Memoire Laroy Ludovic
Laroy_Ludovic
2023-11-01
1 Packages and Working Directory
#setwd("C:/Users/Ludov/Desktop/mémoire/statistiques")library(tidyverse)## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.4.0 ✔ purrr 1.0.1
## ✔ tibble 3.1.8 ✔ dplyr 1.1.0
## ✔ tidyr 1.3.0 ✔ stringr 1.5.0
## ✔ readr 2.1.3 ✔ forcats 1.0.0
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()library(visreg)
library(emmeans)
library(EMSaov)
library(ade4)
library(ggResidpanel)
library(car)## Le chargement a nécessité le package : carData
##
## Attachement du package : 'car'
##
## L'objet suivant est masqué depuis 'package:dplyr':
##
## recode
##
## L'objet suivant est masqué depuis 'package:purrr':
##
## somelibrary(readxl)
library(lme4)## Le chargement a nécessité le package : Matrix
##
## Attachement du package : 'Matrix'
##
## Les objets suivants sont masqués depuis 'package:tidyr':
##
## expand, pack, unpacklibrary(lmerTest)##
## Attachement du package : 'lmerTest'
##
## L'objet suivant est masqué depuis 'package:lme4':
##
## lmer
##
## L'objet suivant est masqué depuis 'package:stats':
##
## steplibrary(knitr)2 Importation des données
Data <- read_excel("data/Data_full.xlsx")
#View(Data)Data_logger_3_Dark <- read.csv2("data/Data_logger_3_Dark.csv")
Data_logger_3_Smart <- read.table("data/3_Smart.csv", header = T, sep = "\t", dec = ".")
Data_logger_3_Full <- read.table("data/3_Full.csv", header = T, sep = "\t", dec = ".")
Data_logger_4_Dark <- read.table("data/4_Dark.csv", header = T, sep = "\t", dec = ".")
Data_logger_4_Smart <- read.table("data/4_Smart.csv", header = T, sep = "\t", dec = ".")
Data_logger_4_Full <- read.table("data/4_Full.csv", header = T, sep = "\t", dec = ".")2.1 Modifications des colonnes
2.1.1 Data_logger
colnames(Data_logger_3_Dark) <- c("Sample", "Date_time", "Temperature","Humidity","Dew_point_temperature")
Data_logger_3_Dark <- Data_logger_3_Dark[2:nrow(Data_logger_3_Dark),]
Data_logger_3_Dark$Treatment <- "Dark"
Data_logger_3_Dark$Sample <- as.numeric(Data_logger_3_Dark$Sample)
Data_logger_3_Dark$Temperature <- as.numeric(Data_logger_3_Dark$Temperature)
Data_logger_3_Dark$Humidity <- as.numeric(Data_logger_3_Dark$Humidity)
Data_logger_3_Dark$Dew_point_temperature <- as.numeric(Data_logger_3_Dark$Dew_point_temperature)
Data_logger_3_Dark$Treatment <- as.factor(Data_logger_3_Dark$Treatment)
Data_logger_3_Dark$Room <- as.factor("3")
Data_logger_3_Dark$Section <- as.factor("3_Dark")colnames(Data_logger_3_Smart) <- c("Sample", "Date_time", "Temperature","Humidity","Dew_point_temperature")
Data_logger_3_Smart$Treatment <- as.factor("Smart")
Data_logger_3_Smart$Room <- as.factor("3")
Data_logger_3_Smart$Section <- as.factor("3_Smart")colnames(Data_logger_3_Full) <- c("Sample", "Date_time", "Temperature","Humidity","Dew_point_temperature")
Data_logger_3_Full$Treatment <- as.factor("Full")
Data_logger_3_Full$Room <- as.factor("3")
Data_logger_3_Full$Section <- as.factor("3_Full")colnames(Data_logger_4_Dark) <- c("Sample", "Date_time", "Temperature","Humidity","Dew_point_temperature")
Data_logger_4_Dark$Treatment <- as.factor("Dark")
Data_logger_4_Dark$Room <- as.factor("4")
Data_logger_4_Dark$Section <- as.factor("4_Dark")colnames(Data_logger_4_Smart) <- c("Sample", "Date_time", "Temperature","Humidity","Dew_point_temperature")
Data_logger_4_Smart$Treatment <- as.factor("Smart")
Data_logger_4_Smart$Room <- as.factor("4")
Data_logger_4_Smart$Section <- as.factor("4_Smart")colnames(Data_logger_4_Full) <- c("Sample", "Date_time", "Temperature","Humidity","Dew_point_temperature")
Data_logger_4_Full$Treatment <- as.factor("Full")
Data_logger_4_Full$Room <- as.factor("4")
Data_logger_4_Full$Section <- as.factor("4_Full")Data_logger <- rbind(Data_logger_3_Dark, Data_logger_3_Smart, Data_logger_3_Full, Data_logger_4_Dark, Data_logger_4_Smart, Data_logger_4_Full)
summary(Data_logger)## Sample Date_time Temperature Humidity
## Min. : 1 Length:100613 Min. :13.64 Min. : 21.87
## 1st Qu.: 4193 Class :character 1st Qu.:20.84 1st Qu.: 52.00
## Median : 8385 Mode :character Median :24.17 Median : 88.64
## Mean : 8385 Mean :23.16 Mean : 75.75
## 3rd Qu.:12577 3rd Qu.:25.11 3rd Qu.: 97.23
## Max. :16769 Max. :27.19 Max. :100.00
## Dew_point_temperature Treatment Room Section
## Min. :-3.621 Dark :33537 3:50307 3_Dark :16769
## 1st Qu.:13.059 Smart:33538 4:50306 3_Smart:16769
## Median :19.627 Full :33538 3_Full :16769
## Mean :17.752 4_Dark :16768
## 3rd Qu.:23.596 4_Smart:16769
## Max. :26.758 4_Full :167692.1.2 Data
Data$Room <- as.factor(Data$Room)
Data$Mother <- as.factor(Data$Mother)
Data$Treatment <- as.factor(Data$Treatment)
Data$Treatment_bis <- as.factor(Data$Treatment_bis)
Data$ID <- as.factor(Data$ID)
Data$Sex <- as.factor(Data$Sex)
Data$Species <- as.factor(Data$Species)
Data$Region <- as.factor(Data$Region)
Data$Site <- as.factor(Data$Site)
Data$M0 <- as.numeric(Data$M0)
Data$M1 <- as.numeric(Data$M1)
Data$M2 <- as.numeric(Data$M2)
Data$M3 <- as.numeric(Data$M3)
Data$M4 <- as.numeric(Data$M4)
Data$M5 <- as.numeric(Data$M5)
Data$M6 <- as.numeric(Data$M6)
Data$M7 <- as.numeric(Data$M7)
Data$M8 <- as.numeric(Data$M8)
Data$M9 <- as.numeric(Data$M9)
Data$M10 <- as.numeric(Data$M10)
Data$M11 <- as.numeric(Data$M11)
Data$M12 <- as.numeric(Data$M12)
Data$M13 <- as.numeric(Data$M13)
Data$M14 <- as.numeric(Data$M14)
Data$M15 <- as.numeric(Data$M15)
Data$M16 <- as.numeric(Data$M16)
Data$M17 <- as.numeric(Data$M17)
Data$M18 <- as.numeric(Data$M18)
Data$M19 <- as.numeric(Data$M19)
Data$M20 <- as.numeric(Data$M20)
Data$Time_alive <- as.numeric(Data$Time_alive)
Data$Pupa_mass <- as.numeric(Data$Pupa_mass)
Data$Did_pupated <- as.factor(Data$Did_pupated)
Data$Did_emerged <- as.factor(Data$Did_emerged)
Data$Larva_survival <- as.factor(Data$Larva_survival)
Data$Diapause <- as.factor(Data$Diapause)
Data$Treatment_FTL <- as.factor(Data$Treatment_FTL)
Data$Light_orientation <- as.factor(Data$Light_orientation)
Data$Did_move <- as.factor(Data$Did_move)
Data$Did_FTL <- as.factor(Data$Did_FTL)
Data$Treatment_bis <- factor(Data$Treatment_bis, levels = c("Dark", "Full", "Smart", "Mixt_smart"))2.2 Création des colonnes “Total_eaten” et “Eaten_per_day”
Mise en place de Total_eaten
Vecteur_total_eaten <- numeric()
for ( Y in (1:450) ) {
B <- 0
for ( X in (seq(73,403, by = 3)) ) {
A <- as.numeric(unname(Data[ Y , X ]))
B <- sum( A , B )
}
Vecteur_total_eaten <- c(Vecteur_total_eaten, B)
}
Data$Total_eaten <- Vecteur_total_eatenMise en place de Eaten_per_day
Data <- Data %>% mutate(Eaten_per_day = Total_eaten / Time_alive )2.3 Speed_to_light
Afin de résoudre prendre en compte tout les individus qui ont n’ont pas voler mais participer à l’expérience (ils ont aucun score dans le temps mis pour voler mais ne participent pas au test stat (car ils ont rien dans la colonne Flight_to_light))
Vecteur_speed <- numeric()
for (X in (1:nrow(Data))) {
A <- ifelse(Data$End_FTL_experiment[X] == 1800, 0, ( 4.5 / (Data$Flight_to_light[X] / 60) ))
Vecteur_speed <- c(Vecteur_speed, A)
}
Data$Speed_to_light <- Vecteur_speed2.4 Ordre des facteurs différents
Data_ref_smart <- Data
Data_ref_smart$Treatment <- relevel(Data$Treatment, ref = "Smart")
Data_ref_smart$Treatment_bis <- relevel(Data$Treatment_bis, ref = "Smart")
Data_ref_full <- Data
Data_ref_full$Treatment <- relevel(Data$Treatment, ref = "Full")
Data_ref_full$Treatment_bis <- relevel(Data$Treatment_bis, ref = "Full")
Data_ref_mixt_smart <- Data
Data_ref_mixt_smart$Treatment_bis <- relevel(Data$Treatment_bis, ref = "Mixt_smart")
Data_refFTL_Night <- Data
Data_refFTL_Night$Treatment_FTL <- relevel(Data$Treatment_FTL, ref = "Night")
Data_refFTL_Night$Treatment_FTL <- relevel(Data$Treatment_FTL, ref = "Night")
Data_refFTL_Mix <- Data
Data_refFTL_Mix$Treatment_FTL <- relevel(Data$Treatment_FTL, ref = "Mix")
Data_refFTL_Mix$Treatment_FTL <- relevel(Data$Treatment_FTL, ref = "Mix")2.5 Séparation des jeux de données en fonction par espèce
Data_OP <- Data %>% filter(Species == "OP")
Data_OP_ref_smart <- Data_ref_smart %>% filter(Species == "OP")
Data_OP_ref_full <- Data_ref_full %>% filter(Species == "OP")
Data_AE <- Data %>% filter(Species == "AE")
Data_AE_ref_smart <- Data_ref_smart %>% filter(Species == "AE")
Data_AE_ref_full <- Data_ref_full %>% filter(Species == "AE")
Data_AE_ref_mixt_smart <- Data_ref_mixt_smart %>% filter(Species == "AE")3 Data logger
summary(Data_logger)## Sample Date_time Temperature Humidity
## Min. : 1 Length:100613 Min. :13.64 Min. : 21.87
## 1st Qu.: 4193 Class :character 1st Qu.:20.84 1st Qu.: 52.00
## Median : 8385 Mode :character Median :24.17 Median : 88.64
## Mean : 8385 Mean :23.16 Mean : 75.75
## 3rd Qu.:12577 3rd Qu.:25.11 3rd Qu.: 97.23
## Max. :16769 Max. :27.19 Max. :100.00
## Dew_point_temperature Treatment Room Section
## Min. :-3.621 Dark :33537 3:50307 3_Dark :16769
## 1st Qu.:13.059 Smart:33538 4:50306 3_Smart:16769
## Median :19.627 Full :33538 3_Full :16769
## Mean :17.752 4_Dark :16768
## 3rd Qu.:23.596 4_Smart:16769
## Max. :26.758 4_Full :167693.1 Température par pièce
Anova_Data_logger_temp_room <- aov(Temperature ~ Room, data = Data_logger)
summary(Anova_Data_logger_temp_room)## Df Sum Sq Mean Sq F value Pr(>F)
## Room 1 9232 9232 1546 <2e-16 ***
## Residuals 100611 600679 6
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1kable(TukeyHSD(Anova_Data_logger_temp_room)$Room,caption = "Test post-hoc de Tukey pour la température en fonction des différentes pièces")| diff | lwr | upr | p adj | |
|---|---|---|---|---|
| 4-3 | 0.6058174 | 0.5756213 | 0.6360134 | 0 |
write.csv2( TukeyHSD(Anova_Data_logger_temp_room)$Room , file = "output/Data_logger_temp_room.csv" )3.2 Température par traitement
Anova_Data_logger_temp_treatment <- aov(Temperature ~ Treatment, data = Data_logger)
summary(Anova_Data_logger_temp_treatment)## Df Sum Sq Mean Sq F value Pr(>F)
## Treatment 2 1717 858.4 142 <2e-16 ***
## Residuals 100610 608194 6.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1kable(TukeyHSD(Anova_Data_logger_temp_treatment)$Treatment,caption = "Test post-hoc de Tukey pour la température en fonction des différents traitements")| diff | lwr | upr | p adj | |
|---|---|---|---|---|
| Smart-Dark | -0.1199718 | -0.1644711 | -0.0754726 | 0 |
| Full-Dark | -0.3168704 | -0.3613696 | -0.2723712 | 0 |
| Full-Smart | -0.1968986 | -0.2413975 | -0.1523997 | 0 |
write.csv2( TukeyHSD(Anova_Data_logger_temp_treatment)$Treatment , file = "output/Data_logger_temp_treatment.csv" )3.3 Température par section
Anova_Data_logger_temp_section <- aov(Temperature ~ Section, data = Data_logger)
summary(Anova_Data_logger_temp_section)## Df Sum Sq Mean Sq F value Pr(>F)
## Section 5 12576 2515.1 423.6 <2e-16 ***
## Residuals 100607 597335 5.9
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1kable(TukeyHSD(Anova_Data_logger_temp_section)$Section,caption = "Test post-hoc de Tukey pour la température en fonction des différentes sections")| diff | lwr | upr | p adj | |
|---|---|---|---|---|
| 3_Smart-3_Dark | -0.3961415 | -0.4719741 | -0.3203088 | 0.0000000 |
| 3_Full-3_Dark | -0.5797694 | -0.6556021 | -0.5039367 | 0.0000000 |
| 4_Dark-3_Dark | 0.2464425 | 0.1706087 | 0.3222763 | 0.0000000 |
| 4_Smart-3_Dark | 0.4026330 | 0.3268003 | 0.4784656 | 0.0000000 |
| 4_Full-3_Dark | 0.1924637 | 0.1166310 | 0.2682964 | 0.0000000 |
| 3_Full-3_Smart | -0.1836279 | -0.2594606 | -0.1077953 | 0.0000000 |
| 4_Dark-3_Smart | 0.6425840 | 0.5667502 | 0.7184178 | 0.0000000 |
| 4_Smart-3_Smart | 0.7987744 | 0.7229417 | 0.8746071 | 0.0000000 |
| 4_Full-3_Smart | 0.5886052 | 0.5127725 | 0.6644378 | 0.0000000 |
| 4_Dark-3_Full | 0.8262119 | 0.7503781 | 0.9020457 | 0.0000000 |
| 4_Smart-3_Full | 0.9824023 | 0.9065697 | 1.0582350 | 0.0000000 |
| 4_Full-3_Full | 0.7722331 | 0.6964004 | 0.8480658 | 0.0000000 |
| 4_Smart-4_Dark | 0.1561904 | 0.0803566 | 0.2320242 | 0.0000001 |
| 4_Full-4_Dark | -0.0539788 | -0.1298126 | 0.0218550 | 0.3260046 |
| 4_Full-4_Smart | -0.2101692 | -0.2860019 | -0.1343366 | 0.0000000 |
write.csv2( TukeyHSD(Anova_Data_logger_temp_section)$Section , file = "output/Data_logger_temp_section.csv" )3.4 Humidité par pièce
Anova_Data_logger_hum_room <- aov(Humidity ~ Room, data = Data_logger)
summary(Anova_Data_logger_hum_room)## Df Sum Sq Mean Sq F value Pr(>F)
## Room 1 558908 558908 950.2 <2e-16 ***
## Residuals 100611 59178188 588
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1kable(TukeyHSD(Anova_Data_logger_hum_room)$Room,caption = "Test post-hoc de Tukey pour l'humidité en fonction des différentes pièces")| diff | lwr | upr | p adj | |
|---|---|---|---|---|
| 4-3 | -4.71382 | -5.013535 | -4.414104 | 0 |
write.csv2( TukeyHSD(Anova_Data_logger_hum_room)$Room , file = "output/Data_logger_hum_room.csv" )3.5 Humidité par traitement
Anova_Data_logger_hum_treatment <- aov(Humidity ~ Treatment, data = Data_logger)
summary(Anova_Data_logger_hum_treatment)## Df Sum Sq Mean Sq F value Pr(>F)
## Treatment 2 408004 204002 345.9 <2e-16 ***
## Residuals 100610 59329092 590
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1kable(TukeyHSD(Anova_Data_logger_hum_treatment)$Treatment,caption = "Test post-hoc de Tukey pour l'humidité en fonction des différents traitements")| diff | lwr | upr | p adj | |
|---|---|---|---|---|
| Smart-Dark | 1.214412 | 0.7749055 | 1.653918 | 0 |
| Full-Dark | 4.747522 | 4.3080161 | 5.187029 | 0 |
| Full-Smart | 3.533111 | 3.0936077 | 3.972614 | 0 |
write.csv2( TukeyHSD(Anova_Data_logger_hum_treatment)$Treatment , file = "output/Data_logger_hum_treatment.csv" )3.6 Humidité par section
Anova_Data_logger_hum_section <- aov(Humidity ~ Section, data = Data_logger)
summary(Anova_Data_logger_hum_section)## Df Sum Sq Mean Sq F value Pr(>F)
## Section 5 1661156 332231 575.5 <2e-16 ***
## Residuals 100607 58075939 577
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1kable(TukeyHSD(Anova_Data_logger_hum_section)$Section,caption = "Test post-hoc de Tukey pour l'humidité en fonction des différentes sections")| diff | lwr | upr | p adj | |
|---|---|---|---|---|
| 3_Smart-3_Dark | 7.641563 | 6.893832 | 8.3892938 | 0.0000000 |
| 3_Full-3_Dark | 7.698508 | 6.950777 | 8.4462388 | 0.0000000 |
| 4_Dark-3_Dark | 1.538324 | 0.790582 | 2.2860664 | 0.0000001 |
| 4_Smart-3_Dark | -3.674461 | -4.422192 | -2.9267300 | 0.0000000 |
| 4_Full-3_Dark | 3.334815 | 2.587084 | 4.0825464 | 0.0000000 |
| 3_Full-3_Smart | 0.056945 | -0.690786 | 0.8046761 | 0.9999343 |
| 4_Dark-3_Smart | -6.103239 | -6.850981 | -5.3554964 | 0.0000000 |
| 4_Smart-3_Smart | -11.316024 | -12.063755 | -10.5682928 | 0.0000000 |
| 4_Full-3_Smart | -4.306748 | -5.054479 | -3.5590164 | 0.0000000 |
| 4_Dark-3_Full | -6.160184 | -6.907926 | -5.4124414 | 0.0000000 |
| 4_Smart-3_Full | -11.372969 | -12.120700 | -10.6252378 | 0.0000000 |
| 4_Full-3_Full | -4.363692 | -5.111423 | -3.6159614 | 0.0000000 |
| 4_Smart-4_Dark | -5.212785 | -5.960527 | -4.4650430 | 0.0000000 |
| 4_Full-4_Dark | 1.796491 | 1.048749 | 2.5442333 | 0.0000000 |
| 4_Full-4_Smart | 7.009276 | 6.261545 | 7.7570074 | 0.0000000 |
write.csv2( TukeyHSD(Anova_Data_logger_hum_section)$Section , file = "output/Data_logger_hum_section.csv" )4 Analyses Développement
4.1 Total_molt
Vu que c’est une variable de comptage, nous comptons faire un glm de type poisson
4.1.1 Test
GLM_Total_molt <- glmer(Total_molt ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex , family = poisson, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')summary(GLM_Total_molt)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 970.3 1033.5 -468.2 936.3 287
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.87904 -0.46734 0.09575 0.30220 1.82167
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.00e+00 0.000e+00
## Site (Intercept) 9.32e-17 9.654e-09
## Room (Intercept) 0.00e+00 0.000e+00
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.22906 0.09861 12.464 < 2e-16 ***
## Treatment_bisFull -0.10802 0.12930 -0.835 0.403
## Treatment_bisSmart 0.01831 0.14233 0.129 0.898
## Treatment_bisMixt_smart 0.01054 0.15924 0.066 0.947
## SexMale 0.03246 0.13058 0.249 0.804
## SpeciesOP -0.73140 0.15269 -4.790 1.67e-06 ***
## RegionLuxembourg 0.14355 0.08255 1.739 0.082 .
## SexMale:SpeciesOP -0.05026 0.16401 -0.306 0.759
## SpeciesOP:RegionLuxembourg -0.09978 0.15673 -0.637 0.524
## Treatment_bisFull:SpeciesOP 0.02977 0.17993 0.165 0.869
## Treatment_bisSmart:SpeciesOP 0.03500 0.23814 0.147 0.883
## Treatment_bisFull:SexMale 0.05893 0.16996 0.347 0.729
## Treatment_bisSmart:SexMale -0.12092 0.21066 -0.574 0.566
## Treatment_bisMixt_smart:SexMale -0.07719 0.23607 -0.327 0.744
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 14 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Pas d’effet significatif autre que l’espèce.
Vérification des hypothèses
resid_panel(GLM_Total_molt, plots = c("resid"), smoother = TRUE)## `geom_smooth()` using formula = 'y ~ x'
Le modèle pourrait être siplifié par AIC (surtout pour les interactions)
4.1.2 Sipmplification du modèle
Simplification par AIC/BIC
drop1(GLM_Total_molt)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')## Single term deletions
##
## Model:
## Total_molt ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex
## npar AIC
## <none> 970.31
## Sex:Species 1 968.40
## Species:Region 1 968.71
## Treatment_bis:Species 2 966.34
## Treatment_bis:Sex 3 965.12GLM_Total_molt2 <- update(GLM_Total_molt, . ~ . - Treatment_bis:Sex)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(GLM_Total_molt2)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## boundary (singular) fit: see help('isSingular')## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')## Single term deletions
##
## Model:
## Total_molt ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Species:Region +
## Treatment_bis:Species
## npar AIC
## <none> 965.12
## Sex:Species 1 963.16
## Species:Region 1 963.54
## Treatment_bis:Species 2 961.16GLM_Total_molt3 <- update(GLM_Total_molt2, . ~ . - Treatment_bis:Species)## boundary (singular) fit: see help('isSingular')drop1(GLM_Total_molt3)## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')## Single term deletions
##
## Model:
## Total_molt ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Species:Region
## npar AIC
## <none> 961.16
## Treatment_bis 3 955.86
## Sex:Species 1 959.19
## Species:Region 1 959.57GLM_Total_molt4 <- update(GLM_Total_molt3, . ~ . - Sex:Species)## boundary (singular) fit: see help('isSingular')# drop1(GLM_Total_molt5) drop1 a cessé de fonctionné donc je compare le modèle avec et sans interactions
GLM_Total_molt5 <- update(GLM_Total_molt4, . ~ . - Species:Region - Room:Treatment_bis)## boundary (singular) fit: see help('isSingular')AIC(GLM_Total_molt4)## [1] 959.1862AIC(GLM_Total_molt5)## [1] 957.5986Modèle final, aucune interactions n’était significative
GLM_Total_molt <- GLM_Total_molt5
summary(GLM_Total_molt5)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 957.6 994.8 -468.8 937.6 294
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8750 -0.4448 0.1580 0.3201 1.8090
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0 0
## Site (Intercept) 0 0
## Room (Intercept) 0 0
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.249363 0.076924 16.242 <2e-16 ***
## Treatment_bisFull -0.071402 0.084509 -0.845 0.398
## Treatment_bisSmart -0.020291 0.102305 -0.198 0.843
## Treatment_bisMixt_smart -0.019024 0.117183 -0.162 0.871
## SexMale 0.007811 0.070677 0.111 0.912
## SpeciesOP -0.789854 0.081302 -9.715 <2e-16 ***
## RegionLuxembourg 0.114200 0.070195 1.627 0.104
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal SpcsOP
## Trtmnt_bsFl -0.499
## Trtmnt_bsSm -0.440 0.384
## Trtmnt_bsM_ -0.446 0.349 0.306
## SexMale -0.362 -0.051 0.017 -0.029
## SpeciesOP -0.372 0.088 0.143 0.269 -0.034
## ReginLxmbrg -0.394 -0.025 -0.076 -0.022 -0.020 -0.057
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Seulement les espèces sont significatives
4.1.3 Treatment VS Treatment_bis
AIC(GLM_Total_molt)## [1] 957.5986AIC(update(GLM_Total_molt, . ~ . - Treatment_bis + Treatment))## boundary (singular) fit: see help('isSingular')## [1] 955.6493summary(GLM_Total_molt)$coeff## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.249362967 0.07692355 16.2416195 2.560733e-59
## Treatment_bisFull -0.071402364 0.08450888 -0.8449096 3.981613e-01
## Treatment_bisSmart -0.020290687 0.10230536 -0.1983345 8.427833e-01
## Treatment_bisMixt_smart -0.019024308 0.11718279 -0.1623473 8.710324e-01
## SexMale 0.007811043 0.07067680 0.1105178 9.119987e-01
## SpeciesOP -0.789853774 0.08130168 -9.7150980 2.599987e-22
## RegionLuxembourg 0.114200258 0.07019497 1.6269008 1.037582e-01summary(update(GLM_Total_molt, . ~ . - Treatment_bis + Treatment))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.2395001210 0.07816780 15.856913745 1.259322e-56
## SexMale 0.0078032917 0.07065795 0.110437559 9.120624e-01
## SpeciesOP -0.7854511296 0.07817605 -10.047209082 9.450604e-24
## RegionLuxembourg 0.1131112397 0.07008653 1.613879843 1.065535e-01
## TreatmentFull -0.0623153922 0.08736703 -0.713259799 4.756850e-01
## TreatmentSmart 0.0008079064 0.08482624 0.009524251 9.924009e-01pas de grosse différence de significativité L’AIC préfère le modèle avec “Treatment”
summary(GLM_Total_molt)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 957.6 994.8 -468.8 937.6 294
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8750 -0.4448 0.1580 0.3201 1.8090
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0 0
## Site (Intercept) 0 0
## Room (Intercept) 0 0
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.249363 0.076924 16.242 <2e-16 ***
## Treatment_bisFull -0.071402 0.084509 -0.845 0.398
## Treatment_bisSmart -0.020291 0.102305 -0.198 0.843
## Treatment_bisMixt_smart -0.019024 0.117183 -0.162 0.871
## SexMale 0.007811 0.070677 0.111 0.912
## SpeciesOP -0.789854 0.081302 -9.715 <2e-16 ***
## RegionLuxembourg 0.114200 0.070195 1.627 0.104
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal SpcsOP
## Trtmnt_bsFl -0.499
## Trtmnt_bsSm -0.440 0.384
## Trtmnt_bsM_ -0.446 0.349 0.306
## SexMale -0.362 -0.051 0.017 -0.029
## SpeciesOP -0.372 0.088 0.143 0.269 -0.034
## ReginLxmbrg -0.394 -0.025 -0.076 -0.022 -0.020 -0.057
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(update(GLM_Total_molt, . ~ . - Treatment_bis + Treatment))## boundary (singular) fit: see help('isSingular')## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Sex + Species + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 955.6 989.1 -468.8 937.6 295
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8657 -0.4425 0.1661 0.3278 1.8034
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000e+00 0.000e+00
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 1.459e-18 1.208e-09
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.2395001 0.0781678 15.857 <2e-16 ***
## SexMale 0.0078033 0.0706580 0.110 0.912
## SpeciesOP -0.7854511 0.0781761 -10.047 <2e-16 ***
## RegionLuxembourg 0.1131112 0.0700865 1.614 0.107
## TreatmentFull -0.0623154 0.0873670 -0.713 0.476
## TreatmentSmart 0.0008079 0.0848262 0.010 0.992
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) SexMal SpcsOP RgnLxm TrtmnF
## SexMale -0.378
## SpeciesOP -0.256 -0.028
## ReginLxmbrg -0.391 -0.020 -0.050
## TreatmntFll -0.526 -0.032 -0.007 -0.023
## TretmntSmrt -0.568 0.031 0.036 -0.053 0.507
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Info_Total_molt <- "
Effet significatif de l'espèce, OP possède moins de mues.
"
Info_Total_molt## [1] "\nEffet significatif de l'espèce, OP possède moins de mues.\n"4.1.4 Visualisation
Résumé des données
Summary_Total_molt <- Data %>%
group_by(Treatment, Species, Region) %>%
summarise(Mean=mean(Total_molt),
Var=var(Total_molt),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))Graphique avec ce résumé
ggplot(Summary_Total_molt, aes(x=Treatment, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_grid(~Region) +
labs(title = "Nombre de mues", x = "Traitement", y = "Nombre de mues", color = "Espèce") +
theme_bw()## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
ggplot(Data, aes(x=Total_molt)) +
geom_histogram(aes(y = ..count.. , fill = Species), position = "dodge", size = 4) +
scale_x_continuous(breaks = seq(0,6)) +
labs(title = "Nombres de mues par espèce", x = "Nombre de mues", y = "Nombre d'individu", fill = "Espèce") +
theme_bw()## Warning: The dot-dot notation (`..count..`) was deprecated in ggplot2 3.4.0.
## ℹ Please use `after_stat(count)` instead.## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
4.2 Diapause
4.2.1 Test
GLM_Diapause <- glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data, family = binomial)
summary(GLM_Diapause)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 195.4 251.2 -82.7 165.4 289
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.8081 -0.2944 -0.2163 -0.1254 5.6179
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.425e-01 0.5852746
## Site (Intercept) 8.894e-01 0.9430726
## Room (Intercept) 1.062e-07 0.0003259
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.69086 0.67160 -4.007 6.16e-05
## Treatment_bisFull 1.29096 0.71956 1.794 0.0728
## Treatment_bisSmart -0.11529 1.03099 -0.112 0.9110
## Treatment_bisMixt_smart -33.98513 5819.93268 -0.006 0.9953
## SexMale 0.07099 0.63243 0.112 0.9106
## RegionLuxembourg -0.57942 0.96440 -0.601 0.5480
## Treatment_bisFull:SexMale -2.08720 1.08502 -1.924 0.0544
## Treatment_bisSmart:SexMale 0.26663 1.51819 0.176 0.8606
## Treatment_bisMixt_smart:SexMale 17.81447 4184.83400 0.004 0.9966
## Treatment_bisFull:RegionLuxembourg -0.82819 0.99234 -0.835 0.4040
## Treatment_bisSmart:RegionLuxembourg -0.99425 1.50602 -0.660 0.5091
## Treatment_bisMixt_smart:RegionLuxembourg 17.28909 4044.59938 0.004 0.9966
##
## (Intercept) ***
## Treatment_bisFull .
## Treatment_bisSmart
## Treatment_bisMixt_smart
## SexMale
## RegionLuxembourg
## Treatment_bisFull:SexMale .
## Treatment_bisSmart:SexMale
## Treatment_bisMixt_smart:SexMale
## Treatment_bisFull:RegionLuxembourg
## Treatment_bisSmart:RegionLuxembourg
## Treatment_bisMixt_smart:RegionLuxembourg
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM T_M_:S
## Trtmnt_bsFl -0.571
## Trtmnt_bsSm -0.362 0.341
## Trtmnt_bsM_ 0.000 0.000 0.000
## SexMale -0.395 0.372 0.271 0.000
## ReginLxmbrg -0.573 0.280 0.170 0.000 -0.036
## Trtmnt_F:SM 0.266 -0.497 -0.163 0.000 -0.576 -0.001
## Trtmnt_S:SM 0.138 -0.129 -0.485 0.000 -0.427 0.033 0.232
## Trtmn_M_:SM 0.000 0.000 0.000 -0.719 0.000 0.000 0.000 0.000
## Trtmnt_F:RL 0.291 -0.571 -0.163 0.000 0.029 -0.480 0.087 -0.037 0.000
## Trtmnt_S:RL 0.181 -0.170 -0.478 0.000 0.016 -0.308 -0.001 -0.090 0.000
## Trtmn_M_:RL 0.000 0.000 0.000 -0.695 0.000 0.000 0.000 0.000 0.000
## T_F:RL T_S:RL
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_F:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## Trtmnt_F:RL
## Trtmnt_S:RL 0.297
## Trtmn_M_:RL 0.000 0.000
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## unable to evaluate scaled gradient
## Model failed to converge: degenerate Hessian with 1 negative eigenvalues4.2.2 Simplification du modèle
drop1(GLM_Diapause)## Single term deletions
##
## Model:
## Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## npar AIC
## <none> 195.41
## Treatment_bis:Sex 3 197.50
## Treatment_bis:Region 3 192.78GLM_Diapause1 <- update(GLM_Diapause, . ~ . - Treatment_bis:Region)
drop1(GLM_Diapause1)## Single term deletions
##
## Model:
## Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex
## npar AIC
## <none> 192.78
## Region 1 191.88
## Treatment_bis:Sex 3 193.70Plus aucune interaction est nécessaire à faire retirer
GLM_Diapause <- GLM_Diapause14.2.3 Treatment VS Treatment_bis
AIC(glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data, family = binomial))## [1] 195.4097AIC(glmer(Diapause ~ Treatment + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data, family = binomial))## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## [1] 196.4034summary(glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data, family = binomial))$coeff## Estimate Std. Error z value
## (Intercept) -2.69085839 0.6716023 -4.006624629
## Treatment_bisFull 1.29095850 0.7195566 1.794102698
## Treatment_bisSmart -0.11528514 1.0309858 -0.111820295
## Treatment_bisMixt_smart -33.98512976 5819.9326829 -0.005839437
## SexMale 0.07098974 0.6324269 0.112249713
## RegionLuxembourg -0.57941581 0.9643999 -0.600804494
## Treatment_bisFull:SexMale -2.08719598 1.0850233 -1.923641542
## Treatment_bisSmart:SexMale 0.26663258 1.5181892 0.175625404
## Treatment_bisMixt_smart:SexMale 17.81447062 4184.8340023 0.004256912
## Treatment_bisFull:RegionLuxembourg -0.82818915 0.9923404 -0.834581753
## Treatment_bisSmart:RegionLuxembourg -0.99425108 1.5060199 -0.660184568
## Treatment_bisMixt_smart:RegionLuxembourg 17.28908514 4044.5993756 0.004274610
## Pr(>|z|)
## (Intercept) 6.159263e-05
## Treatment_bisFull 7.279678e-02
## Treatment_bisSmart 9.109659e-01
## Treatment_bisMixt_smart 9.953408e-01
## SexMale 9.106254e-01
## RegionLuxembourg 5.479702e-01
## Treatment_bisFull:SexMale 5.439953e-02
## Treatment_bisSmart:SexMale 8.605882e-01
## Treatment_bisMixt_smart:SexMale 9.966035e-01
## Treatment_bisFull:RegionLuxembourg 4.039532e-01
## Treatment_bisSmart:RegionLuxembourg 5.091354e-01
## Treatment_bisMixt_smart:RegionLuxembourg 9.965894e-01summary(glmer(Diapause ~ Treatment + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data, family = binomial))$coeff## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## Estimate Std. Error z value
## (Intercept) -2.57720028 0.6894436 -3.738087133
## TreatmentFull -0.96039356 0.9739312 -0.986100028
## TreatmentSmart -0.81024571 0.8598493 -0.942311333
## SexMale 0.08045145 0.6360189 0.126492231
## RegionLuxembourg -0.59885534 0.9803765 -0.610842202
## SexFemale:Treatment_bisFull 2.12416873 1.0931975 1.943078665
## SexFemale:Treatment_bisSmart 0.53662765 1.2667396 0.423629007
## SexMale:Treatment_bisSmart 0.83195584 1.5419772 0.539538362
## SexFemale:Treatment_bisMixt_smart -32.83639589 5143.5970326 -0.006383936
## SexMale:Treatment_bisMixt_smart -15.41720073 3883.8998730 -0.003969515
## RegionLuxembourg:Treatment_bisFull -0.85127285 0.9960992 -0.854606474
## RegionLuxembourg:Treatment_bisSmart -1.01366758 1.5103680 -0.671139475
## RegionLuxembourg:Treatment_bisMixt_smart 17.21961336 3883.9000385 0.004433588
## Pr(>|z|)
## (Intercept) 0.0001854257
## TreatmentFull 0.3240840301
## TreatmentSmart 0.3460332678
## SexMale 0.8993422985
## RegionLuxembourg 0.5413040517
## SexFemale:Treatment_bisFull 0.0520066543
## SexFemale:Treatment_bisSmart 0.6718363969
## SexMale:Treatment_bisSmart 0.5895154342
## SexFemale:Treatment_bisMixt_smart 0.9949063904
## SexMale:Treatment_bisMixt_smart 0.9968327932
## RegionLuxembourg:Treatment_bisFull 0.3927690424
## RegionLuxembourg:Treatment_bisSmart 0.5021316814
## RegionLuxembourg:Treatment_bisMixt_smart 0.9964625200Aucune grosse différence, on peut continuer avec Treatment_bis (qui est meilleur en termes d’AIC)
Analyse des p-val
summary(glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data, family = binomial))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 195.4 251.2 -82.7 165.4 289
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.8081 -0.2944 -0.2163 -0.1254 5.6179
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.425e-01 0.5852746
## Site (Intercept) 8.894e-01 0.9430726
## Room (Intercept) 1.062e-07 0.0003259
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.69086 0.67160 -4.007 6.16e-05
## Treatment_bisFull 1.29096 0.71956 1.794 0.0728
## Treatment_bisSmart -0.11529 1.03099 -0.112 0.9110
## Treatment_bisMixt_smart -33.98513 5819.93268 -0.006 0.9953
## SexMale 0.07099 0.63243 0.112 0.9106
## RegionLuxembourg -0.57942 0.96440 -0.601 0.5480
## Treatment_bisFull:SexMale -2.08720 1.08502 -1.924 0.0544
## Treatment_bisSmart:SexMale 0.26663 1.51819 0.176 0.8606
## Treatment_bisMixt_smart:SexMale 17.81447 4184.83400 0.004 0.9966
## Treatment_bisFull:RegionLuxembourg -0.82819 0.99234 -0.835 0.4040
## Treatment_bisSmart:RegionLuxembourg -0.99425 1.50602 -0.660 0.5091
## Treatment_bisMixt_smart:RegionLuxembourg 17.28909 4044.59938 0.004 0.9966
##
## (Intercept) ***
## Treatment_bisFull .
## Treatment_bisSmart
## Treatment_bisMixt_smart
## SexMale
## RegionLuxembourg
## Treatment_bisFull:SexMale .
## Treatment_bisSmart:SexMale
## Treatment_bisMixt_smart:SexMale
## Treatment_bisFull:RegionLuxembourg
## Treatment_bisSmart:RegionLuxembourg
## Treatment_bisMixt_smart:RegionLuxembourg
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM T_M_:S
## Trtmnt_bsFl -0.571
## Trtmnt_bsSm -0.362 0.341
## Trtmnt_bsM_ 0.000 0.000 0.000
## SexMale -0.395 0.372 0.271 0.000
## ReginLxmbrg -0.573 0.280 0.170 0.000 -0.036
## Trtmnt_F:SM 0.266 -0.497 -0.163 0.000 -0.576 -0.001
## Trtmnt_S:SM 0.138 -0.129 -0.485 0.000 -0.427 0.033 0.232
## Trtmn_M_:SM 0.000 0.000 0.000 -0.719 0.000 0.000 0.000 0.000
## Trtmnt_F:RL 0.291 -0.571 -0.163 0.000 0.029 -0.480 0.087 -0.037 0.000
## Trtmnt_S:RL 0.181 -0.170 -0.478 0.000 0.016 -0.308 -0.001 -0.090 0.000
## Trtmn_M_:RL 0.000 0.000 0.000 -0.695 0.000 0.000 0.000 0.000 0.000
## T_F:RL T_S:RL
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_F:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## Trtmnt_F:RL
## Trtmnt_S:RL 0.297
## Trtmn_M_:RL 0.000 0.000
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## unable to evaluate scaled gradient
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluessummary(glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_ref_smart, family = binomial))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_ref_smart
##
## AIC BIC logLik deviance df.resid
## 195.4 251.2 -82.7 165.4 289
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.8064 -0.2939 -0.2164 -0.1255 5.6141
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.439e-01 0.586425
## Site (Intercept) 8.878e-01 0.942225
## Room (Intercept) 3.767e-06 0.001941
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.8030 1.0360 -2.706 0.00682
## Treatment_bisDark 0.1132 1.0228 0.111 0.91185
## Treatment_bisFull 1.4013 1.0502 1.334 0.18210
## Treatment_bisMixt_smart -33.9365 218.4837 -0.155 0.87656
## SexMale 0.3335 1.3528 0.247 0.80527
## RegionLuxembourg -1.5718 1.5176 -1.036 0.30034
## Treatment_bisDark:SexMale -0.2614 1.5112 -0.173 0.86266
## Treatment_bisFull:SexMale -2.3468 1.6419 -1.429 0.15291
## Treatment_bisMixt_smart:SexMale 17.9553 232.5937 0.077 0.93847
## Treatment_bisDark:RegionLuxembourg 0.9941 1.4674 0.677 0.49814
## Treatment_bisFull:RegionLuxembourg 0.1656 1.4989 0.110 0.91202
## Treatment_bisMixt_smart:RegionLuxembourg 17.9365 203.3988 0.088 0.92973
##
## (Intercept) **
## Treatment_bisDark
## Treatment_bisFull
## Treatment_bisMixt_smart
## SexMale
## RegionLuxembourg
## Treatment_bisDark:SexMale
## Treatment_bisFull:SexMale
## Treatment_bisMixt_smart:SexMale
## Treatment_bisDark:RegionLuxembourg
## Treatment_bisFull:RegionLuxembourg
## Treatment_bisMixt_smart:RegionLuxembourg
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_D:SM T_F:SM T_M_:S
## Trtmnt_bsDr -0.768
## Trtmnt_bsFl -0.799 0.750
## Trtmnt_bsM_ 0.001 -0.001 -0.001
## SexMale -0.462 0.418 0.445 0.000
## ReginLxmbrg -0.435 0.359 0.327 -0.001 -0.103
## Trtmnt_D:SM 0.433 -0.491 -0.412 0.000 -0.908 0.092
## Trtmnt_F:SM 0.411 -0.345 -0.506 0.000 -0.845 0.099 0.772
## Trtmn_M_:SM 0.000 0.000 0.000 -0.595 -0.001 0.000 0.001 0.001
## Trtmnt_D:RL 0.336 -0.476 -0.337 0.001 0.103 -0.775 -0.104 -0.095 0.000
## Trtmnt_F:RL 0.376 -0.368 -0.508 0.001 0.065 -0.747 -0.056 -0.010 0.000
## Trtmn_M_:RL 0.001 -0.001 -0.001 -0.394 -0.002 -0.002 0.002 0.002 -0.504
## T_D:RL T_F:RL
## Trtmnt_bsDr
## Trtmnt_bsFl
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_D:SM
## Trtmnt_F:SM
## Trtmn_M_:SM
## Trtmnt_D:RL
## Trtmnt_F:RL 0.771
## Trtmn_M_:RL 0.002 0.002
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0118311 (tol = 0.002, component 1)
## Model is nearly unidentifiable: large eigenvalue ratio
## - Rescale variables?summary(glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_ref_full, family = binomial))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_ref_full
##
## AIC BIC logLik deviance df.resid
## 195.4 251.2 -82.7 165.4 289
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.8093 -0.2939 -0.2160 -0.1254 5.6213
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.419e-01 0.584756
## Site (Intercept) 8.989e-01 0.948108
## Room (Intercept) 1.947e-06 0.001395
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.4003 0.6468 -2.165 0.0304
## Treatment_bisDark -1.2918 0.7197 -1.795 0.0727
## Treatment_bisSmart -1.4080 1.0370 -1.358 0.1745
## Treatment_bisMixt_smart -34.6146 4936.0524 -0.007 0.9944
## SexMale -2.0169 0.8873 -2.273 0.0230
## RegionLuxembourg -1.4126 1.0003 -1.412 0.1579
## Treatment_bisDark:SexMale 2.0903 1.0850 1.926 0.0540
## Treatment_bisSmart:SexMale 2.3555 1.6489 1.429 0.1531
## Treatment_bisMixt_smart:SexMale 19.4483 3330.5276 0.006 0.9953
## Treatment_bisDark:RegionLuxembourg 0.8258 0.9925 0.832 0.4054
## Treatment_bisSmart:RegionLuxembourg -0.1627 1.5373 -0.106 0.9157
## Treatment_bisMixt_smart:RegionLuxembourg 17.9108 3643.1034 0.005 0.9961
##
## (Intercept) *
## Treatment_bisDark .
## Treatment_bisSmart
## Treatment_bisMixt_smart
## SexMale *
## RegionLuxembourg
## Treatment_bisDark:SexMale .
## Treatment_bisSmart:SexMale
## Treatment_bisMixt_smart:SexMale
## Treatment_bisDark:RegionLuxembourg
## Treatment_bisSmart:RegionLuxembourg
## Treatment_bisMixt_smart:RegionLuxembourg
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_D:SM T_S:SM T_M_:S
## Trtmnt_bsDr -0.519
## Trtmnt_bsSm -0.357 0.355
## Trtmnt_bsM_ 0.000 0.000 0.000
## SexMale -0.335 0.342 0.231 0.000
## ReginLxmbrg -0.608 0.297 0.208 0.000 0.100
## Trtmnt_D:SM 0.276 -0.497 -0.183 0.000 -0.813 -0.085
## Trtmnt_S:SM 0.181 -0.208 -0.481 0.000 -0.554 -0.061 0.445
## Trtmn_M_:SM 0.000 0.000 0.000 -0.675 0.000 0.000 0.000 0.000
## Trtmnt_D:RL 0.334 -0.571 -0.235 0.000 -0.127 -0.529 0.087 0.092 0.000
## Trtmnt_S:RL 0.215 -0.203 -0.502 0.000 -0.072 -0.344 0.057 -0.022 0.000
## Trtmn_M_:RL 0.000 0.000 0.000 -0.738 0.000 0.000 0.000 0.000 0.000
## T_D:RL T_S:RL
## Trtmnt_bsDr
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_D:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## Trtmnt_D:RL
## Trtmnt_S:RL 0.355
## Trtmn_M_:RL 0.000 0.000
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## unable to evaluate scaled gradient
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluesInfo_Diapause <-"
Les individus du traitement Full ont quasiements significativement (p-val = 0.0728) une plus grande probabilité d'être en diapause que les individus du traitement Dark.
Les mâles du traitement Full ont significativements une plus petite probabilité de rentrer en diapause par rapport aux femelles du même traitement.
"4.2.4 Visualisation
ggplot(Data) +
aes(x = Diapause, fill = Treatment) +
geom_bar(position = "dodge") +
scale_fill_hue(direction = 1) +
facet_grid(~Species) +
labs(title = "Nombre de diapause chez AE et OP", y = "Nombre", x = "Diapause", fill = "Traitement") +
theme_minimal()
4.3 TT_pupation
4.3.1 Test
LM_TT_pupation <- lmer(TT_pupation ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')summary(LM_TT_pupation)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_pupation ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: 2134.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.9654 -0.4416 -0.0861 0.2605 5.2458
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 11.38 3.373
## Site (Intercept) 23.20 4.817
## Room (Intercept) 0.00 0.000
## Residual 72.18 8.496
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 43.6897 2.7783 19.0993 15.725
## Treatment_bisFull -2.0835 2.2129 265.4220 -0.942
## Treatment_bisSmart -5.8623 2.6506 263.4238 -2.212
## Treatment_bisMixt_smart -1.6053 3.0843 267.4236 -0.520
## SexMale 0.8035 2.0424 272.9850 0.393
## SpeciesOP -26.0565 3.0826 34.0980 -8.453
## RegionLuxembourg 5.9235 3.6424 16.1600 1.626
## SexMale:SpeciesOP -1.6867 2.1637 268.1280 -0.780
## SpeciesOP:RegionLuxembourg -6.4407 3.7776 20.5335 -1.705
## Treatment_bisFull:SpeciesOP -0.3947 2.3514 264.8778 -0.168
## Treatment_bisSmart:SpeciesOP 9.3164 3.0539 264.2310 3.051
## Treatment_bisFull:SexMale 1.1886 2.3601 268.3797 0.504
## Treatment_bisSmart:SexMale -0.6361 3.1106 274.9649 -0.205
## Treatment_bisMixt_smart:SexMale -6.1167 3.9013 273.4112 -1.568
## Treatment_bisFull:RegionLuxembourg 3.2045 2.3379 264.5498 1.371
## Treatment_bisSmart:RegionLuxembourg -3.8231 2.9792 262.2092 -1.283
## Treatment_bisMixt_smart:RegionLuxembourg 12.4549 3.8213 268.2423 3.259
## Pr(>|t|)
## (Intercept) 2.19e-12 ***
## Treatment_bisFull 0.34730
## Treatment_bisSmart 0.02785 *
## Treatment_bisMixt_smart 0.60316
## SexMale 0.69431
## SpeciesOP 7.00e-10 ***
## RegionLuxembourg 0.12324
## SexMale:SpeciesOP 0.43635
## SpeciesOP:RegionLuxembourg 0.10328
## Treatment_bisFull:SpeciesOP 0.86682
## Treatment_bisSmart:SpeciesOP 0.00252 **
## Treatment_bisFull:SexMale 0.61493
## Treatment_bisSmart:SexMale 0.83811
## Treatment_bisMixt_smart:SexMale 0.11807
## Treatment_bisFull:RegionLuxembourg 0.17165
## Treatment_bisSmart:RegionLuxembourg 0.20054
## Treatment_bisMixt_smart:RegionLuxembourg 0.00126 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 17 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Normalité des résidus
qqnorm(resid(LM_TT_pupation))
qqline(resid(LM_TT_pupation))
Normalité non vérifiée, on modifie les données
LM_TT_pupation <- lmer(log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')Normalité des résidus
qqnorm(resid(LM_TT_pupation))
qqline(resid(LM_TT_pupation))
C’est bien mieux
Homogénité des variances
plot(LM_TT_pupation)
Distance de cook
plot(cooks.distance(LM_TT_pupation))
4.3.2 Simplification du modèle
drop1(LM_TT_pupation)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.08876 0.088757 1 266.356 2.4951 0.115389
## Species:Region 0.07043 0.070426 1 24.272 1.9798 0.172090
## Treatment_bis:Species 0.37054 0.185270 2 262.455 5.2082 0.006051 **
## Treatment_bis:Sex 0.09525 0.031751 3 268.905 0.8926 0.445454
## Treatment_bis:Region 0.48820 0.162732 3 262.288 4.5746 0.003843 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_TT_pupation1 <- update(LM_TT_pupation, . ~ . - Treatment_bis:Sex)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_TT_pupation1)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region + Treatment_bis:Species + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.04739 0.047390 1 269.295 1.3375 0.248507
## Species:Region 0.07172 0.071715 1 24.948 2.0240 0.167218
## Treatment_bis:Species 0.37345 0.186723 2 265.128 5.2698 0.005697 **
## Treatment_bis:Region 0.47669 0.158896 3 265.281 4.4844 0.004328 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_TT_pupation2 <- update(LM_TT_pupation1, . ~ . - Species:Region)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_TT_pupation2)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Treatment_bis:Species + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.04637 0.046373 1 269.57 1.3109 0.253251
## Treatment_bis:Species 0.35527 0.177637 2 266.05 5.0215 0.007234 **
## Treatment_bis:Region 0.51978 0.173260 3 268.64 4.8977 0.002486 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_TT_pupation3 <- update(LM_TT_pupation2, . ~ . - Sex:Species)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_TT_pupation3)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Species + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 0.01930 0.019299 1 271.14 0.5460 0.460606
## Treatment_bis:Species 0.36260 0.181298 2 266.67 5.1289 0.006521 **
## Treatment_bis:Region 0.52963 0.176542 3 269.39 4.9943 0.002184 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_TT_pupation4 <- update(LM_TT_pupation3, . ~ . - Sex)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_TT_pupation4)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_pupation) ~ Treatment_bis + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Species + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Species 0.54568 0.27284 2 278.00 7.0389 0.001042 **
## Treatment_bis:Region 0.48652 0.16217 3 281.36 4.1838 0.006419 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1AIC(LM_TT_pupation)## [1] -3.013188AIC(LM_TT_pupation2)## [1] -20.08038AIC(LM_TT_pupation3)## [1] -25.1234AIC(LM_TT_pupation4)## [1] -12.10204Le meilleur modèle est le dernier (et en plus c’est le plus simple)
LM_TT_pupation <- lmer(log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex , data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')4.3.3 Treatment VS Treatment_bis
AIC(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex , data = Data))## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')## [1] -6.633181AIC(lmer(log(TT_pupation) ~ Treatment + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment:Species + Treatment:Sex , data = Data))## [1] -2.274728summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Region + Treatment_bis:Species , data = Data))$coeff## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 3.77610265 0.05429042 12.938393
## Treatment_bisFull -0.01950870 0.04341651 266.819071
## Treatment_bisSmart -0.11957283 0.05386700 265.169701
## Treatment_bisMixt_smart -0.07251908 0.05767618 271.164010
## SexMale -0.01672386 0.02263342 271.143916
## SpeciesOP -1.10427693 0.05756314 43.691433
## RegionLuxembourg 0.06218835 0.06865808 9.016883
## Treatment_bisFull:RegionLuxembourg 0.07849757 0.05185327 267.789463
## Treatment_bisSmart:RegionLuxembourg -0.06105654 0.06574407 266.735175
## Treatment_bisMixt_smart:RegionLuxembourg 0.26851935 0.08394681 278.353468
## Treatment_bisFull:SpeciesOP -0.03738171 0.05191725 267.548880
## Treatment_bisSmart:SpeciesOP 0.17834786 0.06722218 266.433847
## t value Pr(>|t|)
## (Intercept) 69.5537518 4.863173e-18
## Treatment_bisFull -0.4493384 6.535523e-01
## Treatment_bisSmart -2.2197789 2.727982e-02
## Treatment_bisMixt_smart -1.2573488 2.097092e-01
## SexMale -0.7389014 4.606060e-01
## SpeciesOP -19.1837516 6.615424e-23
## RegionLuxembourg 0.9057688 3.886203e-01
## Treatment_bisFull:RegionLuxembourg 1.5138404 1.312457e-01
## Treatment_bisSmart:RegionLuxembourg -0.9287003 3.538841e-01
## Treatment_bisMixt_smart:RegionLuxembourg 3.1986844 1.540074e-03
## Treatment_bisFull:SpeciesOP -0.7200247 4.721383e-01
## Treatment_bisSmart:SpeciesOP 2.6531103 8.454303e-03summary(lmer(log(TT_pupation) ~ Treatment + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment:Region + Treatment:Species, data = Data))$coeff## Estimate Std. Error df t value
## (Intercept) 3.780751833 0.05640102 11.335252 67.0333941
## TreatmentFull -0.029148130 0.04591439 268.365046 -0.6348366
## TreatmentSmart -0.087902764 0.04575129 270.330492 -1.9213177
## SexMale -0.007683795 0.02352130 272.347985 -0.3266739
## SpeciesOP -1.120694368 0.06128983 56.768536 -18.2851590
## RegionLuxembourg 0.054444947 0.06627489 9.009504 0.8215019
## TreatmentFull:RegionLuxembourg 0.087292304 0.05706355 269.427478 1.5297385
## TreatmentSmart:RegionLuxembourg 0.055271076 0.05659217 268.917444 0.9766558
## TreatmentFull:SpeciesOP -0.032135196 0.05679876 268.538867 -0.5657729
## TreatmentSmart:SpeciesOP 0.067552879 0.05671879 268.781807 1.1910141
## Pr(>|t|)
## (Intercept) 4.305979e-16
## TreatmentFull 5.260759e-01
## TreatmentSmart 5.574309e-02
## SexMale 7.441654e-01
## SpeciesOP 1.837220e-25
## RegionLuxembourg 4.325610e-01
## TreatmentFull:RegionLuxembourg 1.272547e-01
## TreatmentSmart:RegionLuxembourg 3.296173e-01
## TreatmentFull:SpeciesOP 5.720206e-01
## TreatmentSmart:SpeciesOP 2.346988e-01Le modèle treatment_bis a des p-val concernants les traitements plus significatifs et est mieux selon l’AIC.
Analyse des P-val
summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Region + Treatment_bis:Species , data = Data))## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Treatment_bis:Species
## Data: Data
##
## REML criterion at convergence: -57.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.2068 -0.6222 -0.0553 0.4602 3.9758
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.012935 0.11373
## Site (Intercept) 0.005718 0.07562
## Room (Intercept) 0.000000 0.00000
## Residual 0.035349 0.18801
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.77610 0.05429 12.93839 69.554
## Treatment_bisFull -0.01951 0.04342 266.81907 -0.449
## Treatment_bisSmart -0.11957 0.05387 265.16970 -2.220
## Treatment_bisMixt_smart -0.07252 0.05768 271.16401 -1.257
## SexMale -0.01672 0.02263 271.14392 -0.739
## SpeciesOP -1.10428 0.05756 43.69143 -19.184
## RegionLuxembourg 0.06219 0.06866 9.01688 0.906
## Treatment_bisFull:RegionLuxembourg 0.07850 0.05185 267.78946 1.514
## Treatment_bisSmart:RegionLuxembourg -0.06106 0.06574 266.73517 -0.929
## Treatment_bisMixt_smart:RegionLuxembourg 0.26852 0.08395 278.35347 3.199
## Treatment_bisFull:SpeciesOP -0.03738 0.05192 267.54888 -0.720
## Treatment_bisSmart:SpeciesOP 0.17835 0.06722 266.43385 2.653
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisFull 0.65355
## Treatment_bisSmart 0.02728 *
## Treatment_bisMixt_smart 0.20971
## SexMale 0.46061
## SpeciesOP < 2e-16 ***
## RegionLuxembourg 0.38862
## Treatment_bisFull:RegionLuxembourg 0.13125
## Treatment_bisSmart:RegionLuxembourg 0.35388
## Treatment_bisMixt_smart:RegionLuxembourg 0.00154 **
## Treatment_bisFull:SpeciesOP 0.47214
## Treatment_bisSmart:SpeciesOP 0.00845 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal SpcsOP RgnLxm T_F:RL T_S:RL
## Trtmnt_bsFl -0.378
## Trtmnt_bsSm -0.311 0.399
## Trtmnt_bsM_ -0.297 0.387 0.313
## SexMale -0.168 -0.044 0.039 -0.015
## SpeciesOP -0.446 0.267 0.215 0.193 0.020
## ReginLxmbrg -0.606 0.172 0.138 0.155 -0.018 0.002
## Trtmnt_F:RL 0.172 -0.494 -0.184 -0.187 0.032 0.032 -0.351
## Trtmnt_S:RL 0.143 -0.182 -0.593 -0.164 -0.015 0.026 -0.290 0.370
## Trtmn_M_:RL 0.122 -0.147 -0.132 -0.627 -0.014 0.040 -0.253 0.319 0.267
## Trtmn_F:SOP 0.246 -0.584 -0.249 -0.230 -0.042 -0.416 0.024 -0.094 -0.024
## Trtmn_S:SOP 0.194 -0.232 -0.469 -0.165 -0.067 -0.324 0.023 -0.027 -0.083
## T_M_:R T_F:SO
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## SpeciesOP
## ReginLxmbrg
## Trtmnt_F:RL
## Trtmnt_S:RL
## Trtmn_M_:RL
## Trtmn_F:SOP -0.034
## Trtmn_S:SOP -0.030 0.360
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Region + Treatment_bis:Species , data = Data_ref_full))## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Treatment_bis:Species
## Data: Data_ref_full
##
## REML criterion at convergence: -57.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.2068 -0.6222 -0.0553 0.4602 3.9758
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.012935 0.11373
## Site (Intercept) 0.005718 0.07562
## Room (Intercept) 0.000000 0.00000
## Residual 0.035349 0.18801
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.75659 0.05521 14.02771 68.037
## Treatment_bisDark 0.01951 0.04342 266.81907 0.449
## Treatment_bisSmart -0.10006 0.05405 262.21600 -1.851
## Treatment_bisMixt_smart -0.05301 0.05722 265.73700 -0.926
## SexMale -0.01672 0.02263 271.14392 -0.739
## SpeciesOP -1.14166 0.05935 47.95417 -19.236
## RegionLuxembourg 0.14069 0.07004 10.05440 2.009
## Treatment_bisDark:RegionLuxembourg -0.07850 0.05185 267.78946 -1.514
## Treatment_bisSmart:RegionLuxembourg -0.13955 0.06701 265.12660 -2.083
## Treatment_bisMixt_smart:RegionLuxembourg 0.19002 0.08344 273.14728 2.277
## Treatment_bisDark:SpeciesOP 0.03738 0.05192 267.54888 0.720
## Treatment_bisSmart:SpeciesOP 0.21573 0.06859 265.61916 3.145
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisDark 0.65355
## Treatment_bisSmart 0.06523 .
## Treatment_bisMixt_smart 0.35510
## SexMale 0.46061
## SpeciesOP < 2e-16 ***
## RegionLuxembourg 0.07217 .
## Treatment_bisDark:RegionLuxembourg 0.13125
## Treatment_bisSmart:RegionLuxembourg 0.03823 *
## Treatment_bisMixt_smart:RegionLuxembourg 0.02354 *
## Treatment_bisDark:SpeciesOP 0.47214
## Treatment_bisSmart:SpeciesOP 0.00185 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal SpcsOP RgnLxm T_D:RL T_S:RL
## Trtmnt_bsDr -0.414
## Trtmnt_bsSm -0.325 0.406
## Trtmnt_bsM_ -0.302 0.369 0.309
## SexMale -0.199 0.044 0.074 0.018
## SpeciesOP -0.412 0.252 0.193 0.177 -0.018
## ReginLxmbrg -0.613 0.197 0.157 0.163 0.006 -0.015
## Trtmnt_D:RL 0.219 -0.494 -0.214 -0.187 -0.032 0.051 -0.396
## Trtmnt_S:RL 0.167 -0.204 -0.602 -0.171 -0.040 0.043 -0.317 0.411
## Trtmn_M_:RL 0.140 -0.159 -0.146 -0.639 -0.034 0.040 -0.259 0.301 0.270
## Trtmn_D:SOP 0.217 -0.584 -0.222 -0.211 0.042 -0.471 0.046 -0.094 -0.049
## Trtmn_S:SOP 0.173 -0.215 -0.443 -0.151 -0.034 -0.357 0.037 -0.045 -0.096
## T_M_:R T_D:SO
## Trtmnt_bsDr
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## SpeciesOP
## ReginLxmbrg
## Trtmnt_D:RL
## Trtmnt_S:RL
## Trtmn_M_:RL
## Trtmn_D:SOP -0.024
## Trtmn_S:SOP -0.031 0.405
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Region + Treatment_bis:Species , data = Data_ref_smart))## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Treatment_bis:Species
## Data: Data_ref_smart
##
## REML criterion at convergence: -57.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.2068 -0.6222 -0.0553 0.4602 3.9758
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.012935 0.11373
## Site (Intercept) 0.005718 0.07562
## Room (Intercept) 0.000000 0.00000
## Residual 0.035349 0.18801
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 3.656530 0.063466 23.026455
## Treatment_bisDark 0.119573 0.053867 265.169700
## Treatment_bisFull 0.100064 0.054047 262.216001
## Treatment_bisMixt_smart 0.047054 0.065443 264.421486
## SexMale -0.016724 0.022633 271.143916
## SpeciesOP -0.925929 0.072961 101.429192
## RegionLuxembourg 0.001132 0.080137 16.863093
## Treatment_bisDark:RegionLuxembourg 0.061057 0.065744 266.735175
## Treatment_bisFull:RegionLuxembourg 0.139554 0.067005 265.126605
## Treatment_bisMixt_smart:RegionLuxembourg 0.329576 0.091801 270.349382
## Treatment_bisDark:SpeciesOP -0.178348 0.067222 266.433847
## Treatment_bisFull:SpeciesOP -0.215730 0.068588 265.619155
## t value Pr(>|t|)
## (Intercept) 57.614 < 2e-16 ***
## Treatment_bisDark 2.220 0.027280 *
## Treatment_bisFull 1.851 0.065230 .
## Treatment_bisMixt_smart 0.719 0.472773
## SexMale -0.739 0.460606
## SpeciesOP -12.691 < 2e-16 ***
## RegionLuxembourg 0.014 0.988897
## Treatment_bisDark:RegionLuxembourg 0.929 0.353884
## Treatment_bisFull:RegionLuxembourg 2.083 0.038234 *
## Treatment_bisMixt_smart:RegionLuxembourg 3.590 0.000392 ***
## Treatment_bisDark:SpeciesOP -2.653 0.008454 **
## Treatment_bisFull:SpeciesOP -3.145 0.001848 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal SpcsOP RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.582
## Trtmnt_bsFl -0.569 0.676
## Trtmnt_bsM_ -0.469 0.547 0.555
## SexMale -0.110 -0.039 -0.074 -0.045
## SpeciesOP -0.371 0.263 0.260 0.216 -0.046
## ReginLxmbrg -0.657 0.369 0.366 0.302 -0.028 -0.027
## Trtmnt_D:RL 0.382 -0.593 -0.445 -0.344 0.015 0.056 -0.572
## Trtmnt_F:RL 0.368 -0.440 -0.602 -0.348 0.040 0.056 -0.559 0.695
## Trtmn_M_:RL 0.266 -0.304 -0.307 -0.652 -0.002 0.044 -0.408 0.472 0.484
## Trtmn_D:SOP 0.232 -0.469 -0.281 -0.241 0.067 -0.666 0.049 -0.083 -0.061
## Trtmn_F:SOP 0.227 -0.272 -0.443 -0.234 0.034 -0.650 0.049 -0.063 -0.096
## T_M_:R T_D:SO
## Trtmnt_bsDr
## Trtmnt_bsFl
## Trtmnt_bsM_
## SexMale
## SpeciesOP
## ReginLxmbrg
## Trtmnt_D:RL
## Trtmnt_F:RL
## Trtmn_M_:RL
## Trtmn_D:SOP -0.032
## Trtmn_F:SOP -0.042 0.708
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Infos_TT_pupation <- "
OP est plus rapide.
Smart est significativement plus rapide que Dark chez AE mais Smart est significativement plus lent que Dark et Full chez OP.
Full est quasiment significativement (0.082) plus lent que Dark mais uniquement dans le Luxembourg.
Full est quasiment significativement (0.086) plus lent que Smart.
Full est quasiment significativement (0.097) plus lent dans le Luxembourg.
Mixt_smart est plus lent que n'importe quel autre treatment mais uniquement dans le Luxembourg
"
Infos_TT_pupation## [1] "\nOP est plus rapide.\nSmart est significativement plus rapide que Dark chez AE mais Smart est significativement plus lent que Dark et Full chez OP.\nFull est quasiment significativement (0.082) plus lent que Dark mais uniquement dans le Luxembourg.\nFull est quasiment significativement (0.086) plus lent que Smart.\nFull est quasiment significativement (0.097) plus lent dans le Luxembourg.\nMixt_smart est plus lent que n'importe quel autre treatment mais uniquement dans le Luxembourg\n"4.3.4 Visualisation
Summary_TT_pupation <- Data %>%
filter(Did_pupated == "Yes") %>%
group_by(Treatment_bis, Species, Region) %>%
summarise(Mean=mean(log(TT_pupation)),
Var=var(log(TT_pupation)),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_TT_pupation, aes(x=Treatment_bis, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_grid(~Region) +
labs(title = "Temps pour entrer en chrysalide", x = "Traitement", y = "log(Nombre de jours)", color = "Espèce") +
theme_bw()
Summary_TT_pupation2 <- Data %>%
filter(Did_pupated == "Yes") %>%
group_by(Treatment_bis, Species) %>%
summarise(Mean=mean(log(TT_pupation)),
Var=var(log(TT_pupation)),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_TT_pupation2, aes(x=Treatment_bis, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
labs(title = "Time to Pupation", x = "Treatment", y = "log(Days)") +
theme_bw()
4.4 Time_in_pupa
4.4.1 Test
LM_Time_in_pupa <- lmer(Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')summary(LM_TT_pupation)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex
## Data: Data
##
## REML criterion at convergence: -42.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.1358 -0.5872 -0.1119 0.5122 4.1975
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.009186 0.09584
## Site (Intercept) 0.007935 0.08908
## Room (Intercept) 0.000000 0.00000
## Residual 0.037209 0.19290
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.703375 0.059318 17.639677 62.433
## Treatment_bisFull 0.003632 0.045196 270.551334 0.080
## Treatment_bisSmart -0.149036 0.051781 267.531050 -2.878
## Treatment_bisMixt_smart 0.094418 0.060451 273.190577 1.562
## SexMale 0.032073 0.046472 274.662322 0.690
## SpeciesOP -0.978520 0.075109 36.810031 -13.028
## RegionLuxembourg 0.167889 0.072314 11.490685 2.322
## SexMale:SpeciesOP -0.080675 0.049172 270.185399 -1.641
## SpeciesOP:RegionLuxembourg -0.177645 0.093183 22.435976 -1.906
## Treatment_bisFull:SpeciesOP -0.020124 0.053223 266.394454 -0.378
## Treatment_bisSmart:SpeciesOP 0.186982 0.069245 266.224474 2.700
## Treatment_bisFull:SexMale 0.008564 0.053709 269.268432 0.159
## Treatment_bisSmart:SexMale -0.019486 0.070773 277.233351 -0.275
## Treatment_bisMixt_smart:SexMale -0.122305 0.088787 274.741600 -1.378
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisFull 0.93601
## Treatment_bisSmart 0.00432 **
## Treatment_bisMixt_smart 0.11947
## SexMale 0.49068
## SpeciesOP 2.35e-15 ***
## RegionLuxembourg 0.03953 *
## SexMale:SpeciesOP 0.10203
## SpeciesOP:RegionLuxembourg 0.06949 .
## Treatment_bisFull:SpeciesOP 0.70566
## Treatment_bisSmart:SpeciesOP 0.00737 **
## Treatment_bisFull:SexMale 0.87344
## Treatment_bisSmart:SexMale 0.78327
## Treatment_bisMixt_smart:SexMale 0.16947
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 14 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification de la normalité
qqnorm(resid(LM_Time_in_pupa))
qqline(resid(LM_Time_in_pupa))
Homogénité des variances
plot(LM_Time_in_pupa)
Distance de cook
plot(cooks.distance(LM_Time_in_pupa))
4.4.2 Simplification du modèle
drop1(LM_Time_in_pupa)## Single term deletions using Satterthwaite's method:
##
## Model:
## Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.0006 0.0006 1 233.454 0.0007 0.979312
## Species:Region 0.2057 0.2057 1 24.657 0.2453 0.624763
## Treatment_bis:Species 0.0504 0.0252 2 225.751 0.0301 0.970386
## Treatment_bis:Sex 0.4442 0.1481 3 236.799 0.1766 0.912182
## Treatment_bis:Region 10.6469 3.5490 3 226.603 4.2325 0.006184 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Time_in_pupa1 <- update(LM_Time_in_pupa, . ~ . - Treatment_bis:Species)## boundary (singular) fit: see help('isSingular')drop1(LM_Time_in_pupa1)## Single term deletions using Satterthwaite's method:
##
## Model:
## Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.0018 0.0018 1 234.291 0.0021 0.963184
## Species:Region 0.2232 0.2232 1 24.502 0.2685 0.608970
## Treatment_bis:Sex 0.4791 0.1597 3 238.458 0.1921 0.901693
## Treatment_bis:Region 10.6736 3.5579 3 228.099 4.2809 0.005794 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Time_in_pupa2 <- update(LM_Time_in_pupa1, . ~ . - Sex:Species)## boundary (singular) fit: see help('isSingular')drop1(LM_Time_in_pupa2)## Single term deletions using Satterthwaite's method:
##
## Model:
## Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Species:Region 0.2233 0.2233 1 24.508 0.2699 0.608084
## Treatment_bis:Sex 0.4781 0.1594 3 239.938 0.1926 0.901365
## Treatment_bis:Region 10.6700 3.5567 3 228.953 4.2984 0.005659 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Time_in_pupa3 <- update(LM_Time_in_pupa2, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_Time_in_pupa3)## Single term deletions using Satterthwaite's method:
##
## Model:
## Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 14.4272 14.4272 1 240.509 17.5990 3.838e-05 ***
## Species:Region 0.2293 0.2293 1 24.592 0.2797 0.601642
## Treatment_bis:Region 10.6710 3.5570 3 231.728 4.3390 0.005353 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Time_in_pupa4 <- update(LM_Time_in_pupa3, . ~ . - Species:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_Time_in_pupa4)## Single term deletions using Satterthwaite's method:
##
## Model:
## Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 14.5453 14.5453 1 240.987 17.7076 3.637e-05 ***
## Species 7.6276 7.6276 1 25.499 9.2859 0.005316 **
## Treatment_bis:Region 11.7854 3.9285 3 237.395 4.7825 0.002960 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Regardons si les simplifications étaient utiles
AIC(LM_Time_in_pupa4)## [1] 757.3326AIC(LM_Time_in_pupa)## [1] 773.8755Les simplifications étaient utiles
LM_Time_in_pupa <- LM_Time_in_pupa44.4.3 Treatment VS Treatment_bis
AIC(lmer(Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data))## boundary (singular) fit: see help('isSingular')## [1] 757.3326AIC(lmer(Time_in_pupa ~ Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region , data = Data))## boundary (singular) fit: see help('isSingular')## [1] 777.6884summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 13.45331264 0.3249256 1.817888
## Treatment_bisFull 0.45732669 0.1850741 229.313659
## Treatment_bisSmart 0.09052413 0.2551831 228.989561
## Treatment_bisMixt_smart 0.42937690 0.2813087 243.934122
## SexMale 0.49161888 0.1168286 240.987065
## SpeciesOP -0.55825601 0.1831983 25.498629
## RegionLuxembourg -0.06501675 0.2244022 61.155647
## Treatment_bisFull:RegionLuxembourg -0.28437877 0.2675173 228.196157
## Treatment_bisSmart:RegionLuxembourg -0.17391802 0.3339218 231.779821
## Treatment_bisMixt_smart:RegionLuxembourg 1.28735203 0.4186491 251.087106
## t value Pr(>|t|)
## (Intercept) 41.4042883 1.025199e-03
## Treatment_bisFull 2.4710458 1.420013e-02
## Treatment_bisSmart 0.3547418 7.231095e-01
## Treatment_bisMixt_smart 1.5263549 1.282170e-01
## SexMale 4.2080344 3.637027e-05
## SpeciesOP -3.0472775 5.315530e-03
## RegionLuxembourg -0.2897331 7.730005e-01
## Treatment_bisFull:RegionLuxembourg -1.0630294 2.888923e-01
## Treatment_bisSmart:RegionLuxembourg -0.5208345 6.029792e-01
## Treatment_bisMixt_smart:RegionLuxembourg 3.0750143 2.337524e-03summary(lmer(Time_in_pupa ~ Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region , data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 13.54506094 0.4239224 1.480875 31.9517457
## TreatmentFull 0.42000429 0.2040923 227.548411 2.0579139
## TreatmentSmart 0.09595950 0.1998780 229.649815 0.4800903
## SexMale 0.53525851 0.1220365 242.847208 4.3860510
## SpeciesOP -0.75352492 0.1794630 21.626285 -4.1987768
## RegionLuxembourg -0.08781116 0.2481337 88.075803 -0.3538864
## TreatmentFull:RegionLuxembourg -0.18552603 0.2983027 230.389072 -0.6219387
## TreatmentSmart:RegionLuxembourg 0.30029402 0.2907840 230.282277 1.0327048
## Pr(>|t|)
## (Intercept) 4.419164e-03
## TreatmentFull 4.073785e-02
## TreatmentSmart 6.316201e-01
## SexMale 1.720899e-05
## SpeciesOP 3.829421e-04
## RegionLuxembourg 7.242698e-01
## TreatmentFull:RegionLuxembourg 5.345971e-01
## TreatmentSmart:RegionLuxembourg 3.028254e-01Selon les summary le choix de treatment ou treatment_bis est discutable mais on peut alors se pencher sur l’AIC qui nous encourage à prendre treatment_bis.
Analysons les P-val
summary(LM_Time_in_pupa)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: 729.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.0873 -0.6314 -0.0501 0.5971 3.7822
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.1324 0.3639
## Site (Intercept) 0.0000 0.0000
## Room (Intercept) 0.1471 0.3836
## Residual 0.8214 0.9063
## Number of obs: 263, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 13.45331 0.32493 1.81789 41.404
## Treatment_bisFull 0.45733 0.18507 229.31366 2.471
## Treatment_bisSmart 0.09052 0.25518 228.98956 0.355
## Treatment_bisMixt_smart 0.42938 0.28131 243.93412 1.526
## SexMale 0.49162 0.11683 240.98707 4.208
## SpeciesOP -0.55826 0.18320 25.49863 -3.047
## RegionLuxembourg -0.06502 0.22440 61.15565 -0.290
## Treatment_bisFull:RegionLuxembourg -0.28438 0.26752 228.19616 -1.063
## Treatment_bisSmart:RegionLuxembourg -0.17392 0.33392 231.77982 -0.521
## Treatment_bisMixt_smart:RegionLuxembourg 1.28735 0.41865 251.08711 3.075
## Pr(>|t|)
## (Intercept) 0.00103 **
## Treatment_bisFull 0.01420 *
## Treatment_bisSmart 0.72311
## Treatment_bisMixt_smart 0.12822
## SexMale 3.64e-05 ***
## SpeciesOP 0.00532 **
## RegionLuxembourg 0.77300
## Treatment_bisFull:RegionLuxembourg 0.28889
## Treatment_bisSmart:RegionLuxembourg 0.60298
## Treatment_bisMixt_smart:RegionLuxembourg 0.00234 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal SpcsOP RgnLxm T_F:RL T_S:RL
## Trtmnt_bsFl -0.244
## Trtmnt_bsSm -0.203 0.326
## Trtmnt_bsM_ -0.214 0.305 0.174
## SexMale -0.142 -0.100 0.029 -0.043
## SpeciesOP -0.244 0.037 0.044 0.183 -0.003
## ReginLxmbrg -0.319 0.360 0.268 0.254 0.000 -0.013
## Trtmnt_F:RL 0.179 -0.687 -0.212 -0.226 0.032 -0.051 -0.533
## Trtmnt_S:RL 0.146 -0.237 -0.703 -0.174 -0.033 -0.012 -0.450 0.361
## Trtmn_M_:RL 0.120 -0.203 -0.158 -0.610 -0.012 0.014 -0.396 0.299 0.259
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_ref_full
##
## REML criterion at convergence: 729.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.0873 -0.6314 -0.0501 0.5971 3.7822
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.1324 0.3639
## Site (Intercept) 0.0000 0.0000
## Room (Intercept) 0.1471 0.3836
## Residual 0.8214 0.9063
## Number of obs: 263, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 13.91064 0.33232 1.98902 41.859
## Treatment_bisDark -0.45733 0.18507 229.31366 -2.471
## Treatment_bisSmart -0.36680 0.26193 230.47280 -1.400
## Treatment_bisMixt_smart -0.02795 0.28564 234.75630 -0.098
## SexMale 0.49162 0.11683 240.98707 4.208
## SpeciesOP -0.55826 0.18320 25.49863 -3.047
## RegionLuxembourg -0.34940 0.24080 77.02702 -1.451
## Treatment_bisDark:RegionLuxembourg 0.28438 0.26752 228.19616 1.063
## Treatment_bisSmart:RegionLuxembourg 0.11046 0.34428 231.63277 0.321
## Treatment_bisMixt_smart:RegionLuxembourg 1.57173 0.42411 248.36645 3.706
## Pr(>|t|)
## (Intercept) 0.00059 ***
## Treatment_bisDark 0.01420 *
## Treatment_bisSmart 0.16275
## Treatment_bisMixt_smart 0.92214
## SexMale 3.64e-05 ***
## SpeciesOP 0.00532 **
## RegionLuxembourg 0.15085
## Treatment_bisDark:RegionLuxembourg 0.28889
## Treatment_bisSmart:RegionLuxembourg 0.74861
## Treatment_bisMixt_smart:RegionLuxembourg 0.00026 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal SpcsOP RgnLxm T_D:RL T_S:RL
## Trtmnt_bsDr -0.318
## Trtmnt_bsSm -0.241 0.389
## Trtmnt_bsM_ -0.244 0.347 0.206
## SexMale -0.195 0.100 0.099 0.023
## SpeciesOP -0.218 -0.037 0.017 0.156 -0.003
## ReginLxmbrg -0.334 0.427 0.315 0.262 0.035 -0.069
## Trtmnt_D:RL 0.207 -0.687 -0.278 -0.222 -0.032 0.051 -0.615
## Trtmnt_S:RL 0.171 -0.303 -0.718 -0.190 -0.057 0.028 -0.495 0.427
## Trtmn_M_:RL 0.135 -0.232 -0.185 -0.603 -0.032 0.046 -0.424 0.336 0.287
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Time_in_pupa ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_ref_smart
##
## REML criterion at convergence: 729.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.0873 -0.6314 -0.0501 0.5971 3.7822
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.1324 0.3639
## Site (Intercept) 0.0000 0.0000
## Room (Intercept) 0.1471 0.3836
## Residual 0.8214 0.9063
## Number of obs: 263, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 13.54384 0.37027 3.03794 36.578
## Treatment_bisDark -0.09052 0.25518 228.98956 -0.355
## Treatment_bisFull 0.36680 0.26193 230.47280 1.400
## Treatment_bisMixt_smart 0.33885 0.34540 232.77518 0.981
## SexMale 0.49162 0.11683 240.98707 4.208
## SpeciesOP -0.55826 0.18320 25.49863 -3.047
## RegionLuxembourg -0.23893 0.30735 166.21382 -0.777
## Treatment_bisDark:RegionLuxembourg 0.17392 0.33392 231.77982 0.521
## Treatment_bisFull:RegionLuxembourg -0.11046 0.34428 231.63277 -0.321
## Treatment_bisMixt_smart:RegionLuxembourg 1.46127 0.46310 242.04038 3.155
## Pr(>|t|)
## (Intercept) 4.06e-05 ***
## Treatment_bisDark 0.72311
## Treatment_bisFull 0.16275
## Treatment_bisMixt_smart 0.32759
## SexMale 3.64e-05 ***
## SpeciesOP 0.00532 **
## RegionLuxembourg 0.43803
## Treatment_bisDark:RegionLuxembourg 0.60298
## Treatment_bisFull:RegionLuxembourg 0.74861
## Treatment_bisMixt_smart:RegionLuxembourg 0.00181 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal SpcsOP RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.511
## Trtmnt_bsFl -0.491 0.744
## Trtmnt_bsM_ -0.433 0.597 0.588
## SexMale -0.105 -0.029 -0.099 -0.056
## SpeciesOP -0.184 -0.044 -0.017 0.116 -0.003
## ReginLxmbrg -0.457 0.568 0.557 0.416 -0.036 -0.022
## Trtmnt_D:RL 0.357 -0.703 -0.517 -0.377 0.033 0.012 -0.758
## Trtmnt_F:RL 0.354 -0.517 -0.718 -0.387 0.057 -0.028 -0.732 0.689
## Trtmn_M_:RL 0.254 -0.364 -0.364 -0.616 0.013 0.021 -0.554 0.487 0.480
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Info_time_in_pupa <- "
Le traitement Full met significativement plus de temps que le traitement Dark.
Le traitement Smart met significativement moins de temps que le traitement Full.
Le traitement Smart a une p-val de 0.999 quand on le compare à dark. Ces 2 traitements sont donc très simillaires.
Les males sont significatiment plus lent
L'espèce OP est significativement plus rapide
Les chenilles restent plus longtemps en chrysalide dans le traitement Mixt_smart quand elles viennent du luxembourg que quand elles viennent du brabant.
"
Info_time_in_pupa## [1] "\nLe traitement Full met significativement plus de temps que le traitement Dark.\nLe traitement Smart met significativement moins de temps que le traitement Full.\nLe traitement Smart a une p-val de 0.999 quand on le compare à dark. Ces 2 traitements sont donc très simillaires.\nLes males sont significatiment plus lent\nL'espèce OP est significativement plus rapide\nLes chenilles restent plus longtemps en chrysalide dans le traitement Mixt_smart quand elles viennent du luxembourg que quand elles viennent du brabant.\n"4.4.4 Visualisation
Summary_Time_in_pupa <- Data %>%
filter(Did_pupated == "Yes", Did_emerged == "Yes", Sex != "NA") %>%
group_by(Treatment_bis, Species, Region) %>%
summarise(Mean=mean(Time_in_pupa),
Var=var(Time_in_pupa),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_Time_in_pupa, aes(x=Treatment_bis, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_wrap(~Region) +
labs(title = "Temps en chrysalide", x = "Traitement", y = "Nombre de jours", color = "Espèce") +
theme_bw()
Tout se voit super bien sur ce graph sauf le Sex.
Summary_Time_in_pupa2 <- Data %>%
filter(Did_pupated == "Yes", Did_emerged == "Yes", Sex != "NA") %>%
group_by(Treatment_bis, Species, Sex) %>%
summarise(Mean=mean(Time_in_pupa),
Var=var(Time_in_pupa),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_Time_in_pupa2, aes(x=Treatment_bis, y=Mean, color = Sex))+
scale_color_manual(name = "Sex", values = c("Female" = "red", "Male" = "royalblue")) +
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_wrap(~Species) +
labs(title = "Temps en chrysalide", x = "Traitement", y = "Nombre de jours", color = "Espèce") +
theme_bw()
4.5 TT_emerge
4.5.1 Test
LM_TT_emerge <- lmer(TT_emerge ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientsummary(LM_TT_pupation)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex
## Data: Data
##
## REML criterion at convergence: -42.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.1358 -0.5872 -0.1119 0.5122 4.1975
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.009186 0.09584
## Site (Intercept) 0.007935 0.08908
## Room (Intercept) 0.000000 0.00000
## Residual 0.037209 0.19290
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.703375 0.059318 17.639677 62.433
## Treatment_bisFull 0.003632 0.045196 270.551334 0.080
## Treatment_bisSmart -0.149036 0.051781 267.531050 -2.878
## Treatment_bisMixt_smart 0.094418 0.060451 273.190577 1.562
## SexMale 0.032073 0.046472 274.662322 0.690
## SpeciesOP -0.978520 0.075109 36.810031 -13.028
## RegionLuxembourg 0.167889 0.072314 11.490685 2.322
## SexMale:SpeciesOP -0.080675 0.049172 270.185399 -1.641
## SpeciesOP:RegionLuxembourg -0.177645 0.093183 22.435976 -1.906
## Treatment_bisFull:SpeciesOP -0.020124 0.053223 266.394454 -0.378
## Treatment_bisSmart:SpeciesOP 0.186982 0.069245 266.224474 2.700
## Treatment_bisFull:SexMale 0.008564 0.053709 269.268432 0.159
## Treatment_bisSmart:SexMale -0.019486 0.070773 277.233351 -0.275
## Treatment_bisMixt_smart:SexMale -0.122305 0.088787 274.741600 -1.378
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisFull 0.93601
## Treatment_bisSmart 0.00432 **
## Treatment_bisMixt_smart 0.11947
## SexMale 0.49068
## SpeciesOP 2.35e-15 ***
## RegionLuxembourg 0.03953 *
## SexMale:SpeciesOP 0.10203
## SpeciesOP:RegionLuxembourg 0.06949 .
## Treatment_bisFull:SpeciesOP 0.70566
## Treatment_bisSmart:SpeciesOP 0.00737 **
## Treatment_bisFull:SexMale 0.87344
## Treatment_bisSmart:SexMale 0.78327
## Treatment_bisMixt_smart:SexMale 0.16947
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 14 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification de la normalité
qqnorm(resid(LM_TT_emerge))
qqline(resid(LM_TT_emerge))
il faudrait mettre d’autres facteur
LM_TT_emerge <- lmer(log(TT_emerge) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientsummary(LM_TT_pupation)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex
## Data: Data
##
## REML criterion at convergence: -42.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.1358 -0.5872 -0.1119 0.5122 4.1975
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.009186 0.09584
## Site (Intercept) 0.007935 0.08908
## Room (Intercept) 0.000000 0.00000
## Residual 0.037209 0.19290
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.703375 0.059318 17.639677 62.433
## Treatment_bisFull 0.003632 0.045196 270.551334 0.080
## Treatment_bisSmart -0.149036 0.051781 267.531050 -2.878
## Treatment_bisMixt_smart 0.094418 0.060451 273.190577 1.562
## SexMale 0.032073 0.046472 274.662322 0.690
## SpeciesOP -0.978520 0.075109 36.810031 -13.028
## RegionLuxembourg 0.167889 0.072314 11.490685 2.322
## SexMale:SpeciesOP -0.080675 0.049172 270.185399 -1.641
## SpeciesOP:RegionLuxembourg -0.177645 0.093183 22.435976 -1.906
## Treatment_bisFull:SpeciesOP -0.020124 0.053223 266.394454 -0.378
## Treatment_bisSmart:SpeciesOP 0.186982 0.069245 266.224474 2.700
## Treatment_bisFull:SexMale 0.008564 0.053709 269.268432 0.159
## Treatment_bisSmart:SexMale -0.019486 0.070773 277.233351 -0.275
## Treatment_bisMixt_smart:SexMale -0.122305 0.088787 274.741600 -1.378
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisFull 0.93601
## Treatment_bisSmart 0.00432 **
## Treatment_bisMixt_smart 0.11947
## SexMale 0.49068
## SpeciesOP 2.35e-15 ***
## RegionLuxembourg 0.03953 *
## SexMale:SpeciesOP 0.10203
## SpeciesOP:RegionLuxembourg 0.06949 .
## Treatment_bisFull:SpeciesOP 0.70566
## Treatment_bisSmart:SpeciesOP 0.00737 **
## Treatment_bisFull:SexMale 0.87344
## Treatment_bisSmart:SexMale 0.78327
## Treatment_bisMixt_smart:SexMale 0.16947
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 14 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')qqnorm(resid(LM_TT_emerge))
qqline(resid(LM_TT_emerge))
La normalité est bien meilleure
Homogénité des variances
plot(LM_TT_emerge)
Distance de cook
plot(cooks.distance(LM_TT_emerge))
4.5.2 Simplification du modèle
drop1(LM_TT_emerge)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_emerge) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.050181 0.050181 1 226.851 3.7656 0.053555 .
## Species:Region 0.062438 0.062438 1 24.509 4.6854 0.040371 *
## Treatment_bis:Species 0.077601 0.038801 2 222.783 2.9116 0.056460 .
## Treatment_bis:Sex 0.029588 0.009863 3 231.007 0.7401 0.529101
## Treatment_bis:Region 0.161811 0.053937 3 224.073 4.0475 0.007911 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_TT_emerge1 <- update(LM_TT_emerge, . ~ . - Treatment_bis:Sex)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientdrop1(LM_TT_emerge1)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_emerge) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region + Treatment_bis:Species + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.032558 0.032558 1 231.652 2.4589 0.118228
## Species:Region 0.063200 0.063200 1 25.091 4.7731 0.038459 *
## Treatment_bis:Species 0.082017 0.041009 2 225.158 3.0971 0.047110 *
## Treatment_bis:Region 0.157084 0.052361 3 226.910 3.9545 0.008932 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_TT_emerge2 <- update(LM_TT_emerge1, . ~ . - Sex:Species)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientdrop1(LM_TT_emerge2)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_emerge) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Species + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 0.028634 0.028634 1 232.688 2.1554 0.143420
## Species:Region 0.059023 0.059023 1 25.068 4.4429 0.045215 *
## Treatment_bis:Species 0.086589 0.043295 2 225.388 3.2589 0.040248 *
## Treatment_bis:Region 0.161320 0.053773 3 227.310 4.0477 0.007894 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_TT_emerge3 <- update(LM_TT_emerge2, . ~ . - Sex)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientdrop1(LM_TT_emerge3)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_emerge) ~ Treatment_bis + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Species + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Species:Region 0.077673 0.077673 1 23.623 5.5680 0.026907 *
## Treatment_bis:Species 0.118286 0.059143 2 230.317 4.2397 0.015552 *
## Treatment_bis:Region 0.179960 0.059987 3 232.584 4.3002 0.005633 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Regardons si les simplifications étaient utiles
AIC(LM_TT_emerge)## [1] -230.623AIC(LM_TT_emerge3)## [1] -255.422Les simplifications étaient utiles
LM_TT_emerge <- LM_TT_emerge34.5.3 Treatment VS Treatment_bis
AIC(lmer(log(TT_emerge) ~ Treatment_bis + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Species + Treatment_bis:Region, data = Data))## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## [1] -255.422AIC(lmer(log(TT_emerge) ~ Treatment + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment:Species + Treatment:Region, data = Data))## [1] -240.5444summary(lmer(log(TT_emerge) ~ Treatment_bis + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Species + Treatment_bis:Region, data = Data))$coeff## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## Estimate Std. Error df
## (Intercept) 3.95511287 0.03922836 10.86725
## Treatment_bisFull 0.03071693 0.02982998 230.27031
## Treatment_bisSmart -0.02498566 0.03655393 226.81083
## Treatment_bisMixt_smart 0.01850374 0.03861631 230.55791
## SpeciesOP -0.61094803 0.04728140 32.08622
## RegionLuxembourg 0.12977121 0.04817467 20.66081
## SpeciesOP:RegionLuxembourg -0.14641003 0.06204679 23.62279
## Treatment_bisFull:SpeciesOP -0.03994628 0.03529009 231.70760
## Treatment_bisSmart:SpeciesOP 0.09209626 0.04426232 229.36551
## Treatment_bisFull:RegionLuxembourg 0.01203657 0.03482695 229.18573
## Treatment_bisSmart:RegionLuxembourg -0.08467750 0.04340001 229.05798
## Treatment_bisMixt_smart:RegionLuxembourg 0.13212333 0.05662560 239.33271
## t value Pr(>|t|)
## (Intercept) 100.8227848 1.691591e-17
## Treatment_bisFull 1.0297336 3.042155e-01
## Treatment_bisSmart -0.6835286 4.949706e-01
## Treatment_bisMixt_smart 0.4791690 6.322726e-01
## SpeciesOP -12.9215309 2.914775e-14
## RegionLuxembourg 2.6937641 1.371780e-02
## SpeciesOP:RegionLuxembourg -2.3596714 2.690678e-02
## Treatment_bisFull:SpeciesOP -1.1319405 2.588295e-01
## Treatment_bisSmart:SpeciesOP 2.0806924 3.857230e-02
## Treatment_bisFull:RegionLuxembourg 0.3456108 7.299523e-01
## Treatment_bisSmart:RegionLuxembourg -1.9510939 5.226518e-02
## Treatment_bisMixt_smart:RegionLuxembourg 2.3332792 2.046272e-02summary(lmer(log(TT_emerge) ~ Treatment + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment:Species + Treatment:Region, data = Data))$coeff## Estimate Std. Error df
## (Intercept) 3.9562735447 0.04720156 4.787439
## TreatmentFull 0.0271855793 0.03176171 231.679029
## TreatmentSmart 0.0001964454 0.03048215 233.363063
## SpeciesOP -0.6110264019 0.05073851 37.109398
## RegionLuxembourg 0.1362527299 0.04939532 21.758770
## SpeciesOP:RegionLuxembourg -0.1610352195 0.06359414 22.744920
## TreatmentFull:SpeciesOP -0.0362881789 0.03897183 231.487350
## TreatmentSmart:SpeciesOP 0.0113951343 0.03793371 231.155322
## TreatmentFull:RegionLuxembourg 0.0138360443 0.03901176 231.765691
## TreatmentSmart:RegionLuxembourg -0.0122431400 0.03781352 232.754484
## t value Pr(>|t|)
## (Intercept) 83.816592483 9.097349e-09
## TreatmentFull 0.855923007 3.929247e-01
## TreatmentSmart 0.006444605 9.948635e-01
## SpeciesOP -12.042655457 2.194485e-14
## RegionLuxembourg 2.758413625 1.153818e-02
## SpeciesOP:RegionLuxembourg -2.532233499 1.870751e-02
## TreatmentFull:SpeciesOP -0.931138719 3.527519e-01
## TreatmentSmart:SpeciesOP 0.300396017 7.641451e-01
## TreatmentFull:RegionLuxembourg 0.354663397 7.231643e-01
## TreatmentSmart:RegionLuxembourg -0.323776769 7.463978e-01Treatment_bis est meilleur, il explique mieux les résultats obtenus
Analysons les P-val
summary(LM_TT_emerge)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_emerge) ~ Treatment_bis + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Species +
## Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: -287.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4315 -0.6567 -0.0274 0.4973 3.5040
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0043738 0.06613
## Site (Intercept) 0.0017208 0.04148
## Room (Intercept) 0.0005773 0.02403
## Residual 0.0139498 0.11811
## Number of obs: 268, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.95511 0.03923 10.86725 100.823
## Treatment_bisFull 0.03072 0.02983 230.27031 1.030
## Treatment_bisSmart -0.02499 0.03655 226.81083 -0.684
## Treatment_bisMixt_smart 0.01850 0.03862 230.55791 0.479
## SpeciesOP -0.61095 0.04728 32.08622 -12.922
## RegionLuxembourg 0.12977 0.04817 20.66081 2.694
## SpeciesOP:RegionLuxembourg -0.14641 0.06205 23.62279 -2.360
## Treatment_bisFull:SpeciesOP -0.03995 0.03529 231.70760 -1.132
## Treatment_bisSmart:SpeciesOP 0.09210 0.04426 229.36551 2.081
## Treatment_bisFull:RegionLuxembourg 0.01204 0.03483 229.18573 0.346
## Treatment_bisSmart:RegionLuxembourg -0.08468 0.04340 229.05798 -1.951
## Treatment_bisMixt_smart:RegionLuxembourg 0.13212 0.05663 239.33271 2.333
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisFull 0.3042
## Treatment_bisSmart 0.4950
## Treatment_bisMixt_smart 0.6323
## SpeciesOP 2.91e-14 ***
## RegionLuxembourg 0.0137 *
## SpeciesOP:RegionLuxembourg 0.0269 *
## Treatment_bisFull:SpeciesOP 0.2588
## Treatment_bisSmart:SpeciesOP 0.0386 *
## Treatment_bisFull:RegionLuxembourg 0.7300
## Treatment_bisSmart:RegionLuxembourg 0.0523 .
## Treatment_bisMixt_smart:RegionLuxembourg 0.0205 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SpcsOP RgnLxm SOP:RL T_F:SO T_S:SO
## Trtmnt_bsFl -0.374
## Trtmnt_bsSm -0.284 0.371
## Trtmnt_bsM_ -0.338 0.396 0.259
## SpeciesOP -0.522 0.234 0.166 0.256
## ReginLxmbrg -0.608 0.188 0.149 0.210 0.344
## SpcsOP:RgnL 0.326 -0.022 -0.021 -0.103 -0.654 -0.516
## Trtmn_F:SOP 0.229 -0.604 -0.212 -0.260 -0.333 0.007 -0.004
## Trtmn_S:SOP 0.161 -0.231 -0.453 -0.187 -0.247 0.047 -0.049 0.367
## Trtmnt_F:RL 0.178 -0.477 -0.178 -0.190 0.004 -0.325 0.002 -0.110 -0.013
## Trtmnt_S:RL 0.158 -0.182 -0.593 -0.165 -0.025 -0.318 0.073 -0.022 -0.066
## Trtmn_M_:RL 0.179 -0.155 -0.131 -0.590 -0.090 -0.338 0.182 -0.019 -0.038
## T_F:RL T_S:RL
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SpeciesOP
## ReginLxmbrg
## SpcsOP:RgnL
## Trtmn_F:SOP
## Trtmn_S:SOP
## Trtmnt_F:RL
## Trtmnt_S:RL 0.361
## Trtmn_M_:RL 0.293 0.272
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientsummary(lmer(log(TT_emerge) ~ Treatment_bis + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Species + Treatment_bis:Region, data = Data_ref_full))## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_emerge) ~ Treatment_bis + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Species +
## Treatment_bis:Region
## Data: Data_ref_full
##
## REML criterion at convergence: -287.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4315 -0.6567 -0.0274 0.4973 3.5040
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0043738 0.06613
## Site (Intercept) 0.0017208 0.04148
## Room (Intercept) 0.0005773 0.02403
## Residual 0.0139498 0.11811
## Number of obs: 268, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.98583 0.03941 11.39642 101.141
## Treatment_bisDark -0.03072 0.02983 230.27031 -1.030
## Treatment_bisSmart -0.05570 0.03764 227.26576 -1.480
## Treatment_bisMixt_smart -0.01221 0.03833 227.31328 -0.319
## SpeciesOP -0.65089 0.04869 36.17365 -13.369
## RegionLuxembourg 0.14181 0.04942 23.88074 2.869
## SpeciesOP:RegionLuxembourg -0.14641 0.06205 23.62279 -2.360
## Treatment_bisDark:SpeciesOP 0.03995 0.03529 231.70760 1.132
## Treatment_bisSmart:SpeciesOP 0.13204 0.04537 229.72874 2.910
## Treatment_bisDark:RegionLuxembourg -0.01204 0.03483 229.18573 -0.346
## Treatment_bisSmart:RegionLuxembourg -0.09671 0.04479 230.27755 -2.159
## Treatment_bisMixt_smart:RegionLuxembourg 0.12009 0.05715 235.94233 2.101
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisDark 0.30422
## Treatment_bisSmart 0.14030
## Treatment_bisMixt_smart 0.75032
## SpeciesOP 1.45e-15 ***
## RegionLuxembourg 0.00847 **
## SpeciesOP:RegionLuxembourg 0.02691 *
## Treatment_bisDark:SpeciesOP 0.25883
## Treatment_bisSmart:SpeciesOP 0.00397 **
## Treatment_bisDark:RegionLuxembourg 0.72995
## Treatment_bisSmart:RegionLuxembourg 0.03186 *
## Treatment_bisMixt_smart:RegionLuxembourg 0.03667 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SpcsOP RgnLxm SOP:RL T_D:SO T_S:SO
## Trtmnt_bsDr -0.384
## Trtmnt_bsSm -0.306 0.432
## Trtmnt_bsM_ -0.337 0.380 0.274
## SpeciesOP -0.499 0.211 0.174 0.225
## ReginLxmbrg -0.581 0.153 0.140 0.190 0.277
## SpcsOP:RgnL 0.308 0.022 -0.003 -0.086 -0.638 -0.502
## Trtmn_D:SOP 0.229 -0.604 -0.272 -0.208 -0.402 0.071 0.004
## Trtmn_S:SOP 0.164 -0.244 -0.462 -0.170 -0.287 0.090 -0.045 0.420
## Trtmnt_D:RL 0.183 -0.477 -0.205 -0.179 0.076 -0.388 -0.002 -0.110 -0.072
## Trtmnt_S:RL 0.162 -0.195 -0.577 -0.163 0.020 -0.355 0.070 -0.064 -0.103
## Trtmn_M_:RL 0.172 -0.137 -0.129 -0.578 -0.055 -0.359 0.179 -0.048 -0.066
## T_D:RL T_S:RL
## Trtmnt_bsDr
## Trtmnt_bsSm
## Trtmnt_bsM_
## SpeciesOP
## ReginLxmbrg
## SpcsOP:RgnL
## Trtmn_D:SOP
## Trtmn_S:SOP
## Trtmnt_D:RL
## Trtmnt_S:RL 0.428
## Trtmn_M_:RL 0.320 0.296
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientsummary(lmer(log(TT_emerge) ~ Treatment_bis + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Species + Treatment_bis:Region, data = Data_ref_smart))## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_emerge) ~ Treatment_bis + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Species +
## Treatment_bis:Region
## Data: Data_ref_smart
##
## REML criterion at convergence: -287.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4315 -0.6567 -0.0274 0.4973 3.5040
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0043738 0.06613
## Site (Intercept) 0.0017208 0.04148
## Room (Intercept) 0.0005773 0.02403
## Residual 0.0139498 0.11811
## Number of obs: 268, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.93013 0.04541 18.07036 86.551
## Treatment_bisDark 0.02499 0.03655 226.81083 0.684
## Treatment_bisFull 0.05570 0.03764 227.26576 1.480
## Treatment_bisMixt_smart 0.04349 0.04577 195.09444 0.950
## SpeciesOP -0.51885 0.05621 60.35141 -9.231
## RegionLuxembourg 0.04509 0.05363 30.96334 0.841
## SpeciesOP:RegionLuxembourg -0.14641 0.06205 23.62279 -2.360
## Treatment_bisDark:SpeciesOP -0.09210 0.04426 229.36551 -2.081
## Treatment_bisFull:SpeciesOP -0.13204 0.04537 229.72874 -2.910
## Treatment_bisDark:RegionLuxembourg 0.08468 0.04340 229.05797 1.951
## Treatment_bisFull:RegionLuxembourg 0.09671 0.04479 230.27755 2.159
## Treatment_bisMixt_smart:RegionLuxembourg 0.21680 0.06128 236.48764 3.538
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisDark 0.494971
## Treatment_bisFull 0.140302
## Treatment_bisMixt_smart 0.343238
## SpeciesOP 3.83e-13 ***
## RegionLuxembourg 0.406932
## SpeciesOP:RegionLuxembourg 0.026907 *
## Treatment_bisDark:SpeciesOP 0.038572 *
## Treatment_bisFull:SpeciesOP 0.003966 **
## Treatment_bisDark:RegionLuxembourg 0.052265 .
## Treatment_bisFull:RegionLuxembourg 0.031856 *
## Treatment_bisMixt_smart:RegionLuxembourg 0.000485 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SpcsOP RgnLxm SOP:RL T_D:SO T_F:SO
## Trtmnt_bsDr -0.560
## Trtmnt_bsFl -0.563 0.677
## Trtmnt_bsM_ -0.518 0.580 0.593
## SpeciesOP -0.445 0.218 0.223 0.231
## ReginLxmbrg -0.640 0.346 0.353 0.323 0.234
## SpcsOP:RgnL 0.265 0.021 0.003 -0.070 -0.589 -0.405
## Trtmn_D:SOP 0.226 -0.453 -0.257 -0.204 -0.579 0.012 0.049
## Trtmn_F:SOP 0.241 -0.277 -0.462 -0.238 -0.558 0.003 0.045 0.690
## Trtmnt_D:RL 0.341 -0.593 -0.431 -0.334 0.073 -0.524 -0.073 -0.066 -0.048
## Trtmnt_F:RL 0.338 -0.436 -0.577 -0.338 0.065 -0.508 -0.070 -0.054 -0.103
## Trtmn_M_:RL 0.286 -0.299 -0.301 -0.600 -0.046 -0.449 0.116 -0.012 -0.013
## T_D:RL T_F:RL
## Trtmnt_bsDr
## Trtmnt_bsFl
## Trtmnt_bsM_
## SpeciesOP
## ReginLxmbrg
## SpcsOP:RgnL
## Trtmn_D:SOP
## Trtmn_F:SOP
## Trtmnt_D:RL
## Trtmnt_F:RL 0.689
## Trtmn_M_:RL 0.457 0.455
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientInfos_TT_emerge <- "
L'impacte du traitement Smart chez OP est quasiment significativemt (p = 0.051) différent (plus lent que Dark) que l'impacte du traitement smart chez AE.
L'impacte du traitement Smart chez OP est significativemt différent (plus lent que Full) que l'impacte du traitement smart chez AE.
Chez AE, Le traitement smart est également significativement plus rapide que le traitement full.
L'impacte du traitement Mixt_Smart est différent (plus lent) en fonction de la région
L'espèce OP met significativement moins de temps.
La région luxembourg met significativement plus de temps pour l'espèce AE mais met significativement moins de temps pour l'espèce OP.
"
Infos_TT_emerge## [1] "\nL'impacte du traitement Smart chez OP est quasiment significativemt (p = 0.051) différent (plus lent que Dark) que l'impacte du traitement smart chez AE.\nL'impacte du traitement Smart chez OP est significativemt différent (plus lent que Full) que l'impacte du traitement smart chez AE.\nChez AE, Le traitement smart est également significativement plus rapide que le traitement full.\nL'impacte du traitement Mixt_Smart est différent (plus lent) en fonction de la région\nL'espèce OP met significativement moins de temps.\nLa région luxembourg met significativement plus de temps pour l'espèce AE mais met significativement moins de temps pour l'espèce OP.\n"4.5.4 Visualisation
Summary_TT_emerge <- Data %>%
filter(Did_emerged == "Yes") %>%
group_by(Treatment_bis, Species, Region) %>%
summarise(Mean=mean(log(TT_emerge)),
Var=var(log(TT_emerge)),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_TT_emerge, aes(x=Treatment_bis, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_grid(~Region) +
labs(title = "Time to Emerge", x = "Treatment", y = "log(Days)") +
theme_bw()
ggplot(Summary_TT_emerge, aes(x=Region, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_grid(~Treatment_bis) +
labs(title = "Temps pour devenir adulte", x = "Région", y = "log(Nombre de jours)", color = "Espèce") +
theme_bw()
Summary_TT_emerge2 <- Data %>%
filter(Did_emerged == "Yes") %>%
group_by(Treatment_bis, Species) %>%
summarise(Mean=mean(log(TT_emerge)),
Var=var(log(TT_emerge)),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_TT_emerge2, aes(x=Species, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_grid(~Treatment_bis) +
labs(title = "Time to Emerge", x = "Treatment", y = "log(Days)") +
theme_bw()
4.6 Pupa_mass
4.6.1 Test
LM_Pupa_mass <- lmer(Pupa_mass ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientsummary(LM_Pupa_mass)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: -827
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.1746 -0.4147 -0.0613 0.4129 3.1564
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.817e-04 0.024119
## Site (Intercept) 4.711e-04 0.021706
## Room (Intercept) 1.845e-06 0.001358
## Residual 1.942e-03 0.044066
## Number of obs: 288, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 3.236e-01 1.493e-02 1.804e+01
## Treatment_bisFull 1.673e-02 1.172e-02 2.472e+02
## Treatment_bisSmart 3.451e-03 1.403e-02 1.971e+02
## Treatment_bisMixt_smart 5.505e-02 1.623e-02 1.800e+02
## SexMale 2.074e-02 1.090e-02 2.543e+02
## SpeciesOP -1.594e-01 1.841e-02 3.515e+01
## RegionLuxembourg 1.109e-02 1.947e-02 1.575e+01
## SexMale:SpeciesOP -1.823e-02 1.160e-02 2.523e+02
## SpeciesOP:RegionLuxembourg -1.974e-02 2.362e-02 2.302e+01
## Treatment_bisFull:SpeciesOP -1.638e-02 1.257e-02 2.483e+02
## Treatment_bisSmart:SpeciesOP 1.077e-02 1.656e-02 2.522e+02
## Treatment_bisFull:SexMale -5.581e-04 1.265e-02 2.498e+02
## Treatment_bisSmart:SexMale -2.591e-02 1.683e-02 2.603e+02
## Treatment_bisMixt_smart:SexMale -5.771e-02 2.049e-02 2.547e+02
## Treatment_bisFull:RegionLuxembourg 7.998e-03 1.258e-02 2.481e+02
## Treatment_bisSmart:RegionLuxembourg 8.815e-03 1.594e-02 2.494e+02
## Treatment_bisMixt_smart:RegionLuxembourg 4.570e-02 2.014e-02 2.524e+02
## t value Pr(>|t|)
## (Intercept) 21.666 2.29e-14 ***
## Treatment_bisFull 1.427 0.154701
## Treatment_bisSmart 0.246 0.805956
## Treatment_bisMixt_smart 3.393 0.000851 ***
## SexMale 1.902 0.058251 .
## SpeciesOP -8.658 3.08e-10 ***
## RegionLuxembourg 0.570 0.576800
## SexMale:SpeciesOP -1.572 0.117286
## SpeciesOP:RegionLuxembourg -0.836 0.411726
## Treatment_bisFull:SpeciesOP -1.303 0.193808
## Treatment_bisSmart:SpeciesOP 0.650 0.516065
## Treatment_bisFull:SexMale -0.044 0.964832
## Treatment_bisSmart:SexMale -1.539 0.125002
## Treatment_bisMixt_smart:SexMale -2.817 0.005231 **
## Treatment_bisFull:RegionLuxembourg 0.636 0.525643
## Treatment_bisSmart:RegionLuxembourg 0.553 0.580822
## Treatment_bisMixt_smart:RegionLuxembourg 2.270 0.024082 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 17 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientVérification des hypothèses
qqnorm(resid(LM_Pupa_mass))
qqline(resid(LM_Pupa_mass))
Une modification des données est nécessaire
LM_Pupa_mass <- lmer(log(Pupa_mass) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientsummary(LM_Pupa_mass)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Pupa_mass) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: -173.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.7997 -0.5194 -0.0361 0.5925 2.6501
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0081743 0.09041
## Site (Intercept) 0.0016180 0.04022
## Room (Intercept) 0.0002465 0.01570
## Residual 0.0216932 0.14729
## Number of obs: 288, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -1.159437 0.046059 23.082221
## Treatment_bisFull 0.058897 0.039224 247.902786
## Treatment_bisSmart 0.023849 0.047302 236.570590
## Treatment_bisMixt_smart 0.163299 0.054827 231.860153
## SexMale 0.061889 0.036432 255.388721
## SpeciesOP -0.717450 0.062067 41.503349
## RegionLuxembourg 0.044759 0.058080 24.964495
## SexMale:SpeciesOP -0.052370 0.038754 253.584990
## SpeciesOP:RegionLuxembourg -0.081379 0.080940 29.739302
## Treatment_bisFull:SpeciesOP -0.031081 0.042079 249.800337
## Treatment_bisSmart:SpeciesOP 0.027601 0.055488 253.951908
## Treatment_bisFull:SexMale -0.008714 0.042316 250.518122
## Treatment_bisSmart:SexMale -0.051378 0.056344 262.240865
## Treatment_bisMixt_smart:SexMale -0.155689 0.068472 255.857117
## Treatment_bisFull:RegionLuxembourg 0.010560 0.042080 248.995529
## Treatment_bisSmart:RegionLuxembourg 0.017807 0.053329 250.617895
## Treatment_bisMixt_smart:RegionLuxembourg 0.108362 0.067306 253.671981
## t value Pr(>|t|)
## (Intercept) -25.173 < 2e-16 ***
## Treatment_bisFull 1.502 0.13448
## Treatment_bisSmart 0.504 0.61460
## Treatment_bisMixt_smart 2.978 0.00321 **
## SexMale 1.699 0.09058 .
## SpeciesOP -11.559 1.48e-14 ***
## RegionLuxembourg 0.771 0.44815
## SexMale:SpeciesOP -1.351 0.17780
## SpeciesOP:RegionLuxembourg -1.005 0.32280
## Treatment_bisFull:SpeciesOP -0.739 0.46083
## Treatment_bisSmart:SpeciesOP 0.497 0.61932
## Treatment_bisFull:SexMale -0.206 0.83702
## Treatment_bisSmart:SexMale -0.912 0.36268
## Treatment_bisMixt_smart:SexMale -2.274 0.02381 *
## Treatment_bisFull:RegionLuxembourg 0.251 0.80207
## Treatment_bisSmart:RegionLuxembourg 0.334 0.73873
## Treatment_bisMixt_smart:RegionLuxembourg 1.610 0.10864
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 17 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientqqnorm(resid(LM_Pupa_mass))
qqline(resid(LM_Pupa_mass))
Je pense que la normalité est ok.
Homogénité des variances
plot(LM_Pupa_mass)
Distance de cook
plot(cooks.distance(LM_Pupa_mass))
4.6.2 Simplification du modèle
drop1(LM_Pupa_mass)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.039613 0.039613 1 253.585 1.8261 0.1778
## Species:Region 0.021929 0.021929 1 29.739 1.0109 0.3228
## Treatment_bis:Species 0.026189 0.013094 2 251.109 0.6036 0.5476
## Treatment_bis:Sex 0.123487 0.041162 3 255.779 1.8975 0.1304
## Treatment_bis:Region 0.058108 0.019369 3 250.167 0.8929 0.4454LM_Pupa_mass1 <- update(LM_Pupa_mass, . ~ . - Treatment_bis:Region)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientdrop1(LM_Pupa_mass1)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region + Treatment_bis:Species + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.038991 0.038991 1 256.876 1.7934 0.1817
## Species:Region 0.036320 0.036320 1 28.519 1.6705 0.2066
## Treatment_bis:Species 0.026841 0.013421 2 254.612 0.6173 0.5402
## Treatment_bis:Sex 0.115544 0.038515 3 259.087 1.7715 0.1530LM_Pupa_mass2 <- update(LM_Pupa_mass1, . ~ . - Treatment_bis:Species)
drop1(LM_Pupa_mass2)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.043904 0.043904 1 258.563 2.0241 0.1560
## Species:Region 0.033971 0.033971 1 28.494 1.5662 0.2209
## Treatment_bis:Sex 0.114387 0.038129 3 260.779 1.7579 0.1556LM_Pupa_mass3 <- update(LM_Pupa_mass2, . ~ . - Treatment_bis:Sex)
drop1(LM_Pupa_mass3)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.36788 0.122627 3 97.951 5.5939 0.001391 **
## Sex:Species 0.01144 0.011445 1 262.323 0.5221 0.470602
## Species:Region 0.03591 0.035906 1 28.636 1.6379 0.210882
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass4 <- update(LM_Pupa_mass3, . ~ . - Sex:Species)
drop1(LM_Pupa_mass4)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.36156 0.120520 3 105.202 5.5140 0.00148 **
## Sex 0.01126 0.011259 1 264.072 0.5151 0.47357
## Species:Region 0.03635 0.036346 1 28.587 1.6629 0.20755
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass5 <- update(LM_Pupa_mass4, . ~ . - Sex)
drop1(LM_Pupa_mass5)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ Treatment_bis + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.303763 0.101254 3 144.503 4.3892 0.005471 **
## Species:Region 0.034196 0.034196 1 29.637 1.4823 0.233015
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass6 <- update(LM_Pupa_mass5, . ~ . - Species:Region)
drop1(LM_Pupa_mass6)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ Treatment_bis + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room)
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.3048 0.1016 3 140.053 4.3994 0.005439 **
## Species 8.7078 8.7078 1 31.820 377.0611 < 2.2e-16 ***
## Region 0.0183 0.0183 1 7.837 0.7908 0.400328
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Il n’y a plus aucune interaction, nous arrêtons la simplification du modèle
Regardons si les simplifications étaient utiles
AIC(LM_Pupa_mass6)## [1] -176.5115AIC(LM_Pupa_mass)## [1] -131.2767Elle l’a été
LM_Pupa_mass <- LM_Pupa_mass64.6.3 Treatment VS Treatment_bis
AIC(lmer(log(Pupa_mass) ~ Treatment_bis + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))## [1] -176.5115AIC(lmer(log(Pupa_mass) ~ Treatment + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))## boundary (singular) fit: see help('isSingular')## [1] -177.1378summary(lmer(log(Pupa_mass) ~ Treatment_bis + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))$coeff## Estimate Std. Error df t value
## (Intercept) -1.11485370 0.03641410 10.022152 -30.6159861
## Treatment_bisFull 0.03366768 0.02126123 261.847742 1.5835245
## Treatment_bisSmart 0.01026932 0.02828342 158.542150 0.3630862
## Treatment_bisMixt_smart 0.12571078 0.03537482 204.036224 3.5536798
## SpeciesOP -0.79298016 0.04083725 31.820207 -19.4180610
## RegionLuxembourg 0.03502196 0.03938257 7.836814 0.8892758
## Pr(>|t|)
## (Intercept) 3.111105e-11
## Treatment_bisFull 1.145090e-01
## Treatment_bisSmart 7.170241e-01
## Treatment_bisMixt_smart 4.719401e-04
## SpeciesOP 3.319481e-19
## RegionLuxembourg 4.003276e-01summary(lmer(log(Pupa_mass) ~ Treatment + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.11264604 0.04159904 5.848142 -26.7469137 2.436948e-07
## TreatmentFull 0.04130535 0.02235363 262.595199 1.8478136 6.575383e-02
## TreatmentSmart 0.05503177 0.02243855 265.235145 2.4525549 1.482914e-02
## SpeciesOP -0.81478596 0.04048370 30.261326 -20.1262729 4.490787e-19
## RegionLuxembourg 0.03477702 0.03884826 32.002473 0.8952017 3.773634e-01Les AIC sont assez proche mais pour une fois je serais plus d’avis de sélectionner la colonne Treatment et non treatment_bis au vu des p-val. Je pars sur Treatment.
Analyse des p-val
summary(lmer(log(Pupa_mass) ~ Treatment + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Pupa_mass) ~ Treatment + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data
##
## REML criterion at convergence: -195.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6328 -0.5054 0.0294 0.5453 3.5681
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 9.449e-03 9.721e-02
## Site (Intercept) 9.867e-11 9.933e-06
## Room (Intercept) 1.218e-03 3.490e-02
## Residual 2.342e-02 1.530e-01
## Number of obs: 292, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.11265 0.04160 5.84814 -26.747 2.44e-07 ***
## TreatmentFull 0.04131 0.02235 262.59520 1.848 0.0658 .
## TreatmentSmart 0.05503 0.02244 265.23515 2.453 0.0148 *
## SpeciesOP -0.81479 0.04048 30.26133 -20.126 < 2e-16 ***
## RegionLuxembourg 0.03478 0.03885 32.00247 0.895 0.3774
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnF TrtmnS SpcsOP
## TreatmntFll -0.267
## TretmntSmrt -0.276 0.510
## SpeciesOP -0.366 -0.003 0.033
## ReginLxmbrg -0.455 0.005 -0.029 0.024
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Pupa_mass) ~ Treatment + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Pupa_mass) ~ Treatment + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data_ref_full
##
## REML criterion at convergence: -195.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6328 -0.5054 0.0294 0.5453 3.5681
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 9.449e-03 9.721e-02
## Site (Intercept) 9.867e-11 9.933e-06
## Room (Intercept) 1.218e-03 3.490e-02
## Residual 2.342e-02 1.530e-01
## Number of obs: 292, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.07134 0.04163 5.86668 -25.735 2.94e-07 ***
## TreatmentDark -0.04131 0.02235 262.59520 -1.848 0.0658 .
## TreatmentSmart 0.01373 0.02218 261.32124 0.619 0.5365
## SpeciesOP -0.81479 0.04048 30.26133 -20.126 < 2e-16 ***
## RegionLuxembourg 0.03478 0.03885 32.00251 0.895 0.3774
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnS SpcsOP
## TreatmntDrk -0.270
## TretmntSmrt -0.274 0.492
## SpeciesOP -0.367 0.003 0.036
## ReginLxmbrg -0.452 -0.005 -0.034 0.024
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Pupa_mass) ~ Treatment + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Pupa_mass) ~ Treatment + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data_ref_smart
##
## REML criterion at convergence: -195.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6328 -0.5054 0.0294 0.5453 3.5681
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 9.449e-03 9.721e-02
## Site (Intercept) 9.867e-11 9.933e-06
## Room (Intercept) 1.218e-03 3.490e-02
## Residual 2.342e-02 1.530e-01
## Number of obs: 292, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.05761 0.04146 5.76879 -25.510 3.74e-07 ***
## TreatmentDark -0.05503 0.02244 265.23515 -2.453 0.0148 *
## TreatmentFull -0.01373 0.02218 261.32124 -0.619 0.5365
## SpeciesOP -0.81479 0.04048 30.26133 -20.126 < 2e-16 ***
## RegionLuxembourg 0.03478 0.03885 32.00248 0.895 0.3774
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnF SpcsOP
## TreatmntDrk -0.264
## TreatmntFll -0.260 0.498
## SpeciesOP -0.349 -0.033 -0.036
## ReginLxmbrg -0.472 0.029 0.034 0.024
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Info_Pupa_mass <- "
Le traitement Full (P = 0.0658) est presque significativement plus lourd que le le traitement Dark.
Le traitement Smart est significativement plus lourd que le traitement Dark.
L'espèce OP est significativement plus légère.
"
Info_Pupa_mass## [1] "\nLe traitement Full (P = 0.0658) est presque significativement plus lourd que le le traitement Dark.\nLe traitement Smart est significativement plus lourd que le traitement Dark.\nL'espèce OP est significativement plus légère.\n"4.6.4 Visualisation
Summary_Pupa_mass <- Data %>%
filter(Pupa_mass != "NA") %>%
group_by(Treatment, Species, Region) %>%
summarise(Mean=mean(log(Pupa_mass)),
Var=var(log(Pupa_mass)),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_Pupa_mass, aes(x=Treatment, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_grid(~Region) +
labs(title = "Poids des chrysalides", x = "Traitement", y = "log(Poids des chrysalides (g) )", color = "Espèce") +
theme_bw()
4.7 Adult_mass
4.7.1 Test
LM_Adult_mass <- lmer(Adult_mass ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientsummary(LM_Adult_mass)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Adult_mass ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: -964.5
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.0550 -0.4644 -0.0047 0.4095 4.1061
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.950e-04 0.013964
## Site (Intercept) 1.210e-04 0.010999
## Room (Intercept) 1.648e-05 0.004059
## Residual 8.733e-04 0.029551
## Number of obs: 267, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 1.917e-01 9.558e-03 1.962e+01
## Treatment_bisFull 2.209e-02 8.420e-03 2.252e+02
## Treatment_bisSmart 1.035e-02 1.011e-02 2.177e+02
## Treatment_bisMixt_smart 4.010e-02 1.137e-02 2.273e+02
## SexMale -1.988e-02 7.638e-03 2.365e+02
## SpeciesOP -9.715e-02 1.148e-02 3.775e+01
## RegionLuxembourg 7.836e-03 1.160e-02 2.278e+01
## SexMale:SpeciesOP 6.198e-03 8.090e-03 2.283e+02
## SpeciesOP:RegionLuxembourg -1.099e-02 1.419e-02 2.325e+01
## Treatment_bisFull:SpeciesOP -1.655e-02 8.859e-03 2.273e+02
## Treatment_bisSmart:SpeciesOP 2.690e-03 1.153e-02 2.248e+02
## Treatment_bisFull:SexMale 1.803e-03 8.877e-03 2.325e+02
## Treatment_bisSmart:SexMale -4.729e-03 1.179e-02 2.408e+02
## Treatment_bisMixt_smart:SexMale -3.741e-02 1.443e-02 2.403e+02
## Treatment_bisFull:RegionLuxembourg -8.193e-04 8.723e-03 2.238e+02
## Treatment_bisSmart:RegionLuxembourg -4.877e-03 1.116e-02 2.216e+02
## Treatment_bisMixt_smart:RegionLuxembourg 2.390e-02 1.411e-02 2.324e+02
## t value Pr(>|t|)
## (Intercept) 20.052 1.54e-14 ***
## Treatment_bisFull 2.623 0.009304 **
## Treatment_bisSmart 1.024 0.307114
## Treatment_bisMixt_smart 3.528 0.000506 ***
## SexMale -2.603 0.009831 **
## SpeciesOP -8.465 2.98e-10 ***
## RegionLuxembourg 0.676 0.506052
## SexMale:SpeciesOP 0.766 0.444375
## SpeciesOP:RegionLuxembourg -0.774 0.446603
## Treatment_bisFull:SpeciesOP -1.868 0.063068 .
## Treatment_bisSmart:SpeciesOP 0.233 0.815795
## Treatment_bisFull:SexMale 0.203 0.839200
## Treatment_bisSmart:SexMale -0.401 0.688646
## Treatment_bisMixt_smart:SexMale -2.592 0.010112 *
## Treatment_bisFull:RegionLuxembourg -0.094 0.925256
## Treatment_bisSmart:RegionLuxembourg -0.437 0.662522
## Treatment_bisMixt_smart:RegionLuxembourg 1.693 0.091783 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 17 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientVérification des hypothèses
qqnorm(resid(LM_Adult_mass))
qqline(resid(LM_Adult_mass))
Une modification des données est nécessaire.
LM_Adult_mass <- lmer(log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientsummary(LM_Adult_mass)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: -67
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.4145 -0.5848 0.0962 0.5492 2.7251
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0049108 0.07008
## Site (Intercept) 0.0020527 0.04531
## Room (Intercept) 0.0005858 0.02420
## Residual 0.0328065 0.18113
## Number of obs: 267, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) -1.69468 0.05205 19.48485 -32.558
## Treatment_bisFull 0.13766 0.05144 228.20505 2.676
## Treatment_bisSmart 0.07193 0.06178 220.02668 1.164
## Treatment_bisMixt_smart 0.20067 0.06923 230.07090 2.898
## SexMale -0.11432 0.04643 240.96571 -2.462
## SpeciesOP -0.71263 0.06290 43.18709 -11.329
## RegionLuxembourg 0.06343 0.06129 31.88112 1.035
## SexMale:SpeciesOP -0.06067 0.04930 232.67779 -1.231
## SpeciesOP:RegionLuxembourg -0.09203 0.07576 23.88701 -1.215
## Treatment_bisFull:SpeciesOP -0.05461 0.05408 230.29959 -1.010
## Treatment_bisSmart:SpeciesOP 0.01466 0.07045 228.19172 0.208
## Treatment_bisFull:SexMale 0.01757 0.05408 236.62925 0.325
## Treatment_bisSmart:SexMale 0.02017 0.07153 244.59652 0.282
## Treatment_bisMixt_smart:SexMale -0.14667 0.08753 245.17031 -1.676
## Treatment_bisFull:RegionLuxembourg -0.03240 0.05329 226.55231 -0.608
## Treatment_bisSmart:RegionLuxembourg -0.04387 0.06825 224.50158 -0.643
## Treatment_bisMixt_smart:RegionLuxembourg 0.09566 0.08596 235.72876 1.113
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisFull 0.00799 **
## Treatment_bisSmart 0.24558
## Treatment_bisMixt_smart 0.00411 **
## SexMale 0.01450 *
## SpeciesOP 1.61e-14 ***
## RegionLuxembourg 0.30855
## SexMale:SpeciesOP 0.21963
## SpeciesOP:RegionLuxembourg 0.23635
## Treatment_bisFull:SpeciesOP 0.31363
## Treatment_bisSmart:SpeciesOP 0.83539
## Treatment_bisFull:SexMale 0.74559
## Treatment_bisSmart:SexMale 0.77818
## Treatment_bisMixt_smart:SexMale 0.09507 .
## Treatment_bisFull:RegionLuxembourg 0.54379
## Treatment_bisSmart:RegionLuxembourg 0.52102
## Treatment_bisMixt_smart:RegionLuxembourg 0.26692
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 17 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientqqnorm(resid(LM_Adult_mass))
qqline(resid(LM_Adult_mass))
Homogénité des variances
plot(LM_Adult_mass)
Distance de cook
plot(cooks.distance(LM_Adult_mass))
4.7.2 Simplification du modèle
drop1(LM_Adult_mass)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.049701 0.049701 1 232.678 1.5150 0.2196
## Species:Region 0.048405 0.048405 1 23.887 1.4755 0.2364
## Treatment_bis:Species 0.045458 0.022729 2 228.905 0.6928 0.5012
## Treatment_bis:Sex 0.127423 0.042474 3 240.167 1.2947 0.2769
## Treatment_bis:Region 0.089449 0.029816 3 228.924 0.9089 0.4375LM_Adult_mass1 <- update(LM_Adult_mass, . ~ . - Treatment_bis:Species)
drop1(LM_Adult_mass1)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.059771 0.059771 1 233.527 1.8303 0.1774
## Species:Region 0.045475 0.045475 1 24.003 1.3925 0.2495
## Treatment_bis:Sex 0.134890 0.044963 3 241.690 1.3768 0.2504
## Treatment_bis:Region 0.097870 0.032623 3 230.856 0.9990 0.3941LM_Adult_mass2 <- update(LM_Adult_mass1, . ~ . - Treatment_bis:Region)
drop1(LM_Adult_mass2)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.058300 0.058300 1 237.467 1.7771 0.1838
## Species:Region 0.074952 0.074952 1 21.922 2.2847 0.1449
## Treatment_bis:Sex 0.128122 0.042707 3 245.517 1.3018 0.2744LM_Adult_mass3 <- update(LM_Adult_mass2, . ~ . - Treatment_bis:Sex)
drop1(LM_Adult_mass3)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.72726 0.242421 3 129.321 7.3485 0.000138 ***
## Sex:Species 0.02244 0.022439 1 242.655 0.6802 0.410334
## Species:Region 0.08141 0.081406 1 22.513 2.4677 0.130161
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Adult_mass4 <- update(LM_Adult_mass3, . ~ . - Sex:Species)
drop1(LM_Adult_mass4)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.71349 0.23783 3 134.474 7.2238 0.0001568 ***
## Sex 1.33152 1.33152 1 246.586 40.4433 9.747e-10 ***
## Species:Region 0.08083 0.08083 1 22.385 2.4550 0.1311777
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Adult_mass5 <- update(LM_Adult_mass4, . ~ . - Species:Region)
drop1(LM_Adult_mass5)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room)
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.6924 0.2308 3 128.767 7.0119 0.0002095 ***
## Sex 1.3324 1.3324 1 245.959 40.4801 9.625e-10 ***
## Species 14.7698 14.7698 1 26.531 448.7142 < 2.2e-16 ***
## Region 0.0063 0.0063 1 10.270 0.1901 0.6718326
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Nous n’avons plus d’interaction, nous arrêtons la simplification du modèle.
Est ce que la simplification a été utile ?
AIC(LM_Adult_mass5)## [1] -70.68366AIC(LM_Adult_mass)## [1] -24.95704Oui, clairement
LM_Adult_mass <- LM_Adult_mass54.7.3 Treatment VS Treatment_bis
AIC(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))## [1] -70.68366AIC(lmer(log(Adult_mass) ~ Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))## [1] -70.01737summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))$coeff## Estimate Std. Error df t value
## (Intercept) -1.64384714 0.04150109 8.551585 -39.6097346
## Treatment_bisFull 0.09951414 0.02659351 237.979846 3.7420464
## Treatment_bisSmart 0.05444616 0.03562532 135.161913 1.5282997
## Treatment_bisMixt_smart 0.15819770 0.04376917 197.571796 3.6143636
## SexMale -0.14750246 0.02318346 245.958656 -6.3624010
## SpeciesOP -0.81080683 0.03827652 26.530707 -21.1828747
## RegionLuxembourg 0.01828273 0.04192918 10.269655 0.4360383
## Pr(>|t|)
## (Intercept) 5.440142e-11
## Treatment_bisFull 2.288521e-04
## Treatment_bisSmart 1.287750e-01
## Treatment_bisMixt_smart 3.820347e-04
## SexMale 9.624769e-10
## SpeciesOP 3.748241e-18
## RegionLuxembourg 6.718326e-01summary(lmer(log(Adult_mass) ~ Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))$coeff## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.63464765 0.04415767 6.906927 -37.0184321 3.352957e-09
## TreatmentFull 0.10344866 0.02852921 237.210830 3.6260614 3.522174e-04
## TreatmentSmart 0.07396902 0.02804199 238.354540 2.6377947 8.893944e-03
## SexMale -0.14043353 0.02336806 245.362410 -6.0096361 6.682904e-09
## SpeciesOP -0.84544727 0.03809351 23.921155 -22.1939976 1.814242e-17
## RegionLuxembourg 0.01604739 0.04111075 9.518202 0.3903453 7.048740e-01summary(lmer(log(Adult_mass) ~ Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_smart))$coeff## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.56067864 0.04359782 6.585044 -35.7971723 8.564833e-09
## TreatmentDark -0.07396902 0.02804199 238.354540 -2.6377947 8.893944e-03
## TreatmentFull 0.02947964 0.02751896 236.390513 1.0712486 2.851501e-01
## SexMale -0.14043353 0.02336806 245.362410 -6.0096361 6.682904e-09
## SpeciesOP -0.84544727 0.03809351 23.921155 -22.1939976 1.814242e-17
## RegionLuxembourg 0.01604739 0.04111075 9.518202 0.3903453 7.048740e-01Les AIC sont plus ou moins simillaires mais vu qu’il y a une différence significative entre Mixt_smart et Smart je pense qu’il est plus correcte scientifiquement parlant de prendre Treatment_bis
Analyse des P-val
summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room)
## Data: Data
##
## REML criterion at convergence: -92.7
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6044 -0.5960 0.0509 0.6052 2.9552
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0053883 0.07340
## Site (Intercept) 0.0015578 0.03947
## Room (Intercept) 0.0006429 0.02535
## Residual 0.0329157 0.18143
## Number of obs: 267, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.64385 0.04150 8.55158 -39.610 5.44e-11 ***
## Treatment_bisFull 0.09951 0.02659 237.97985 3.742 0.000229 ***
## Treatment_bisSmart 0.05445 0.03563 135.16191 1.528 0.128775
## Treatment_bisMixt_smart 0.15820 0.04377 197.57180 3.614 0.000382 ***
## SexMale -0.14750 0.02318 245.95866 -6.362 9.62e-10 ***
## SpeciesOP -0.81081 0.03828 26.53071 -21.183 < 2e-16 ***
## RegionLuxembourg 0.01828 0.04193 10.26965 0.436 0.671833
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal SpcsOP
## Trtmnt_bsFl -0.275
## Trtmnt_bsSm -0.233 0.361
## Trtmnt_bsM_ -0.275 0.287 0.160
## SexMale -0.216 -0.108 0.009 -0.062
## SpeciesOP -0.393 0.019 0.061 0.226 -0.010
## ReginLxmbrg -0.485 0.001 -0.058 0.006 -0.012 -0.001summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_full))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room)
## Data: Data_ref_full
##
## REML criterion at convergence: -92.7
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6044 -0.5960 0.0509 0.6052 2.9552
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0053883 0.07340
## Site (Intercept) 0.0015578 0.03947
## Room (Intercept) 0.0006429 0.02535
## Residual 0.0329157 0.18143
## Number of obs: 267, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.54433 0.04270 9.62358 -36.170 1.32e-11 ***
## Treatment_bisDark -0.09951 0.02659 237.97985 -3.742 0.000229 ***
## Treatment_bisSmart -0.04507 0.03596 172.73269 -1.253 0.211817
## Treatment_bisMixt_smart 0.05868 0.04421 169.57954 1.327 0.186191
## SexMale -0.14750 0.02318 245.95866 -6.362 9.62e-10 ***
## SpeciesOP -0.81081 0.03828 26.53071 -21.183 < 2e-16 ***
## RegionLuxembourg 0.01828 0.04193 10.26965 0.436 0.671833
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal SpcsOP
## Trtmnt_bsDr -0.356
## Trtmnt_bsSm -0.265 0.382
## Trtmnt_bsM_ -0.302 0.317 0.176
## SexMale -0.278 0.108 0.089 0.004
## SpeciesOP -0.370 -0.019 0.046 0.212 -0.010
## ReginLxmbrg -0.471 -0.001 -0.058 0.005 -0.012 -0.001summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Adult_mass) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room)
## Data: Data_ref_smart
##
## REML criterion at convergence: -92.7
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6044 -0.5960 0.0509 0.6052 2.9552
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0053883 0.07340
## Site (Intercept) 0.0015578 0.03947
## Room (Intercept) 0.0006429 0.02535
## Residual 0.0329157 0.18143
## Number of obs: 267, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.58940 0.04797 12.58720 -33.131 1.26e-13 ***
## Treatment_bisDark -0.05445 0.03563 135.16191 -1.528 0.1288
## Treatment_bisFull 0.04507 0.03596 172.73269 1.253 0.2118
## Treatment_bisMixt_smart 0.10375 0.05184 66.06313 2.002 0.0494 *
## SexMale -0.14750 0.02318 245.95866 -6.362 9.62e-10 ***
## SpeciesOP -0.81081 0.03828 26.53071 -21.183 < 2e-16 ***
## RegionLuxembourg 0.01828 0.04193 10.26965 0.436 0.6718
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal SpcsOP
## Trtmnt_bsDr -0.541
## Trtmnt_bsFl -0.513 0.724
## Trtmnt_bsM_ -0.472 0.552 0.543
## SexMale -0.181 -0.009 -0.089 -0.058
## SpeciesOP -0.294 -0.061 -0.046 0.149 -0.010
## ReginLxmbrg -0.462 0.058 0.058 0.044 -0.012 -0.001Info_Adult_mass <- "
classsement croissant de poids : Dark < Smart < Full et Mixt_smart
Les males sont moins lourds
OP est moins lourds
"
Info_Adult_mass## [1] "\nclasssement croissant de poids : Dark < Smart < Full et Mixt_smart\nLes males sont moins lourds\nOP est moins lourds\n"4.7.4 Visualisation
Summary_Adult_mass <- Data %>%
filter(Adult_mass != "NA", Sex != "NA") %>%
group_by(Treatment_bis, Species, Sex) %>%
summarise(Mean=mean(log(Adult_mass)),
Var=var(log(Adult_mass)),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_Adult_mass, aes(x=Treatment_bis, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_grid(~Sex) +
labs(title = "Poids des adultes", x = "Traitement", y = "log(Poids des adultes (g))", color = "Espèce") +
theme_bw()
4.8 M0
4.8.1 Test
LM_M0 <- lmer(M0 ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')summary(LM_M0)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: M0 ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: -1752.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3630 -0.5563 -0.0803 0.4921 4.6891
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.608e-05 0.006007
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 0.000e+00 0.000000
## Residual 9.359e-05 0.009674
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 1.385e-02 2.604e-03 7.190e+01
## Treatment_bisFull -7.228e-04 2.530e-03 2.635e+02
## Treatment_bisSmart -3.336e-03 3.026e-03 2.624e+02
## Treatment_bisMixt_smart -2.461e-04 3.533e-03 2.660e+02
## SexMale 1.359e-04 2.335e-03 2.711e+02
## SpeciesOP 2.144e-02 3.851e-03 3.959e+01
## RegionLuxembourg 1.074e-03 3.393e-03 5.279e+01
## SexMale:SpeciesOP -5.843e-06 2.466e-03 2.676e+02
## SpeciesOP:RegionLuxembourg -3.803e-03 4.984e-03 2.810e+01
## Treatment_bisFull:SpeciesOP 1.549e-03 2.681e-03 2.644e+02
## Treatment_bisSmart:SpeciesOP -1.655e-03 3.487e-03 2.621e+02
## Treatment_bisFull:SexMale 5.835e-04 2.701e-03 2.650e+02
## Treatment_bisSmart:SexMale 2.238e-03 3.567e-03 2.747e+02
## Treatment_bisMixt_smart:SexMale 3.039e-03 4.460e-03 2.715e+02
## Treatment_bisFull:RegionLuxembourg -2.304e-03 2.668e-03 2.634e+02
## Treatment_bisSmart:RegionLuxembourg 6.598e-04 3.399e-03 2.603e+02
## Treatment_bisMixt_smart:RegionLuxembourg -3.525e-03 4.365e-03 2.672e+02
## t value Pr(>|t|)
## (Intercept) 5.317 1.14e-06 ***
## Treatment_bisFull -0.286 0.775
## Treatment_bisSmart -1.102 0.271
## Treatment_bisMixt_smart -0.070 0.945
## SexMale 0.058 0.954
## SpeciesOP 5.568 1.97e-06 ***
## RegionLuxembourg 0.316 0.753
## SexMale:SpeciesOP -0.002 0.998
## SpeciesOP:RegionLuxembourg -0.763 0.452
## Treatment_bisFull:SpeciesOP 0.578 0.564
## Treatment_bisSmart:SpeciesOP -0.475 0.635
## Treatment_bisFull:SexMale 0.216 0.829
## Treatment_bisSmart:SexMale 0.627 0.531
## Treatment_bisMixt_smart:SexMale 0.681 0.496
## Treatment_bisFull:RegionLuxembourg -0.864 0.389
## Treatment_bisSmart:RegionLuxembourg 0.194 0.846
## Treatment_bisMixt_smart:RegionLuxembourg -0.808 0.420
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 17 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_M0))
qqline(resid(LM_M0))
Je pense que ca va
Homogénité des variances
plot(LM_M0)
Il faudrait quand même un sqrt ou quelque chose dans le style
LM_M0 <- lmer(sqrt(M0) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')summary(LM_M0)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: sqrt(M0) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: -1110.5
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4434 -0.6501 -0.0323 0.6353 3.5364
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.869e-04 1.967e-02
## Site (Intercept) 3.323e-06 1.823e-03
## Room (Intercept) 1.790e-13 4.231e-07
## Residual 8.647e-04 2.941e-02
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 1.147e-01 8.245e-03 3.534e+01
## Treatment_bisFull -4.472e-03 7.697e-03 2.633e+02
## Treatment_bisSmart -1.388e-02 9.206e-03 2.624e+02
## Treatment_bisMixt_smart -6.030e-04 1.075e-02 2.654e+02
## SexMale 2.872e-03 7.110e-03 2.702e+02
## SpeciesOP 6.894e-02 1.232e-02 3.871e+01
## RegionLuxembourg 1.275e-03 1.081e-02 2.989e+01
## SexMale:SpeciesOP -9.482e-04 7.506e-03 2.670e+02
## SpeciesOP:RegionLuxembourg -1.116e-02 1.607e-02 2.903e+01
## Treatment_bisFull:SpeciesOP 6.273e-03 8.159e-03 2.642e+02
## Treatment_bisSmart:SpeciesOP -2.447e-03 1.061e-02 2.618e+02
## Treatment_bisFull:SexMale 8.007e-04 8.219e-03 2.644e+02
## Treatment_bisSmart:SexMale 4.260e-03 1.087e-02 2.735e+02
## Treatment_bisMixt_smart:SexMale 8.559e-03 1.358e-02 2.704e+02
## Treatment_bisFull:RegionLuxembourg -4.421e-03 8.117e-03 2.633e+02
## Treatment_bisSmart:RegionLuxembourg 5.933e-03 1.034e-02 2.603e+02
## Treatment_bisMixt_smart:RegionLuxembourg -1.119e-02 1.329e-02 2.668e+02
## t value Pr(>|t|)
## (Intercept) 13.916 6.57e-16 ***
## Treatment_bisFull -0.581 0.562
## Treatment_bisSmart -1.508 0.133
## Treatment_bisMixt_smart -0.056 0.955
## SexMale 0.404 0.687
## SpeciesOP 5.598 1.92e-06 ***
## RegionLuxembourg 0.118 0.907
## SexMale:SpeciesOP -0.126 0.900
## SpeciesOP:RegionLuxembourg -0.695 0.493
## Treatment_bisFull:SpeciesOP 0.769 0.443
## Treatment_bisSmart:SpeciesOP -0.231 0.818
## Treatment_bisFull:SexMale 0.097 0.922
## Treatment_bisSmart:SexMale 0.392 0.695
## Treatment_bisMixt_smart:SexMale 0.630 0.529
## Treatment_bisFull:RegionLuxembourg -0.545 0.586
## Treatment_bisSmart:RegionLuxembourg 0.574 0.567
## Treatment_bisMixt_smart:RegionLuxembourg -0.842 0.400
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 17 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')qqnorm(resid(LM_M0))
qqline(resid(LM_M0))
C’est NICKEL
Homogénité des variances
plot(LM_M0)
c’est correcte
Distance de cook
plot(cooks.distance(LM_M0))
4.8.2 Simplification du modèle
drop1(LM_M0)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(M0) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.00001380 0.00001380 1 267.035 0.0160 0.8996
## Species:Region 0.00041714 0.00041714 1 29.027 0.4824 0.4929
## Treatment_bis:Species 0.00076234 0.00038117 2 262.804 0.4408 0.6440
## Treatment_bis:Sex 0.00041812 0.00013937 3 268.786 0.1612 0.9224
## Treatment_bis:Region 0.00150859 0.00050286 3 262.399 0.5815 0.6276LM_M0_1 <- update(LM_M0, . ~ . - Treatment_bis:Sex)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_M0_1)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(M0) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region + Treatment_bis:Species + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.00011537 0.00011537 1 269.609 0.1349 0.7137
## Species:Region 0.00040419 0.00040419 1 29.345 0.4725 0.4972
## Treatment_bis:Species 0.00072899 0.00036449 2 265.358 0.4261 0.6535
## Treatment_bis:Region 0.00149749 0.00049916 3 265.265 0.5836 0.6263LM_M0_2 <- update(LM_M0_1, . ~ . - Treatment_bis:Species)## boundary (singular) fit: see help('isSingular')drop1(LM_M0_2)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(M0) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.00007388 0.00007388 1 270.952 0.0869 0.7684
## Species:Region 0.00041528 0.00041528 1 29.263 0.4885 0.4901
## Treatment_bis:Region 0.00135376 0.00045125 3 266.977 0.5308 0.6615LM_M0_3 <- update(LM_M0_2, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_M0_3)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(M0) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.00290152 0.00096717 3 269.908 1.1446 0.3315
## Sex:Species 0.00005642 0.00005642 1 273.657 0.0668 0.7963
## Species:Region 0.00032532 0.00032532 1 28.091 0.3850 0.5399LM_M0_4 <- update(LM_M0_3, . ~ . - Sex:Species)## boundary (singular) fit: see help('isSingular')drop1(LM_M0_4)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(M0) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.0029891 0.00099637 3 270.732 1.1834 0.3164
## Sex 0.0012278 0.00122776 1 275.632 1.4583 0.2282
## Species:Region 0.0003225 0.00032250 1 28.103 0.3830 0.5410LM_M0_5 <- update(LM_M0_4, . ~ . - Species:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_M0_5)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(M0) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room)
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.003020 0.001007 3 270.466 1.1941 0.3124
## Sex 0.001235 0.001235 1 275.539 1.4653 0.2271
## Species 0.055808 0.055808 1 29.780 66.1935 4.662e-09 ***
## Region 0.000202 0.000202 1 11.855 0.2398 0.6333
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1summary(LM_M0_5)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: sqrt(M0) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data
##
## REML criterion at convergence: -1181.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4960 -0.6258 -0.0644 0.6407 3.5925
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.728e-04 0.019307
## Site (Intercept) 2.333e-05 0.004831
## Room (Intercept) 0.000e+00 0.000000
## Residual 8.431e-04 0.029036
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.158e-01 6.848e-03 2.128e+01 16.916 8.08e-14 ***
## Treatment_bisFull -3.067e-03 3.991e-03 2.715e+02 -0.769 0.4428
## Treatment_bisSmart -9.212e-03 5.057e-03 2.688e+02 -1.822 0.0696 .
## Treatment_bisMixt_smart -3.091e-04 6.507e-03 2.744e+02 -0.048 0.9621
## SexMale 4.215e-03 3.482e-03 2.755e+02 1.211 0.2271
## SpeciesOP 6.510e-02 8.001e-03 2.978e+01 8.136 4.66e-09 ***
## RegionLuxembourg -3.933e-03 8.031e-03 1.185e+01 -0.490 0.6333
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal SpcsOP
## Trtmnt_bsFl -0.256
## Trtmnt_bsSm -0.222 0.372
## Trtmnt_bsM_ -0.236 0.322 0.271
## SexMale -0.192 -0.089 -0.013 -0.054
## SpeciesOP -0.443 0.028 0.064 0.138 -0.001
## ReginLxmbrg -0.567 -0.007 -0.047 -0.009 -0.012 -0.004
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Nous n’avons plus d’interactions nous pouvons nous arrêter là. Vu qu’il y a aucune différence significative peut-importe le modèle à part pour l’espèce (ce qui est logique), nous pouvons nous arrêter là. Notons cependant que l’espèce OP est significativement plus lourde au départ de l’expérience et que nous avions presque un effet significatif du traitement Smart.
4.9 Total_eaten
4.9.1 Test
LM_Total_eaten <- lmer(Total_eaten ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')summary(LM_Total_eaten)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Total_eaten ~ Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: 2429.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.9815 -0.3975 -0.0501 0.2431 6.1844
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 159.019 12.61
## Site (Intercept) 8.408 2.90
## Room (Intercept) 0.000 0.00
## Residual 184.906 13.60
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 65.69025 4.75387 20.46260 13.818
## Treatment_bisFull 0.28380 3.57395 259.15138 0.079
## Treatment_bisSmart -4.56156 4.27250 258.14206 -1.068
## Treatment_bisMixt_smart -0.86996 4.99650 260.49839 -0.174
## SexMale -1.05641 3.31250 263.74935 -0.319
## SpeciesOP -46.44854 7.32533 33.84382 -6.341
## RegionLuxembourg 7.55825 6.39414 19.57261 1.182
## SexMale:SpeciesOP -0.80946 3.49097 260.81398 -0.232
## SpeciesOP:RegionLuxembourg -8.79301 9.83654 27.30592 -0.894
## Treatment_bisFull:SpeciesOP -2.80734 3.78947 258.90055 -0.741
## Treatment_bisSmart:SpeciesOP 7.99767 4.92063 256.98722 1.625
## Treatment_bisFull:SexMale 2.27051 3.81680 258.92059 0.595
## Treatment_bisSmart:SexMale -0.09876 5.07313 265.51280 -0.019
## Treatment_bisMixt_smart:SexMale -12.15096 6.32696 262.55831 -1.921
## Treatment_bisFull:RegionLuxembourg 3.92577 3.76817 258.32976 1.042
## Treatment_bisSmart:RegionLuxembourg -2.89676 4.79245 255.93432 -0.604
## Treatment_bisMixt_smart:RegionLuxembourg 21.80175 6.18031 260.77765 3.528
## Pr(>|t|)
## (Intercept) 7.67e-12 ***
## Treatment_bisFull 0.936769
## Treatment_bisSmart 0.286674
## Treatment_bisMixt_smart 0.861912
## SexMale 0.750041
## SpeciesOP 3.18e-07 ***
## RegionLuxembourg 0.251345
## SexMale:SpeciesOP 0.816819
## SpeciesOP:RegionLuxembourg 0.379180
## Treatment_bisFull:SpeciesOP 0.459471
## Treatment_bisSmart:SpeciesOP 0.105318
## Treatment_bisFull:SexMale 0.552448
## Treatment_bisSmart:SexMale 0.984482
## Treatment_bisMixt_smart:SexMale 0.055877 .
## Treatment_bisFull:RegionLuxembourg 0.298467
## Treatment_bisSmart:RegionLuxembourg 0.546085
## Treatment_bisMixt_smart:RegionLuxembourg 0.000495 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 17 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_Total_eaten))
qqline(resid(LM_Total_eaten))
Il faut modifier les variables
LM_Total_eaten <- lmer(log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')summary(LM_Total_eaten)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: 55.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3890 -0.6520 -0.0160 0.5467 4.2463
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.03671 0.1916
## Site (Intercept) 0.00000 0.0000
## Room (Intercept) 0.00000 0.0000
## Residual 0.04796 0.2190
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 4.109019 0.070890 51.778948
## Treatment_bisFull 0.028851 0.057515 259.766080
## Treatment_bisSmart -0.038988 0.068760 258.843388
## Treatment_bisMixt_smart 0.026992 0.080401 261.213801
## SexMale -0.011909 0.053271 264.976901
## SpeciesOP -1.229018 0.110638 34.499910
## RegionLuxembourg 0.125369 0.094892 41.706761
## SexMale:SpeciesOP -0.064999 0.056155 262.128923
## SpeciesOP:RegionLuxembourg -0.189256 0.148241 27.896870
## Treatment_bisFull:SpeciesOP -0.032808 0.060971 260.041568
## Treatment_bisSmart:SpeciesOP 0.134356 0.079204 257.725410
## Treatment_bisFull:SexMale 0.025316 0.061426 259.711623
## Treatment_bisSmart:SexMale 0.005673 0.081553 267.207544
## Treatment_bisMixt_smart:SexMale -0.189421 0.101747 264.216262
## Treatment_bisFull:RegionLuxembourg 0.053287 0.060638 259.259502
## Treatment_bisSmart:RegionLuxembourg -0.053152 0.077148 256.613088
## Treatment_bisMixt_smart:RegionLuxembourg 0.285749 0.099412 262.097512
## t value Pr(>|t|)
## (Intercept) 57.963 < 2e-16 ***
## Treatment_bisFull 0.502 0.61636
## Treatment_bisSmart -0.567 0.57120
## Treatment_bisMixt_smart 0.336 0.73735
## SexMale -0.224 0.82328
## SpeciesOP -11.108 6.1e-13 ***
## RegionLuxembourg 1.321 0.19365
## SexMale:SpeciesOP -1.157 0.24813
## SpeciesOP:RegionLuxembourg -1.277 0.21224
## Treatment_bisFull:SpeciesOP -0.538 0.59097
## Treatment_bisSmart:SpeciesOP 1.696 0.09103 .
## Treatment_bisFull:SexMale 0.412 0.68058
## Treatment_bisSmart:SexMale 0.070 0.94460
## Treatment_bisMixt_smart:SexMale -1.862 0.06376 .
## Treatment_bisFull:RegionLuxembourg 0.879 0.38034
## Treatment_bisSmart:RegionLuxembourg -0.689 0.49147
## Treatment_bisMixt_smart:RegionLuxembourg 2.874 0.00438 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 17 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')qqnorm(resid(LM_Total_eaten))
qqline(resid(LM_Total_eaten))
C’est très bon.
Homogénité des variances
plot(LM_Total_eaten)
c’est correcte
Distance de cook
plot(cooks.distance(LM_Total_eaten))
4.9.2 Simplification du modèle
drop1(LM_Total_eaten)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.06426 0.064261 1 262.129 1.3398 0.24813
## Species:Region 0.07818 0.078178 1 27.897 1.6299 0.21224
## Treatment_bis:Species 0.20958 0.104789 2 258.694 2.1847 0.11458
## Treatment_bis:Sex 0.22396 0.074653 3 263.066 1.5564 0.20038
## Treatment_bis:Region 0.51971 0.173237 3 258.456 3.6118 0.01387 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Total_eaten1 <- update(LM_Total_eaten, . ~ . - Species:Region)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_Total_eaten1)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.06473 0.064729 1 261.97 1.3489 0.246523
## Treatment_bis:Species 0.19891 0.099456 2 259.09 2.0726 0.127938
## Treatment_bis:Sex 0.22640 0.075466 3 262.89 1.5727 0.196369
## Treatment_bis:Region 0.55805 0.186017 3 260.58 3.8765 0.009752 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Total_eaten2 <- update(LM_Total_eaten1, . ~ . - Treatment_bis:Sex)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_Total_eaten2)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Treatment_bis:Species + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.01721 0.017207 1 264.67 0.3565 0.55095
## Treatment_bis:Species 0.20780 0.103899 2 261.82 2.1528 0.11822
## Treatment_bis:Region 0.53729 0.179098 3 263.53 3.7108 0.01214 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Total_eaten3 <- update(LM_Total_eaten2, . ~ . - Treatment_bis:Species)## boundary (singular) fit: see help('isSingular')drop1(LM_Total_eaten3)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.02175 0.021749 1 266.54 0.4458 0.50493
## Treatment_bis:Region 0.51887 0.172958 3 265.60 3.5450 0.01512 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Total_eaten4 <- update(LM_Total_eaten3, . ~ . - Sex:Species)## boundary (singular) fit: see help('isSingular')drop1(LM_Total_eaten4)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 0.1604 0.1604 1 268.211 3.3010 0.07035 .
## Species 15.6461 15.6461 1 29.051 321.9056 < 2e-16 ***
## Treatment_bis:Region 0.5259 0.1753 3 266.479 3.6068 0.01393 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1On arrête la simplification de modèle.
Est-ce qu’elle a été utile ?
AIC(LM_Total_eaten4)## [1] 71.16486AIC(LM_Total_eaten)## [1] 97.17414Oui, elle a été utile.
LM_Total_eaten <- LM_Total_eaten44.9.3 Treatment VS Treatment_bis
AIC(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data))## boundary (singular) fit: see help('isSingular')## [1] 71.16486AIC(lmer(log(Total_eaten) ~ Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region, data = Data))## boundary (singular) fit: see help('isSingular')## [1] 71.2323summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 4.153477797 0.06162099 42.75638
## Treatment_bisFull 0.026942383 0.04139184 263.71600
## Treatment_bisSmart 0.001836929 0.05562459 263.48985
## Treatment_bisMixt_smart -0.057136020 0.06589460 268.02789
## SexMale -0.048291898 0.02657985 268.21073
## SpeciesOP -1.341061221 0.07474538 29.05099
## RegionLuxembourg 0.057172203 0.07819417 43.35920
## Treatment_bisFull:RegionLuxembourg 0.048278571 0.06070793 264.98118
## Treatment_bisSmart:RegionLuxembourg -0.037782694 0.07703579 264.33955
## Treatment_bisMixt_smart:RegionLuxembourg 0.296840489 0.09922843 274.18593
## t value Pr(>|t|)
## (Intercept) 67.40361965 4.773598e-45
## Treatment_bisFull 0.65091055 5.156710e-01
## Treatment_bisSmart 0.03302369 9.736807e-01
## Treatment_bisMixt_smart -0.86708199 3.866727e-01
## SexMale -1.81686101 7.035444e-02
## SpeciesOP -17.94172764 2.925529e-17
## RegionLuxembourg 0.73115685 4.686164e-01
## Treatment_bisFull:RegionLuxembourg 0.79525965 4.271742e-01
## Treatment_bisSmart:RegionLuxembourg -0.49045637 6.242179e-01
## Treatment_bisMixt_smart:RegionLuxembourg 2.99148627 3.028778e-03summary(lmer(log(Total_eaten) ~ Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region, data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 4.179562911 0.06209529 39.21607 67.3088600
## TreatmentFull 0.002713428 0.04393433 264.59305 0.0617610
## TreatmentSmart -0.065998225 0.04431099 266.81199 -1.4894324
## SexMale -0.044336781 0.02697193 268.84668 -1.6438119
## SpeciesOP -1.355694902 0.07366708 28.20778 -18.4029960
## RegionLuxembourg 0.033581997 0.07999868 49.27363 0.4197819
## TreatmentFull:RegionLuxembourg 0.075263856 0.06518564 265.68145 1.1546079
## TreatmentSmart:RegionLuxembourg 0.112034388 0.06481134 266.03931 1.7286233
## Pr(>|t|)
## (Intercept) 3.852278e-42
## TreatmentFull 9.507998e-01
## TreatmentSmart 1.375546e-01
## SexMale 1.013839e-01
## SpeciesOP 2.986756e-17
## RegionLuxembourg 6.764696e-01
## TreatmentFull:RegionLuxembourg 2.492885e-01
## TreatmentSmart:RegionLuxembourg 8.503673e-02Au vu des summary et de l’AIC je préfère le modèle avec Treatment_bis
Analyse des P-val
summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: 43.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3680 -0.7088 -0.0252 0.5633 4.0709
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.03747 0.1936
## Site (Intercept) 0.00000 0.0000
## Room (Intercept) 0.00000 0.0000
## Residual 0.04860 0.2205
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 4.153478 0.061621 42.756384
## Treatment_bisFull 0.026942 0.041392 263.716002
## Treatment_bisSmart 0.001837 0.055625 263.489850
## Treatment_bisMixt_smart -0.057136 0.065895 268.027894
## SexMale -0.048292 0.026580 268.210731
## SpeciesOP -1.341061 0.074745 29.050986
## RegionLuxembourg 0.057172 0.078194 43.359200
## Treatment_bisFull:RegionLuxembourg 0.048279 0.060708 264.981179
## Treatment_bisSmart:RegionLuxembourg -0.037783 0.077036 264.339547
## Treatment_bisMixt_smart:RegionLuxembourg 0.296840 0.099228 274.185928
## t value Pr(>|t|)
## (Intercept) 67.404 < 2e-16 ***
## Treatment_bisFull 0.651 0.51567
## Treatment_bisSmart 0.033 0.97368
## Treatment_bisMixt_smart -0.867 0.38667
## SexMale -1.817 0.07035 .
## SpeciesOP -17.942 < 2e-16 ***
## RegionLuxembourg 0.731 0.46862
## Treatment_bisFull:RegionLuxembourg 0.795 0.42717
## Treatment_bisSmart:RegionLuxembourg -0.490 0.62422
## Treatment_bisMixt_smart:RegionLuxembourg 2.991 0.00303 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal SpcsOP RgnLxm T_F:RL T_S:RL
## Trtmnt_bsFl -0.294
## Trtmnt_bsSm -0.244 0.343
## Trtmnt_bsM_ -0.241 0.321 0.261
## SexMale -0.162 -0.086 0.008 -0.029
## SpeciesOP -0.441 0.019 0.040 0.074 0.002
## ReginLxmbrg -0.610 0.236 0.177 0.168 -0.008 -0.007
## Trtmnt_F:RL 0.203 -0.679 -0.234 -0.218 0.027 -0.008 -0.357
## Trtmnt_S:RL 0.169 -0.246 -0.721 -0.187 -0.023 -0.006 -0.298 0.372
## Trtmn_M_:RL 0.140 -0.209 -0.171 -0.658 -0.021 0.011 -0.261 0.320 0.268
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_ref_full
##
## REML criterion at convergence: 43.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3680 -0.7088 -0.0252 0.5633 4.0709
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.03747 0.1936
## Site (Intercept) 0.00000 0.0000
## Room (Intercept) 0.00000 0.0000
## Residual 0.04860 0.2205
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 4.18042 0.06333 46.80351 66.012
## Treatment_bisDark -0.02694 0.04139 263.71600 -0.651
## Treatment_bisSmart -0.02511 0.05680 261.26579 -0.442
## Treatment_bisMixt_smart -0.08408 0.06560 263.83927 -1.282
## SexMale -0.04829 0.02658 268.21073 -1.817
## SpeciesOP -1.34106 0.07475 29.05099 -17.942
## RegionLuxembourg 0.10545 0.08006 47.12933 1.317
## Treatment_bisDark:RegionLuxembourg -0.04828 0.06071 264.98118 -0.795
## Treatment_bisSmart:RegionLuxembourg -0.08606 0.07839 262.85878 -1.098
## Treatment_bisMixt_smart:RegionLuxembourg 0.24856 0.09839 269.34321 2.526
## Pr(>|t|)
## (Intercept) <2e-16 ***
## Treatment_bisDark 0.5157
## Treatment_bisSmart 0.6589
## Treatment_bisMixt_smart 0.2011
## SexMale 0.0704 .
## SpeciesOP <2e-16 ***
## RegionLuxembourg 0.1942
## Treatment_bisDark:RegionLuxembourg 0.4272
## Treatment_bisSmart:RegionLuxembourg 0.2733
## Treatment_bisMixt_smart:RegionLuxembourg 0.0121 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal SpcsOP RgnLxm T_D:RL T_S:RL
## Trtmnt_bsDr -0.367
## Trtmnt_bsSm -0.281 0.392
## Trtmnt_bsM_ -0.257 0.308 0.270
## SexMale -0.214 0.086 0.070 0.025
## SpeciesOP -0.416 -0.019 0.025 0.062 0.002
## ReginLxmbrg -0.615 0.284 0.203 0.178 0.012 -0.013
## Trtmnt_D:RL 0.246 -0.679 -0.266 -0.210 -0.027 0.008 -0.410
## Trtmnt_S:RL 0.194 -0.284 -0.724 -0.194 -0.043 0.000 -0.327 0.409
## Trtmn_M_:RL 0.152 -0.209 -0.180 -0.664 -0.038 0.016 -0.265 0.295 0.269
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Total_eaten) ~ Treatment_bis + Sex + Species + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_ref_smart
##
## REML criterion at convergence: 43.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3680 -0.7088 -0.0252 0.5633 4.0709
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.03747 0.1936
## Site (Intercept) 0.00000 0.0000
## Room (Intercept) 0.00000 0.0000
## Residual 0.04860 0.2205
## Number of obs: 304, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 4.155315 0.072226 76.123886
## Treatment_bisDark -0.001837 0.055625 263.489850
## Treatment_bisFull 0.025105 0.056799 261.265795
## Treatment_bisMixt_smart -0.058973 0.074297 262.138708
## SexMale -0.048292 0.026580 268.210731
## SpeciesOP -1.341061 0.074745 29.050986
## RegionLuxembourg 0.019390 0.091948 79.727756
## Treatment_bisDark:RegionLuxembourg 0.037783 0.077036 264.339547
## Treatment_bisFull:RegionLuxembourg 0.086061 0.078388 262.858779
## Treatment_bisMixt_smart:RegionLuxembourg 0.334623 0.108067 267.149739
## t value Pr(>|t|)
## (Intercept) 57.532 < 2e-16 ***
## Treatment_bisDark -0.033 0.97368
## Treatment_bisFull 0.442 0.65885
## Treatment_bisMixt_smart -0.794 0.42806
## SexMale -1.817 0.07035 .
## SpeciesOP -17.942 < 2e-16 ***
## RegionLuxembourg 0.211 0.83352
## Treatment_bisDark:RegionLuxembourg 0.490 0.62422
## Treatment_bisFull:RegionLuxembourg 1.098 0.27326
## Treatment_bisMixt_smart:RegionLuxembourg 3.096 0.00217 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal SpcsOP RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.562
## Trtmnt_bsFl -0.540 0.729
## Trtmnt_bsM_ -0.425 0.517 0.526
## SexMale -0.133 -0.008 -0.070 -0.032
## SpeciesOP -0.346 -0.040 -0.025 0.036 0.002
## ReginLxmbrg -0.671 0.453 0.440 0.328 -0.026 -0.011
## Trtmnt_D:RL 0.411 -0.721 -0.527 -0.375 0.023 0.006 -0.584
## Trtmnt_F:RL 0.399 -0.528 -0.724 -0.382 0.043 0.000 -0.568 0.695
## Trtmn_M_:RL 0.282 -0.357 -0.361 -0.685 -0.003 0.015 -0.414 0.466 0.481
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Info_Total_eaten <- "
Aucun traitement n'a d'effet significatif.
Les chenilles mangent significativement plus dans le traitement Mixt_smart quand elles viennent du luxembourg que quand elles viennent du brabant.
L'espèce OP mange moins que l'espèce AE
Les mangent presquent significativement (P = 0.0659) moins que les femelles.
"
Info_Total_eaten## [1] "\nAucun traitement n'a d'effet significatif.\nLes chenilles mangent significativement plus dans le traitement Mixt_smart quand elles viennent du luxembourg que quand elles viennent du brabant.\nL'espèce OP mange moins que l'espèce AE\nLes mangent presquent significativement (P = 0.0659) moins que les femelles.\n"4.9.4 Visualisation
Summary_Total_eaten <- Data %>%
filter(Sex != "NA") %>%
group_by(Treatment_bis, Species, Sex) %>%
summarise(Mean=mean(log(Total_eaten)),
Var=var(log(Total_eaten)),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_Total_eaten, aes(x=Treatment_bis, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_wrap(~Sex) +
labs(title = "Quantité mangée", x = "Traitement", y = "log(Quantitée mangée (morceaux de feuilles))", color = "Species") +
theme_bw()
Summary_Total_eaten2 <- Data %>%
filter(Sex != "NA") %>%
group_by(Treatment_bis, Species, Region) %>%
summarise(Mean=mean(log(Total_eaten)),
Var=var(log(Total_eaten)),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_Total_eaten2, aes(x=Treatment_bis, y=Mean, color = Species))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5) +
geom_point(alpha = 0.8) +
facet_wrap(~Region) +
labs(title = "Total Eaten", x = "Treatment", y = "log(Total eaten)") +
theme_bw()
4.10 Pupa_mass * TT_pupation
4.10.1 Test
LM_Pupa_mass_by_TT_pupation <- lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Species + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis, data = Data)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')summary(LM_Pupa_mass_by_TT_pupation)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Species + Region +
## (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region +
## TT_pupation:Species + TT_pupation:Sex + TT_pupation:Region +
## TT_pupation:Treatment_bis
## Data: Data
##
## REML criterion at convergence: -821.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.3269 -0.4150 -0.0055 0.4755 2.9868
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.899e-04 0.019745
## Site (Intercept) 3.958e-05 0.006291
## Room (Intercept) 0.000e+00 0.000000
## Residual 1.525e-03 0.039049
## Number of obs: 288, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 1.794e-01 2.338e-02 2.274e+02
## TT_pupation 3.294e-03 4.753e-04 2.585e+02
## Treatment_bisFull 2.867e-03 2.893e-02 2.504e+02
## Treatment_bisSmart 2.476e-02 4.284e-02 2.590e+02
## Treatment_bisMixt_smart 8.283e-02 4.307e-02 2.617e+02
## SexMale 2.783e-03 2.598e-02 2.537e+02
## SpeciesOP -5.444e-02 3.332e-02 2.030e+02
## RegionLuxembourg 8.107e-02 3.168e-02 1.894e+02
## SexMale:SpeciesOP -3.426e-03 1.894e-02 2.509e+02
## SpeciesOP:RegionLuxembourg -5.911e-02 2.644e-02 7.214e+01
## Treatment_bisFull:SpeciesOP -2.729e-03 2.239e-02 2.452e+02
## Treatment_bisSmart:SpeciesOP -1.248e-02 2.945e-02 2.593e+02
## Treatment_bisFull:SexMale -4.715e-03 1.128e-02 2.430e+02
## Treatment_bisSmart:SexMale -2.113e-02 1.490e-02 2.586e+02
## Treatment_bisMixt_smart:SexMale -4.986e-02 1.880e-02 2.537e+02
## Treatment_bisFull:RegionLuxembourg -1.676e-03 1.134e-02 2.395e+02
## Treatment_bisSmart:RegionLuxembourg 9.368e-03 1.452e-02 2.458e+02
## Treatment_bisMixt_smart:RegionLuxembourg 2.335e-02 2.254e-02 2.553e+02
## TT_pupation:SpeciesOP -1.448e-03 1.721e-03 2.535e+02
## TT_pupation:SexMale 3.473e-04 5.505e-04 2.568e+02
## TT_pupation:RegionLuxembourg -1.821e-03 6.337e-04 2.593e+02
## TT_pupation:Treatment_bisFull 4.949e-04 6.368e-04 2.502e+02
## TT_pupation:Treatment_bisSmart -1.904e-04 1.021e-03 2.609e+02
## TT_pupation:Treatment_bisMixt_smart -4.068e-04 9.588e-04 2.634e+02
## t value Pr(>|t|)
## (Intercept) 7.674 4.88e-13 ***
## TT_pupation 6.930 3.33e-11 ***
## Treatment_bisFull 0.099 0.92114
## Treatment_bisSmart 0.578 0.56376
## Treatment_bisMixt_smart 1.923 0.05551 .
## SexMale 0.107 0.91478
## SpeciesOP -1.634 0.10384
## RegionLuxembourg 2.559 0.01129 *
## SexMale:SpeciesOP -0.181 0.85663
## SpeciesOP:RegionLuxembourg -2.236 0.02846 *
## Treatment_bisFull:SpeciesOP -0.122 0.90310
## Treatment_bisSmart:SpeciesOP -0.424 0.67214
## Treatment_bisFull:SexMale -0.418 0.67634
## Treatment_bisSmart:SexMale -1.418 0.15741
## Treatment_bisMixt_smart:SexMale -2.653 0.00848 **
## Treatment_bisFull:RegionLuxembourg -0.148 0.88258
## Treatment_bisSmart:RegionLuxembourg 0.645 0.51942
## Treatment_bisMixt_smart:RegionLuxembourg 1.036 0.30136
## TT_pupation:SpeciesOP -0.842 0.40085
## TT_pupation:SexMale 0.631 0.52864
## TT_pupation:RegionLuxembourg -2.873 0.00440 **
## TT_pupation:Treatment_bisFull 0.777 0.43781
## TT_pupation:Treatment_bisSmart -0.186 0.85225
## TT_pupation:Treatment_bisMixt_smart -0.424 0.67174
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 24 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Test des hypothèses
Normalité des réisuds
qqnorm(resid(LM_Pupa_mass_by_TT_pupation))
qqline(resid(LM_Pupa_mass_by_TT_pupation))
On doit modifier les données (comme dans Pupa_mass en fait)
LM_Pupa_mass_by_TT_pupation <- lmer(log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Species + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis, data = Data[-239,])## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient# Honnêtement sans trop savoir pourquoi, la ligne 239 possédait des distance de cook très élevée par rapport au reste des points, nous l'avons donc retirée)
summary(LM_Pupa_mass_by_TT_pupation)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species +
## Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species +
## Region:Species + Treatment_bis:Species + Treatment_bis:Sex +
## Treatment_bis:Region + TT_pupation:Species + TT_pupation:Sex +
## TT_pupation:Region + TT_pupation:Treatment_bis
## Data: Data[-239, ]
##
## REML criterion at convergence: -169.5
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6546 -0.5198 0.0452 0.6318 2.3606
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0054514 0.07383
## Site (Intercept) 0.0002879 0.01697
## Room (Intercept) 0.0003800 0.01949
## Residual 0.0176782 0.13296
## Number of obs: 287, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -1.587e+00 8.141e-02 1.712e+02
## TT_pupation 9.778e-03 1.624e-03 2.555e+02
## Treatment_bisFull 8.045e-02 1.024e-01 2.482e+02
## Treatment_bisSmart 1.421e-01 1.469e-01 2.569e+02
## Treatment_bisMixt_smart 3.249e-01 1.492e-01 2.587e+02
## SexMale 3.605e-02 8.960e-02 2.528e+02
## SpeciesOP -4.404e-01 1.153e-01 2.099e+02
## RegionLuxembourg 1.505e-01 1.114e-01 2.056e+02
## SexMale:SpeciesOP -2.187e-02 6.526e-02 2.510e+02
## SpeciesOP:RegionLuxembourg -1.357e-01 9.408e-02 8.364e+01
## Treatment_bisFull:SpeciesOP -2.142e-02 7.796e-02 2.443e+02
## Treatment_bisSmart:SpeciesOP -6.654e-02 1.008e-01 2.567e+02
## Treatment_bisFull:SexMale -3.039e-02 3.855e-02 2.432e+02
## Treatment_bisSmart:SexMale -5.646e-02 5.108e-02 2.576e+02
## Treatment_bisMixt_smart:SexMale -1.475e-01 6.430e-02 2.521e+02
## Treatment_bisFull:RegionLuxembourg -2.538e-02 3.869e-02 2.400e+02
## Treatment_bisSmart:RegionLuxembourg 1.734e-02 4.951e-02 2.450e+02
## Treatment_bisMixt_smart:RegionLuxembourg 3.646e-02 7.702e-02 2.536e+02
## TT_pupation:SpeciesOP -1.219e-03 5.919e-03 2.563e+02
## TT_pupation:SexMale 6.251e-04 1.915e-03 2.563e+02
## TT_pupation:RegionLuxembourg -2.723e-03 2.252e-03 2.623e+02
## TT_pupation:Treatment_bisFull -4.661e-05 2.271e-03 2.471e+02
## TT_pupation:Treatment_bisSmart -1.739e-03 3.496e-03 2.580e+02
## TT_pupation:Treatment_bisMixt_smart -3.240e-03 3.328e-03 2.612e+02
## t value Pr(>|t|)
## (Intercept) -19.490 < 2e-16 ***
## TT_pupation 6.019 6.05e-09 ***
## Treatment_bisFull 0.786 0.432709
## Treatment_bisSmart 0.967 0.334204
## Treatment_bisMixt_smart 2.177 0.030348 *
## SexMale 0.402 0.687776
## SpeciesOP -3.819 0.000176 ***
## RegionLuxembourg 1.350 0.178402
## SexMale:SpeciesOP -0.335 0.737831
## SpeciesOP:RegionLuxembourg -1.442 0.153030
## Treatment_bisFull:SpeciesOP -0.275 0.783733
## Treatment_bisSmart:SpeciesOP -0.660 0.509683
## Treatment_bisFull:SexMale -0.788 0.431236
## Treatment_bisSmart:SexMale -1.105 0.270043
## Treatment_bisMixt_smart:SexMale -2.293 0.022648 *
## Treatment_bisFull:RegionLuxembourg -0.656 0.512568
## Treatment_bisSmart:RegionLuxembourg 0.350 0.726503
## Treatment_bisMixt_smart:RegionLuxembourg 0.473 0.636326
## TT_pupation:SpeciesOP -0.206 0.836945
## TT_pupation:SexMale 0.326 0.744356
## TT_pupation:RegionLuxembourg -1.209 0.227852
## TT_pupation:Treatment_bisFull -0.021 0.983645
## TT_pupation:Treatment_bisSmart -0.497 0.619355
## TT_pupation:Treatment_bisMixt_smart -0.973 0.331265
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 24 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficientqqnorm(resid(LM_Pupa_mass_by_TT_pupation))
qqline(resid(LM_Pupa_mass_by_TT_pupation))
Homogénité des variances
plot(LM_Pupa_mass_by_TT_pupation)
Distance de cook
plot(cooks.distance(LM_Pupa_mass_by_TT_pupation))
4.10.2 Simplification du modèle
drop1(LM_Pupa_mass_by_TT_pupation)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Species + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.001985 0.001985 1 250.962 0.1123 0.7378
## Species:Region 0.036761 0.036761 1 83.642 2.0794 0.1530
## Treatment_bis:Species 0.007894 0.003947 2 251.745 0.2233 0.8000
## Treatment_bis:Sex 0.097729 0.032576 3 250.714 1.8427 0.1399
## Treatment_bis:Region 0.020074 0.006691 3 246.020 0.3785 0.7686
## TT_pupation:Species 0.000750 0.000750 1 256.293 0.0424 0.8369
## TT_pupation:Sex 0.001884 0.001884 1 256.266 0.1066 0.7444
## TT_pupation:Region 0.025829 0.025829 1 262.299 1.4610 0.2279
## TT_pupation:Treatment_bis 0.019920 0.006640 3 256.153 0.3756 0.7707LM_Pupa_mass_by_TT_pupation1 <- update(LM_Pupa_mass_by_TT_pupation, . ~ . - Treatment_bis:Species)
drop1(LM_Pupa_mass_by_TT_pupation1)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Species:Region + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Species + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex:Species 0.001443 0.001443 1 251.532 0.0821 0.7747
## Species:Region 0.043063 0.043063 1 81.936 2.4513 0.1213
## Treatment_bis:Sex 0.097602 0.032534 3 252.475 1.8519 0.1383
## Treatment_bis:Region 0.020266 0.006755 3 247.619 0.3845 0.7642
## TT_pupation:Species 0.001072 0.001072 1 256.998 0.0610 0.8051
## TT_pupation:Sex 0.003093 0.003093 1 255.639 0.1761 0.6751
## TT_pupation:Region 0.031108 0.031108 1 263.844 1.7708 0.1844
## TT_pupation:Treatment_bis 0.018195 0.006065 3 253.321 0.3452 0.7926LM_Pupa_mass_by_TT_pupation2 <- update(LM_Pupa_mass_by_TT_pupation1, . ~ . - Sex:Species)
drop1(LM_Pupa_mass_by_TT_pupation2)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Species + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Species:Region 0.044235 0.044235 1 82.113 2.5267 0.1158
## Treatment_bis:Sex 0.096293 0.032098 3 253.896 1.8334 0.1415
## Treatment_bis:Region 0.019830 0.006610 3 248.511 0.3776 0.7693
## TT_pupation:Species 0.000903 0.000903 1 256.864 0.0516 0.8205
## TT_pupation:Sex 0.024855 0.024855 1 253.429 1.4197 0.2346
## TT_pupation:Region 0.033297 0.033297 1 265.257 1.9019 0.1690
## TT_pupation:Treatment_bis 0.017084 0.005695 3 254.057 0.3253 0.8071LM_Pupa_mass_by_TT_pupation3 <- update(LM_Pupa_mass_by_TT_pupation2, . ~ . - TT_pupation:Treatment_bis)
drop1(LM_Pupa_mass_by_TT_pupation3)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Species + TT_pupation:Sex + TT_pupation:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Species:Region 0.056247 0.056247 1 77.793 3.2391 0.07578 .
## Treatment_bis:Sex 0.088611 0.029537 3 256.477 1.7009 0.16727
## Treatment_bis:Region 0.012252 0.004084 3 250.230 0.2352 0.87180
## TT_pupation:Species 0.000361 0.000361 1 259.452 0.0208 0.88549
## TT_pupation:Sex 0.037050 0.037050 1 253.799 2.1336 0.14534
## TT_pupation:Region 0.048337 0.048337 1 268.287 2.7836 0.09640 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation4 <- update(LM_Pupa_mass_by_TT_pupation3, . ~ . - Treatment_bis:Region)
drop1(LM_Pupa_mass_by_TT_pupation4)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Sex + TT_pupation:Species + TT_pupation:Sex + TT_pupation:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Species:Region 0.064527 0.064527 1 75.041 3.7545 0.05643 .
## Treatment_bis:Sex 0.091127 0.030376 3 259.237 1.7674 0.15380
## TT_pupation:Species 0.000201 0.000201 1 260.379 0.0117 0.91400
## TT_pupation:Sex 0.037723 0.037723 1 257.457 2.1949 0.13969
## TT_pupation:Region 0.058942 0.058942 1 271.293 3.4295 0.06513 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation5 <- update(LM_Pupa_mass_by_TT_pupation4, . ~ . - TT_pupation:Species)
drop1(LM_Pupa_mass_by_TT_pupation5)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Sex + TT_pupation:Sex + TT_pupation:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Species:Region 0.065196 0.065196 1 75.514 3.8071 0.05474 .
## Treatment_bis:Sex 0.091469 0.030490 3 259.817 1.7804 0.15128
## TT_pupation:Sex 0.037526 0.037526 1 257.804 2.1914 0.14001
## TT_pupation:Region 0.059161 0.059161 1 272.314 3.4547 0.06415 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation6 <- update(LM_Pupa_mass_by_TT_pupation5, . ~ . - TT_pupation:Sex)
drop1(LM_Pupa_mass_by_TT_pupation6)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + Treatment_bis:Sex + TT_pupation:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Species:Region 0.056033 0.056033 1 74.33 3.2595 0.07506 .
## Treatment_bis:Sex 0.064650 0.021550 3 260.87 1.2536 0.29082
## TT_pupation:Region 0.043988 0.043988 1 273.20 2.5588 0.11084
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation7 <- update(LM_Pupa_mass_by_TT_pupation6, . ~ . - Treatment_bis:Sex)
drop1(LM_Pupa_mass_by_TT_pupation7)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + TT_pupation:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.263460 0.087820 3 179.730 5.0593 0.002181 **
## Sex 0.015079 0.015079 1 262.846 0.8687 0.352165
## Species:Region 0.052682 0.052682 1 78.211 3.0350 0.085419 .
## TT_pupation:Region 0.039184 0.039184 1 276.350 2.2574 0.134119
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Il n’y a plus d’interactions qui n’ont pas de P-val proche de 0.05, nous décidons d’arrêter la simplification du modèle.
Est ce que cela a été utile
AIC(LM_Pupa_mass_by_TT_pupation7)## [1] -222.0473AIC(LM_Pupa_mass_by_TT_pupation)## [1] -113.4576Oui ca a été utile
LM_Pupa_mass_by_TT_pupation <- LM_Pupa_mass_by_TT_pupation74.10.3 Treatment VS Teatment_bis
AIC(lmer(log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + TT_pupation:Region, data = Data[-239, ]))## [1] -222.0473AIC(lmer(log(Pupa_mass) ~ TT_pupation + Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + TT_pupation:Region, data = Data[-239, ]))## [1] -228.6703summary(lmer(log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + TT_pupation:Region, data = Data[-239, ]))$coeff## Estimate Std. Error df t value
## (Intercept) -1.547771401 0.064737203 97.97408 -23.9085308
## TT_pupation 0.009558839 0.001293654 271.80224 7.3890239
## Treatment_bisFull 0.043837913 0.018740127 256.16154 2.3392538
## Treatment_bisSmart 0.045327051 0.025261519 192.00066 1.7943122
## Treatment_bisMixt_smart 0.113047807 0.031811171 213.66832 3.5537141
## SexMale 0.015146918 0.016251137 262.84560 0.9320528
## SpeciesOP -0.494393265 0.056804500 62.78089 -8.7034173
## RegionLuxembourg 0.157038324 0.093896862 199.90792 1.6724555
## SpeciesOP:RegionLuxembourg -0.148618061 0.085308846 78.21129 -1.7421178
## TT_pupation:RegionLuxembourg -0.002853817 0.001899422 276.35014 -1.5024660
## Pr(>|t|)
## (Intercept) 1.120606e-42
## TT_pupation 1.825583e-12
## Treatment_bisFull 2.009134e-02
## Treatment_bisSmart 7.433663e-02
## Treatment_bisMixt_smart 4.674550e-04
## SexMale 3.521645e-01
## SpeciesOP 2.175405e-12
## RegionLuxembourg 9.599884e-02
## SpeciesOP:RegionLuxembourg 8.541896e-02
## TT_pupation:RegionLuxembourg 1.341186e-01summary(lmer(log(Pupa_mass) ~ TT_pupation + Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + TT_pupation:Region, data = Data[-239, ]))$coeff## Estimate Std. Error df t value
## (Intercept) -1.550743349 0.065084697 89.78554 -23.826543
## TT_pupation 0.009553083 0.001289698 274.37716 7.407225
## TreatmentFull 0.053087820 0.019506369 256.49045 2.721563
## TreatmentSmart 0.074016135 0.019582554 259.89089 3.779698
## SexMale 0.019457352 0.016211507 263.08195 1.200219
## SpeciesOP -0.513696512 0.056012610 60.89865 -9.171087
## RegionLuxembourg 0.124370484 0.091095223 231.10858 1.365280
## SpeciesOP:RegionLuxembourg -0.125697749 0.084027319 77.06904 -1.495915
## TT_pupation:RegionLuxembourg -0.002184368 0.001842344 277.04849 -1.185646
## Pr(>|t|)
## (Intercept) 1.371737e-40
## TT_pupation 1.594799e-12
## TreatmentFull 6.942490e-03
## TreatmentSmart 1.947912e-04
## SexMale 2.311341e-01
## SpeciesOP 4.451227e-13
## RegionLuxembourg 1.734925e-01
## SpeciesOP:RegionLuxembourg 1.387597e-01
## TT_pupation:RegionLuxembourg 2.367780e-01L’AIC suggère de prendre Treatment mais les p-val disent que Mixt_Smart a un effet fort significatif Je vais rester avec Treatment_bis
Analyse des pval
summary(lmer(log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + TT_pupation:Region, data = Data[-239, ]))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species +
## Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region +
## TT_pupation:Region
## Data: Data[-239, ]
##
## REML criterion at convergence: -250
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6241 -0.5310 0.0713 0.5905 2.4619
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0051734 0.07193
## Site (Intercept) 0.0001168 0.01081
## Room (Intercept) 0.0004170 0.02042
## Residual 0.0173582 0.13175
## Number of obs: 287, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.547771 0.064737 97.974081 -23.909 < 2e-16
## TT_pupation 0.009559 0.001294 271.802239 7.389 1.83e-12
## Treatment_bisFull 0.043838 0.018740 256.161545 2.339 0.020091
## Treatment_bisSmart 0.045327 0.025262 192.000658 1.794 0.074337
## Treatment_bisMixt_smart 0.113048 0.031811 213.668324 3.554 0.000467
## SexMale 0.015147 0.016251 262.845603 0.932 0.352165
## SpeciesOP -0.494393 0.056804 62.780890 -8.703 2.18e-12
## RegionLuxembourg 0.157038 0.093897 199.907918 1.672 0.095999
## SpeciesOP:RegionLuxembourg -0.148618 0.085309 78.211290 -1.742 0.085419
## TT_pupation:RegionLuxembourg -0.002854 0.001899 276.350138 -1.502 0.134119
##
## (Intercept) ***
## TT_pupation ***
## Treatment_bisFull *
## Treatment_bisSmart .
## Treatment_bisMixt_smart ***
## SexMale
## SpeciesOP ***
## RegionLuxembourg .
## SpeciesOP:RegionLuxembourg .
## TT_pupation:RegionLuxembourg
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TT_ppt Trtm_F Trtm_S Trt_M_ SexMal SpcsOP RgnLxm SOP:RL
## TT_pupation -0.860
## Trtmnt_bsFl -0.183 0.055
## Trtmnt_bsSm -0.164 0.062 0.358
## Trtmnt_bsM_ -0.197 0.092 0.311 0.140
## SexMale -0.122 0.027 -0.083 0.011 -0.039
## SpeciesOP -0.748 0.633 0.067 0.079 0.157 0.014
## ReginLxmbrg -0.633 0.585 0.080 -0.087 0.199 0.055 0.511
## SpcsOP:RgnL 0.501 -0.420 -0.069 0.048 -0.149 -0.048 -0.666 -0.792
## TT_pptn:RgL 0.608 -0.689 -0.082 0.071 -0.223 -0.064 -0.448 -0.911 0.670summary(lmer(log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + TT_pupation:Region, data = Data_ref_full[-239, ]))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species +
## Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region +
## TT_pupation:Region
## Data: Data_ref_full[-239, ]
##
## REML criterion at convergence: -250
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6241 -0.5310 0.0713 0.5905 2.4619
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0051734 0.07193
## Site (Intercept) 0.0001168 0.01081
## Room (Intercept) 0.0004170 0.02042
## Residual 0.0173582 0.13175
## Number of obs: 287, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.503933 0.064015 94.547793 -23.494 < 2e-16
## TT_pupation 0.009559 0.001294 271.802240 7.389 1.83e-12
## Treatment_bisDark -0.043838 0.018740 256.161545 -2.339 0.0201
## Treatment_bisSmart 0.001489 0.025511 211.071795 0.058 0.9535
## Treatment_bisMixt_smart 0.069210 0.031501 195.364408 2.197 0.0292
## SexMale 0.015147 0.016251 262.845603 0.932 0.3522
## SpeciesOP -0.494393 0.056804 62.780890 -8.703 2.18e-12
## RegionLuxembourg 0.157038 0.093897 199.907914 1.672 0.0960
## SpeciesOP:RegionLuxembourg -0.148618 0.085309 78.211290 -1.742 0.0854
## TT_pupation:RegionLuxembourg -0.002854 0.001899 276.350137 -1.502 0.1341
##
## (Intercept) ***
## TT_pupation ***
## Treatment_bisDark *
## Treatment_bisSmart
## Treatment_bisMixt_smart *
## SexMale
## SpeciesOP ***
## RegionLuxembourg .
## SpeciesOP:RegionLuxembourg .
## TT_pupation:RegionLuxembourg
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TT_ppt Trtm_D Trtm_S Trt_M_ SexMal SpcsOP RgnLxm SOP:RL
## TT_pupation -0.853
## Trtmnt_bsDr -0.108 -0.055
## Trtmnt_bsSm -0.139 0.021 0.381
## Trtmnt_bsM_ -0.173 0.060 0.281 0.136
## SexMale -0.148 0.027 0.083 0.072 0.010
## SpeciesOP -0.737 0.633 -0.067 0.029 0.119 0.014
## ReginLxmbrg -0.617 0.585 -0.080 -0.144 0.154 0.055 0.511
## SpcsOP:RgnL 0.486 -0.420 0.069 0.098 -0.110 -0.048 -0.666 -0.792
## TT_pptn:RgL 0.591 -0.689 0.082 0.130 -0.177 -0.064 -0.448 -0.911 0.670summary(lmer(log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region + TT_pupation:Region, data = Data_ref_smart[-239, ]))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Pupa_mass) ~ TT_pupation + Treatment_bis + Sex + Species +
## Region + (1 | Mother) + (1 | Site) + (1 | Room) + Species:Region +
## TT_pupation:Region
## Data: Data_ref_smart[-239, ]
##
## REML criterion at convergence: -250
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6241 -0.5310 0.0713 0.5905 2.4619
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0051734 0.07193
## Site (Intercept) 0.0001168 0.01081
## Room (Intercept) 0.0004170 0.02042
## Residual 0.0173582 0.13175
## Number of obs: 287, groups: Mother, 35; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.502444 0.065528 90.683165 -22.928 < 2e-16
## TT_pupation 0.009559 0.001294 271.802245 7.389 1.83e-12
## Treatment_bisDark -0.045327 0.025262 192.000658 -1.794 0.0743
## Treatment_bisFull -0.001489 0.025511 211.071795 -0.058 0.9535
## Treatment_bisMixt_smart 0.067721 0.037746 97.773751 1.794 0.0759
## SexMale 0.015147 0.016251 262.845604 0.932 0.3522
## SpeciesOP -0.494393 0.056804 62.780890 -8.703 2.18e-12
## RegionLuxembourg 0.157038 0.093897 199.907920 1.672 0.0960
## SpeciesOP:RegionLuxembourg -0.148618 0.085309 78.211291 -1.742 0.0854
## TT_pupation:RegionLuxembourg -0.002854 0.001899 276.350138 -1.502 0.1341
##
## (Intercept) ***
## TT_pupation ***
## Treatment_bisDark .
## Treatment_bisFull
## Treatment_bisMixt_smart .
## SexMale
## SpeciesOP ***
## RegionLuxembourg .
## SpeciesOP:RegionLuxembourg .
## TT_pupation:RegionLuxembourg
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TT_ppt Trtm_D Trtm_F Trt_M_ SexMal SpcsOP RgnLxm SOP:RL
## TT_pupation -0.825
## Trtmnt_bsDr -0.224 -0.062
## Trtmnt_bsFl -0.253 -0.021 0.728
## Trtmnt_bsM_ -0.268 0.036 0.551 0.562
## SexMale -0.116 0.027 -0.011 -0.072 -0.040
## SpeciesOP -0.709 0.633 -0.079 -0.029 0.080 0.014
## ReginLxmbrg -0.659 0.585 0.087 0.144 0.226 0.055 0.511
## SpcsOP:RgnL 0.513 -0.420 -0.048 -0.098 -0.158 -0.048 -0.666 -0.792
## TT_pptn:RgL 0.628 -0.689 -0.071 -0.130 -0.236 -0.064 -0.448 -0.911 0.670Info_Pupa_mass_by_TT_pupation <- "
Au plus le temps pour entrer en chrysalide est élevé, au plus la chrysalide sera lourde.
ordre de croissance de masse : Dark < Full et Smart (les deux sont très simillaires) < Mixt_smart
OP est plus légère
Les chrysalides provenants de la région Luxembourg sont quasiment significativement (pval = 0.065) plus lourde.
L'impacte de la région Luxembourg est presque significativement différent (pval = 0.068) en fonction de l'espèce (OP plus légère)
L'impacte du temps avant d'atteindre la chrysalide est quasiment significativement différent fonction de la région d'ou vient la chenille (luxembourgeoise plus légère pour un même temps d'atteinte de chrysalide)
"
Info_Pupa_mass_by_TT_pupation## [1] "\nAu plus le temps pour entrer en chrysalide est élevé, au plus la chrysalide sera lourde.\nordre de croissance de masse : Dark < Full et Smart (les deux sont très simillaires) < Mixt_smart\nOP est plus légère\nLes chrysalides provenants de la région Luxembourg sont quasiment significativement (pval = 0.065) plus lourde.\nL'impacte de la région Luxembourg est presque significativement différent (pval = 0.068) en fonction de l'espèce (OP plus légère)\nL'impacte du temps avant d'atteindre la chrysalide est quasiment significativement différent fonction de la région d'ou vient la chenille (luxembourgeoise plus légère pour un même temps d'atteinte de chrysalide)\n"4.10.4 Visualisation
ggplot(data = Data[-239,], aes(x = TT_pupation, y = Pupa_mass)) +
geom_point(aes(color = Treatment_bis, shape = Species)) +
geom_smooth(method = "lm", aes(linetype = Species)) +
labs(title = "Masse des chrysalides en fonction du temps passé pour entrer en chrysalide", x = "Temps pour entrer en chrysalide (jours)", y = "Poids des chrysalides (g)", color = "Traitement", linetype = "Espèce", shape = "Espèce") +
theme_bw()## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 158 rows containing non-finite values (`stat_smooth()`).## Warning: Removed 158 rows containing missing values (`geom_point()`).
ggplot(data = Data[-239,], aes(x = TT_pupation, y = log(Pupa_mass))) +
geom_point(aes(color = Treatment_bis, shape = Species)) +
geom_smooth(method = "lm", aes(color= Treatment_bis, linetype = Species)) +
facet_wrap(~Region) +
labs(title = "Pupa Mass by Time to pupa", x = "Time to pupation", y = "log(Pupa_mass)") +
theme_bw()## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 158 rows containing non-finite values (`stat_smooth()`).## Warning: Removed 158 rows containing missing values (`geom_point()`).
4.11 Mass_by_Time
Dévelloppement du jeux de données
Data_mass <- Data[,1:31] %>% pivot_longer(cols = M0:M20, names_to = "Numéro_de_masse", values_to = "Mass")
Data_mass$Time <- rep(0:20, length.out = nrow(Data_mass))Data_mass_ref_smart <- Data_mass
Data_mass_ref_smart$Treatment <- relevel(Data_mass$Treatment, ref = "Smart")
Data_mass_ref_smart$Treatment_bis <- relevel(Data_mass$Treatment_bis, ref = "Smart")
Data_mass_ref_full <- Data_mass
Data_mass_ref_full$Treatment <- relevel(Data_mass$Treatment, ref = "Full")
Data_mass_ref_full$Treatment_bis <- relevel(Data_mass$Treatment_bis, ref = "Full")4.11.1 Test
LM_mass_by_time <- lmer(Mass ~ Time + Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region + Time:Species + Time:Sex + Time:Region + Time:Treatment_bis, data = Data_mass)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')summary(LM_mass_by_time)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Mass ~ Time + Treatment_bis + Sex + Species + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Sex:Species + Region:Species +
## Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region +
## Time:Species + Time:Sex + Time:Region + Time:Treatment_bis
## Data: Data_mass
##
## REML criterion at convergence: -1873.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.0175 -0.5296 -0.1481 0.3834 4.4012
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.001171 0.03422
## Site (Intercept) 0.000000 0.00000
## Room (Intercept) 0.000000 0.00000
## Residual 0.019175 0.13847
## Number of obs: 1863, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 2.428e-02 1.710e-02 1.245e+02
## Time 5.480e-02 2.146e-03 1.836e+03
## Treatment_bisFull -2.017e-02 1.759e-02 1.839e+03
## Treatment_bisSmart -8.095e-02 2.227e-02 1.837e+03
## Treatment_bisMixt_smart -3.022e-02 2.182e-02 1.839e+03
## SexMale -2.664e-02 1.607e-02 1.832e+03
## SpeciesOP 3.325e-02 2.694e-02 8.059e+01
## RegionLuxembourg -6.650e-03 2.131e-02 7.580e+01
## SexMale:SpeciesOP 2.400e-02 1.940e-02 1.839e+03
## SpeciesOP:RegionLuxembourg 4.669e-03 3.163e-02 3.937e+01
## Treatment_bisFull:SpeciesOP 3.754e-02 2.154e-02 1.832e+03
## Treatment_bisSmart:SpeciesOP 4.433e-03 2.858e-02 1.838e+03
## Treatment_bisFull:SexMale -4.356e-03 1.633e-02 1.822e+03
## Treatment_bisSmart:SexMale -8.969e-03 2.146e-02 1.725e+03
## Treatment_bisMixt_smart:SexMale 1.046e-02 2.178e-02 1.775e+03
## Treatment_bisFull:RegionLuxembourg -2.995e-02 1.630e-02 1.823e+03
## Treatment_bisSmart:RegionLuxembourg 7.347e-02 2.007e-02 1.838e+03
## Treatment_bisMixt_smart:RegionLuxembourg -4.617e-02 2.138e-02 1.809e+03
## Time:SpeciesOP 6.469e-02 1.034e-02 1.829e+03
## Time:SexMale 5.026e-03 2.188e-03 1.823e+03
## Time:RegionLuxembourg -6.661e-03 2.251e-03 1.838e+03
## Time:Treatment_bisFull 1.249e-02 2.601e-03 1.830e+03
## Time:Treatment_bisSmart 2.782e-02 3.730e-03 1.824e+03
## Time:Treatment_bisMixt_smart 1.744e-02 3.163e-03 1.822e+03
## t value Pr(>|t|)
## (Intercept) 1.420 0.158191
## Time 25.539 < 2e-16 ***
## Treatment_bisFull -1.146 0.251820
## Treatment_bisSmart -3.635 0.000286 ***
## Treatment_bisMixt_smart -1.385 0.166227
## SexMale -1.657 0.097604 .
## SpeciesOP 1.235 0.220579
## RegionLuxembourg -0.312 0.755882
## SexMale:SpeciesOP 1.237 0.216189
## SpeciesOP:RegionLuxembourg 0.148 0.883382
## Treatment_bisFull:SpeciesOP 1.743 0.081502 .
## Treatment_bisSmart:SpeciesOP 0.155 0.876744
## Treatment_bisFull:SexMale -0.267 0.789701
## Treatment_bisSmart:SexMale -0.418 0.676009
## Treatment_bisMixt_smart:SexMale 0.480 0.631071
## Treatment_bisFull:RegionLuxembourg -1.838 0.066250 .
## Treatment_bisSmart:RegionLuxembourg 3.660 0.000260 ***
## Treatment_bisMixt_smart:RegionLuxembourg -2.159 0.030969 *
## Time:SpeciesOP 6.256 4.91e-10 ***
## Time:SexMale 2.297 0.021729 *
## Time:RegionLuxembourg -2.959 0.003123 **
## Time:Treatment_bisFull 4.804 1.68e-06 ***
## Time:Treatment_bisSmart 7.459 1.34e-13 ***
## Time:Treatment_bisMixt_smart 5.513 4.04e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 24 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_mass_by_time))
qqline(resid(LM_mass_by_time))
Il faudrait modifier les données
LM_mass_by_time <- lmer(log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1|Mother) + (1|Site) + (1|Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region + Time:Species + Time:Sex + Time:Region + Time:Treatment_bis, data = Data_mass)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')#summary(LM_mass_by_time)qqnorm(resid(LM_mass_by_time))
qqline(resid(LM_mass_by_time))
Homogénité des variances
plot(LM_mass_by_time)
Distance de cook
plot(cooks.distance(LM_mass_by_time))
On pourrait retirer quelques outlier mais cela semle bon
4.11.2 Simplification du modèle
drop1(LM_mass_by_time)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Region:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region + Time:Species + Time:Sex + Time:Region + Time:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## sqrt(Time) 388.31 388.31 1 1808.32 1447.1310 < 2.2e-16 ***
## Sex:Species 0.45 0.45 1 1829.32 1.6611 0.19762
## Species:Region 0.03 0.03 1 33.41 0.1274 0.72337
## Treatment_bis:Species 1.44 0.72 2 1827.60 2.6822 0.06868 .
## Treatment_bis:Sex 1.08 0.36 3 1833.87 1.3365 0.26080
## Treatment_bis:Region 14.63 4.88 3 1828.35 18.1705 1.281e-11 ***
## Species:Time 523.11 261.56 2 1813.45 974.7464 < 2.2e-16 ***
## Sex:Time 0.52 0.52 1 1810.94 1.9561 0.16211
## Region:Time 0.06 0.06 1 1821.25 0.2160 0.64215
## Treatment_bis:Time 12.73 4.24 3 1811.10 15.8120 3.762e-10 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_mass_by_time1 <- update(LM_mass_by_time, . ~ . - Species:Region)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_mass_by_time1)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region + Species:Time + Sex:Time + Region:Time + Treatment_bis:Time
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## sqrt(Time) 388.36 388.36 1 1809.6 1447.4462 < 2.2e-16 ***
## Sex:Species 0.45 0.45 1 1830.0 1.6661 0.19695
## Treatment_bis:Species 1.44 0.72 2 1830.0 2.6782 0.06896 .
## Treatment_bis:Sex 1.08 0.36 3 1834.8 1.3361 0.26091
## Treatment_bis:Region 14.62 4.87 3 1829.8 18.1613 1.298e-11 ***
## Species:Time 523.11 261.56 2 1814.3 974.8424 < 2.2e-16 ***
## Sex:Time 0.53 0.53 1 1811.6 1.9599 0.16169
## Region:Time 0.08 0.08 1 1801.5 0.2904 0.59006
## Treatment_bis:Time 12.77 4.26 3 1813.1 15.8641 3.491e-10 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_mass_by_time2 <- update(LM_mass_by_time1, . ~ . - Region:Time)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_mass_by_time2)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Treatment_bis:Species + Treatment_bis:Sex + Treatment_bis:Region + Species:Time + Sex:Time + Treatment_bis:Time
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## sqrt(Time) 393.59 393.59 1 1809.7 1467.5926 < 2.2e-16 ***
## Sex:Species 0.44 0.44 1 1830.9 1.6462 0.19964
## Treatment_bis:Species 1.41 0.71 2 1830.9 2.6325 0.07217 .
## Treatment_bis:Sex 1.11 0.37 3 1835.7 1.3779 0.24776
## Treatment_bis:Region 14.88 4.96 3 1831.1 18.4954 8.047e-12 ***
## Species:Time 528.46 264.23 2 1814.9 985.2394 < 2.2e-16 ***
## Sex:Time 0.50 0.50 1 1812.5 1.8585 0.17297
## Treatment_bis:Time 12.69 4.23 3 1813.0 15.7734 3.975e-10 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_mass_by_time3 <- update(LM_mass_by_time2, . ~ . - Treatment_bis:Sex)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_mass_by_time3)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Species + Treatment_bis:Species + Treatment_bis:Region + Species:Time + Sex:Time + Treatment_bis:Time
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## sqrt(Time) 394.21 394.21 1 1812.9 1468.5471 < 2.2e-16 ***
## Sex:Species 0.30 0.30 1 1832.1 1.1291 0.28811
## Treatment_bis:Species 1.54 0.77 2 1833.5 2.8731 0.05678 .
## Treatment_bis:Region 14.50 4.83 3 1833.8 18.0059 1.620e-11 ***
## Species:Time 529.01 264.51 2 1818.1 985.3598 < 2.2e-16 ***
## Sex:Time 0.57 0.57 1 1816.1 2.1394 0.14373
## Treatment_bis:Time 12.54 4.18 3 1816.2 15.5681 5.331e-10 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_mass_by_time4 <- update(LM_mass_by_time3, . ~ . - Sex:Species)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_mass_by_time4)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Species + Treatment_bis:Region + Species:Time + Sex:Time + Treatment_bis:Time
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## sqrt(Time) 394.41 394.41 1 1813.9 1469.3043 < 2.2e-16 ***
## Treatment_bis:Species 1.65 0.83 2 1834.1 3.0767 0.04635 *
## Treatment_bis:Region 14.62 4.87 3 1834.6 18.1498 1.318e-11 ***
## Species:Time 528.91 264.45 2 1819.0 985.1865 < 2.2e-16 ***
## Sex:Time 0.34 0.34 1 1823.5 1.2534 0.26305
## Treatment_bis:Time 12.50 4.17 3 1817.3 15.5213 5.700e-10 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_mass_by_time5 <- update(LM_mass_by_time4, . ~ . - Sex:Time)## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')drop1(LM_mass_by_time5)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Species + Treatment_bis:Region + Species:Time + Treatment_bis:Time
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## sqrt(Time) 395.39 395.39 1 1814.8 1472.5616 < 2.2e-16 ***
## Sex 0.03 0.03 1 1844.8 0.1214 0.72760
## Treatment_bis:Species 1.68 0.84 2 1835.1 3.1275 0.04406 *
## Treatment_bis:Region 14.65 4.88 3 1835.7 18.1881 1.248e-11 ***
## Species:Time 530.24 265.12 2 1820.0 987.4125 < 2.2e-16 ***
## Treatment_bis:Time 12.36 4.12 3 1818.2 15.3499 7.284e-10 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_mass_by_time6 <- update(LM_mass_by_time5, . ~ . - Treatment_bis:Species)## boundary (singular) fit: see help('isSingular')drop1(LM_mass_by_time6)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Species:Time + Treatment_bis:Time
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## sqrt(Time) 395.60 395.60 1 1816.5 1470.3721 < 2.2e-16 ***
## Sex 0.03 0.03 1 1846.7 0.1111 0.739
## Treatment_bis:Region 14.22 4.74 3 1837.4 17.6237 2.798e-11 ***
## Species:Time 27.00 13.50 2 1827.4 50.1861 < 2.2e-16 ***
## Treatment_bis:Time 15.26 5.09 3 1824.4 18.9102 4.453e-12 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Plus aucune interaction ne peut être retirée, on arrête la simplification ici.
A-t-elle été utile ?
AIC(LM_mass_by_time6)## [1] 3026.15AIC(LM_mass_by_time)## [1] 3068.17Oui
LM_mass_by_time <- LM_mass_by_time64.11.3 Treatment VS Teatment_bis
AIC(lmer(log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Species:Time + Treatment_bis:Time, data = Data_mass))## boundary (singular) fit: see help('isSingular')## [1] 3026.15AIC(lmer(log(Mass) ~ sqrt(Time) + Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Species:Time + Treatment:Time, data = Data_mass))## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## boundary (singular) fit: see help('isSingular')## [1] 3035.473summary(lmer(log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Species:Time + Treatment_bis:Time, data = Data_mass))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Species:Time + Treatment_bis:Time
## Data: Data_mass
##
## REML criterion at convergence: 2986.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.5577 -0.6370 0.0238 0.7028 2.4030
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.04871 0.2207
## Site (Intercept) 0.00000 0.0000
## Room (Intercept) 0.00000 0.0000
## Residual 0.26905 0.5187
## Number of obs: 1863, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -4.589e+00 7.752e-02 7.049e+01
## sqrt(Time) 1.648e+00 4.297e-02 1.817e+03
## Treatment_bisFull -2.681e-02 5.089e-02 1.835e+03
## Treatment_bisSmart -3.438e-01 6.988e-02 1.831e+03
## Treatment_bisMixt_smart -2.860e-04 7.135e-02 1.834e+03
## SexMale -8.582e-03 2.575e-02 1.847e+03
## SpeciesOP 1.301e+00 9.684e-02 5.280e+01
## RegionLuxembourg -1.871e-01 8.523e-02 4.018e+01
## Treatment_bisFull:RegionLuxembourg -8.154e-02 6.130e-02 1.845e+03
## Treatment_bisSmart:RegionLuxembourg 3.997e-01 7.474e-02 1.837e+03
## Treatment_bisMixt_smart:RegionLuxembourg -1.824e-01 8.044e-02 1.846e+03
## SpeciesAE:Time -1.104e-01 1.262e-02 1.827e+03
## SpeciesOP:Time -5.760e-02 5.038e-02 1.825e+03
## Treatment_bisFull:Time 2.627e-02 8.552e-03 1.832e+03
## Treatment_bisSmart:Time 9.477e-02 1.296e-02 1.826e+03
## Treatment_bisMixt_smart:Time 3.932e-02 1.147e-02 1.821e+03
## t value Pr(>|t|)
## (Intercept) -59.196 < 2e-16 ***
## sqrt(Time) 38.345 < 2e-16 ***
## Treatment_bisFull -0.527 0.598402
## Treatment_bisSmart -4.920 9.44e-07 ***
## Treatment_bisMixt_smart -0.004 0.996802
## SexMale -0.333 0.738977
## SpeciesOP 13.433 < 2e-16 ***
## RegionLuxembourg -2.195 0.034023 *
## Treatment_bisFull:RegionLuxembourg -1.330 0.183608
## Treatment_bisSmart:RegionLuxembourg 5.347 1.00e-07 ***
## Treatment_bisMixt_smart:RegionLuxembourg -2.267 0.023496 *
## SpeciesAE:Time -8.744 < 2e-16 ***
## SpeciesOP:Time -1.143 0.253072
## Treatment_bisFull:Time 3.072 0.002160 **
## Treatment_bisSmart:Time 7.310 3.97e-13 ***
## Treatment_bisMixt_smart:Time 3.427 0.000623 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 16 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Mass) ~ sqrt(Time) + Treatment + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Species:Time + Treatment:Time, data = Data_mass))## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Mass) ~ sqrt(Time) + Treatment + Sex + Species + Region +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Species:Time + Treatment:Time
## Data: Data_mass
##
## REML criterion at convergence: 2995.5
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.5774 -0.6274 0.0307 0.6941 2.6562
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.854e-02 0.220307
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 6.679e-05 0.008172
## Residual 2.709e-01 0.520485
## Number of obs: 1863, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -4.582e+00 7.810e-02 6.236e+01
## sqrt(Time) 1.661e+00 4.296e-02 1.815e+03
## TreatmentFull -1.246e-01 5.725e-02 1.834e+03
## TreatmentSmart -1.397e-01 7.714e-02 4.376e+02
## SexMale -9.992e-03 2.587e-02 1.844e+03
## SpeciesOP 1.313e+00 9.748e-02 5.427e+01
## RegionLuxembourg -1.867e-01 8.521e-02 4.015e+01
## RegionBrabant:Treatment_bisFull 8.317e-02 6.156e-02 1.845e+03
## RegionBrabant:Treatment_bisSmart -9.974e-02 9.043e-02 8.647e+01
## RegionLuxembourg:Treatment_bisSmart 2.798e-01 8.852e-02 1.129e+02
## RegionBrabant:Treatment_bisMixt_smart 3.370e-02 9.322e-02 1.828e+03
## RegionLuxembourg:Treatment_bisMixt_smart -1.801e-01 9.667e-02 1.839e+03
## SpeciesAE:Time -1.157e-01 1.263e-02 1.826e+03
## SpeciesOP:Time -7.683e-02 5.049e-02 1.824e+03
## TreatmentFull:Time 2.780e-02 8.719e-03 1.825e+03
## TreatmentSmart:Time 6.339e-02 9.612e-03 1.825e+03
## t value Pr(>|t|)
## (Intercept) -58.670 < 2e-16 ***
## sqrt(Time) 38.663 < 2e-16 ***
## TreatmentFull -2.176 0.02968 *
## TreatmentSmart -1.811 0.07082 .
## SexMale -0.386 0.69940
## SpeciesOP 13.466 < 2e-16 ***
## RegionLuxembourg -2.191 0.03433 *
## RegionBrabant:Treatment_bisFull 1.351 0.17684
## RegionBrabant:Treatment_bisSmart -1.103 0.27310
## RegionLuxembourg:Treatment_bisSmart 3.161 0.00202 **
## RegionBrabant:Treatment_bisMixt_smart 0.362 0.71771
## RegionLuxembourg:Treatment_bisMixt_smart -1.863 0.06261 .
## SpeciesAE:Time -9.161 < 2e-16 ***
## SpeciesOP:Time -1.522 0.12825
## TreatmentFull:Time 3.189 0.00145 **
## TreatmentSmart:Time 6.595 5.56e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 16 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')On a des p-val plus intéressentes avec le treatment mais treatment_bis montre des effets différents pour smart et mixt_smart. Si je me base sur les AIC je continue avec treatment_bis
Analyse des P-val
summary(lmer(log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Species:Time + Treatment_bis:Time, data = Data_mass))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Species:Time + Treatment_bis:Time
## Data: Data_mass
##
## REML criterion at convergence: 2986.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.5577 -0.6370 0.0238 0.7028 2.4030
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.04871 0.2207
## Site (Intercept) 0.00000 0.0000
## Room (Intercept) 0.00000 0.0000
## Residual 0.26905 0.5187
## Number of obs: 1863, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -4.589e+00 7.752e-02 7.049e+01
## sqrt(Time) 1.648e+00 4.297e-02 1.817e+03
## Treatment_bisFull -2.681e-02 5.089e-02 1.835e+03
## Treatment_bisSmart -3.438e-01 6.988e-02 1.831e+03
## Treatment_bisMixt_smart -2.860e-04 7.135e-02 1.834e+03
## SexMale -8.582e-03 2.575e-02 1.847e+03
## SpeciesOP 1.301e+00 9.684e-02 5.280e+01
## RegionLuxembourg -1.871e-01 8.523e-02 4.018e+01
## Treatment_bisFull:RegionLuxembourg -8.154e-02 6.130e-02 1.845e+03
## Treatment_bisSmart:RegionLuxembourg 3.997e-01 7.474e-02 1.837e+03
## Treatment_bisMixt_smart:RegionLuxembourg -1.824e-01 8.044e-02 1.846e+03
## SpeciesAE:Time -1.104e-01 1.262e-02 1.827e+03
## SpeciesOP:Time -5.760e-02 5.038e-02 1.825e+03
## Treatment_bisFull:Time 2.627e-02 8.552e-03 1.832e+03
## Treatment_bisSmart:Time 9.477e-02 1.296e-02 1.826e+03
## Treatment_bisMixt_smart:Time 3.932e-02 1.147e-02 1.821e+03
## t value Pr(>|t|)
## (Intercept) -59.196 < 2e-16 ***
## sqrt(Time) 38.345 < 2e-16 ***
## Treatment_bisFull -0.527 0.598402
## Treatment_bisSmart -4.920 9.44e-07 ***
## Treatment_bisMixt_smart -0.004 0.996802
## SexMale -0.333 0.738977
## SpeciesOP 13.433 < 2e-16 ***
## RegionLuxembourg -2.195 0.034023 *
## Treatment_bisFull:RegionLuxembourg -1.330 0.183608
## Treatment_bisSmart:RegionLuxembourg 5.347 1.00e-07 ***
## Treatment_bisMixt_smart:RegionLuxembourg -2.267 0.023496 *
## SpeciesAE:Time -8.744 < 2e-16 ***
## SpeciesOP:Time -1.143 0.253072
## Treatment_bisFull:Time 3.072 0.002160 **
## Treatment_bisSmart:Time 7.310 3.97e-13 ***
## Treatment_bisMixt_smart:Time 3.427 0.000623 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 16 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Species:Time + Treatment_bis:Time, data = Data_mass_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Species:Time + Treatment_bis:Time
## Data: Data_mass_ref_full
##
## REML criterion at convergence: 2986.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.5577 -0.6370 0.0238 0.7028 2.4030
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.04871 0.2207
## Site (Intercept) 0.00000 0.0000
## Room (Intercept) 0.00000 0.0000
## Residual 0.26905 0.5187
## Number of obs: 1863, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -4.616e+00 7.862e-02 7.404e+01
## sqrt(Time) 1.648e+00 4.297e-02 1.817e+03
## Treatment_bisDark 2.681e-02 5.089e-02 1.835e+03
## Treatment_bisSmart -3.170e-01 7.047e-02 1.822e+03
## Treatment_bisMixt_smart 2.652e-02 7.072e-02 1.822e+03
## SexMale -8.582e-03 2.575e-02 1.847e+03
## SpeciesOP 1.301e+00 9.684e-02 5.280e+01
## RegionLuxembourg -2.686e-01 8.721e-02 4.378e+01
## Treatment_bisDark:RegionLuxembourg 8.154e-02 6.130e-02 1.845e+03
## Treatment_bisSmart:RegionLuxembourg 4.812e-01 7.536e-02 1.827e+03
## Treatment_bisMixt_smart:RegionLuxembourg -1.008e-01 7.915e-02 1.841e+03
## SpeciesAE:Time -8.410e-02 1.321e-02 1.822e+03
## SpeciesOP:Time -3.133e-02 5.071e-02 1.825e+03
## Treatment_bisDark:Time -2.627e-02 8.552e-03 1.832e+03
## Treatment_bisSmart:Time 6.850e-02 1.320e-02 1.823e+03
## Treatment_bisMixt_smart:Time 1.305e-02 1.179e-02 1.819e+03
## t value Pr(>|t|)
## (Intercept) -58.709 < 2e-16 ***
## sqrt(Time) 38.345 < 2e-16 ***
## Treatment_bisDark 0.527 0.59840
## Treatment_bisSmart -4.498 7.29e-06 ***
## Treatment_bisMixt_smart 0.375 0.70765
## SexMale -0.333 0.73898
## SpeciesOP 13.433 < 2e-16 ***
## RegionLuxembourg -3.080 0.00357 **
## Treatment_bisDark:RegionLuxembourg 1.330 0.18361
## Treatment_bisSmart:RegionLuxembourg 6.385 2.17e-10 ***
## Treatment_bisMixt_smart:RegionLuxembourg -1.274 0.20283
## SpeciesAE:Time -6.369 2.41e-10 ***
## SpeciesOP:Time -0.618 0.53675
## Treatment_bisDark:Time -3.072 0.00216 **
## Treatment_bisSmart:Time 5.190 2.34e-07 ***
## Treatment_bisMixt_smart:Time 1.107 0.26841
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 16 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Species:Time + Treatment_bis:Time, data = Data_mass_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Mass) ~ sqrt(Time) + Treatment_bis + Sex + Species + Region +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Species:Time + Treatment_bis:Time
## Data: Data_mass_ref_smart
##
## REML criterion at convergence: 2986.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.5577 -0.6370 0.0238 0.7028 2.4030
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.04871 0.2207
## Site (Intercept) 0.00000 0.0000
## Room (Intercept) 0.00000 0.0000
## Residual 0.26905 0.5187
## Number of obs: 1863, groups: Mother, 36; Site, 15; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -4.933e+00 8.970e-02 1.225e+02
## sqrt(Time) 1.648e+00 4.297e-02 1.817e+03
## Treatment_bisDark 3.438e-01 6.988e-02 1.831e+03
## Treatment_bisFull 3.170e-01 7.047e-02 1.822e+03
## Treatment_bisMixt_smart 3.435e-01 8.511e-02 1.821e+03
## SexMale -8.582e-03 2.575e-02 1.847e+03
## SpeciesOP 1.301e+00 9.684e-02 5.280e+01
## RegionLuxembourg 2.126e-01 9.742e-02 6.774e+01
## Treatment_bisDark:RegionLuxembourg -3.997e-01 7.474e-02 1.837e+03
## Treatment_bisFull:RegionLuxembourg -4.812e-01 7.536e-02 1.827e+03
## Treatment_bisMixt_smart:RegionLuxembourg -5.821e-01 9.070e-02 1.838e+03
## SpeciesAE:Time -1.561e-02 1.750e-02 1.824e+03
## SpeciesOP:Time 3.717e-02 5.267e-02 1.825e+03
## Treatment_bisDark:Time -9.477e-02 1.296e-02 1.826e+03
## Treatment_bisFull:Time -6.850e-02 1.320e-02 1.823e+03
## Treatment_bisMixt_smart:Time -5.545e-02 1.516e-02 1.819e+03
## t value Pr(>|t|)
## (Intercept) -54.990 < 2e-16 ***
## sqrt(Time) 38.345 < 2e-16 ***
## Treatment_bisDark 4.920 9.44e-07 ***
## Treatment_bisFull 4.498 7.29e-06 ***
## Treatment_bisMixt_smart 4.036 5.67e-05 ***
## SexMale -0.333 0.738977
## SpeciesOP 13.433 < 2e-16 ***
## RegionLuxembourg 2.182 0.032556 *
## Treatment_bisDark:RegionLuxembourg -5.347 1.00e-07 ***
## Treatment_bisFull:RegionLuxembourg -6.385 2.17e-10 ***
## Treatment_bisMixt_smart:RegionLuxembourg -6.418 1.76e-10 ***
## SpeciesAE:Time -0.892 0.372689
## SpeciesOP:Time 0.706 0.480475
## Treatment_bisDark:Time -7.310 3.97e-13 ***
## Treatment_bisFull:Time -5.190 2.34e-07 ***
## Treatment_bisMixt_smart:Time -3.656 0.000263 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 16 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Info_Mass_by_Time <- "
temps a un effet significatif positif
Pour un même temps, Les smart sont significativements plus légère que les Dark
Pour un même temps, l'Espèce OP est plus lourde.
Pour un même temps, les individus de la région Luxembourg sont moins lourds
Les individus Smart réagissent différement en fonction de si ils viennent du Luxembourg ou pas (si ils viennent du Luxembourg ils sont plus lourds pour un même temps).
Idem pour Mixt_smart mais ils sont moinds lourds
L'espèce AE réagit différement que OP à l'augmentation de temps (les p val)
"
Info_Mass_by_Time## [1] "\ntemps a un effet significatif positif\nPour un même temps, Les smart sont significativements plus légère que les Dark\nPour un même temps, l'Espèce OP est plus lourde.\nPour un même temps, les individus de la région Luxembourg sont moins lourds\nLes individus Smart réagissent différement en fonction de si ils viennent du Luxembourg ou pas (si ils viennent du Luxembourg ils sont plus lourds pour un même temps).\nIdem pour Mixt_smart mais ils sont moinds lourds\nL'espèce AE réagit différement que OP à l'augmentation de temps (les p val)\n"4.11.4 Visualisation
ggplot(data = Data_mass, aes(x = log(Time), y = log(Mass))) +
geom_jitter(aes(color = Treatment_bis, shape = Region), alpha = 0.33) +
geom_smooth(method = "lm", aes(linetype = Region)) +
facet_wrap(~Species) +
labs(title = "Poids des individus en fonction du temps", x = "Temps (log(Numéro de mesure))", y = "log(Poids (g))", color = "Traitement", linetype = "Région", shape = "Région") +
theme_bw()## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 7160 rows containing non-finite values (`stat_smooth()`).## Warning: Removed 6710 rows containing missing values (`geom_point()`).
ggplot(data = Data_mass, aes(x = sqrt(Time), y = log(Mass))) +
geom_point(aes(color = Treatment_bis, shape = Species), alpha = 0.5) +
geom_smooth(method = "lm", aes(color= Treatment_bis, linetype = Species)) +
facet_wrap(~Region) +
labs(title = "Mass by Time", x = "Time (sqrt(Weeks)", y = "log(Mass)") +
theme_bw()## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 6710 rows containing non-finite values (`stat_smooth()`).## Warning: Removed 6710 rows containing missing values (`geom_point()`).
5 Analyses Lumière
5.1 Jeux de donnée avec références
Data_refFTL_Night <- Data
Data_refFTL_Night$Treatment_FTL <- relevel(Data$Treatment_FTL, ref = "Night")
Data_refFTL_Night$Treatment_FTL <- relevel(Data$Treatment_FTL, ref = "Night")
Data_refFTL_Mix <- Data
Data_refFTL_Mix$Treatment_FTL <- relevel(Data$Treatment_FTL, ref = "Mix")
Data_refFTL_Mix$Treatment_FTL <- relevel(Data$Treatment_FTL, ref = "Mix")5.2 Did_move
5.2.1 Test
GLM_Did_move <- glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis, family = binomial, data = Data)
summary(GLM_Did_move)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex +
## Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region +
## Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region +
## Light_orientation:Treatment_bis
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 82.8 174.3 -8.4 16.8 85
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.46643 0.00000 0.00000 0.00006 0.68193
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.186e-06 0.002277
## Site (Intercept) 2.288e+01 4.783051
## Room (Intercept) 3.841e+00 1.959892
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value
## (Intercept) -1.245e-01 4.374e+00 -0.028
## Treatment_bisFull 4.224e+01 1.792e+05 0.000
## Treatment_bisSmart 2.513e+01 3.133e+04 0.001
## Treatment_bisMixt_smart 3.993e+01 1.878e+07 0.000
## SexMale 2.833e+01 6.058e+04 0.000
## RegionLuxembourg 2.899e+01 5.317e+05 0.000
## Treatment_FTLMix 8.404e+00 4.910e+00 1.711
## Treatment_FTLNight 2.522e+01 1.516e+04 0.002
## Light_orientationSouth -1.542e+00 2.623e+00 -0.588
## Treatment_bisFull:SexMale -1.202e+01 5.961e+04 0.000
## Treatment_bisSmart:SexMale -2.898e+01 6.058e+04 0.000
## Treatment_bisMixt_smart:SexMale 6.995e+00 1.399e+05 0.000
## Treatment_bisFull:RegionLuxembourg -3.109e+01 5.318e+05 0.000
## Treatment_bisSmart:RegionLuxembourg -4.115e+01 5.326e+05 0.000
## Treatment_bisMixt_smart:RegionLuxembourg -1.471e+02 1.878e+07 0.000
## SexMale:Treatment_FTLMix -9.663e+00 1.121e+04 -0.001
## SexMale:Treatment_FTLNight 1.558e+01 1.643e+07 0.000
## RegionLuxembourg:Treatment_FTLMix -6.756e+00 1.129e+04 -0.001
## RegionLuxembourg:Treatment_FTLNight 2.178e+01 2.630e+05 0.000
## Treatment_bisFull:Treatment_FTLMix -3.151e+01 1.792e+05 0.000
## Treatment_bisSmart:Treatment_FTLMix 1.002e+01 1.268e+03 0.008
## Treatment_bisMixt_smart:Treatment_FTLMix 7.479e+01 1.616e+05 0.000
## Treatment_bisFull:Treatment_FTLNight -4.782e+01 1.798e+05 0.000
## Treatment_bisSmart:Treatment_FTLNight -3.107e+01 3.481e+04 -0.001
## Treatment_bisMixt_smart:Treatment_FTLNight 2.322e+01 2.943e+05 0.000
## SexMale:Light_orientationSouth 3.548e+00 3.838e+03 0.001
## RegionLuxembourg:Light_orientationSouth 1.809e+01 3.118e+04 0.001
## Treatment_bisFull:Light_orientationSouth -1.420e+01 2.045e+03 -0.007
## Treatment_bisSmart:Light_orientationSouth -2.162e+01 3.133e+04 -0.001
## Treatment_bisMixt_smart:Light_orientationSouth 9.310e+00 1.050e+05 0.000
## Pr(>|z|)
## (Intercept) 0.977
## Treatment_bisFull 1.000
## Treatment_bisSmart 0.999
## Treatment_bisMixt_smart 1.000
## SexMale 1.000
## RegionLuxembourg 1.000
## Treatment_FTLMix 0.087 .
## Treatment_FTLNight 0.999
## Light_orientationSouth 0.557
## Treatment_bisFull:SexMale 1.000
## Treatment_bisSmart:SexMale 1.000
## Treatment_bisMixt_smart:SexMale 1.000
## Treatment_bisFull:RegionLuxembourg 1.000
## Treatment_bisSmart:RegionLuxembourg 1.000
## Treatment_bisMixt_smart:RegionLuxembourg 1.000
## SexMale:Treatment_FTLMix 0.999
## SexMale:Treatment_FTLNight 1.000
## RegionLuxembourg:Treatment_FTLMix 1.000
## RegionLuxembourg:Treatment_FTLNight 1.000
## Treatment_bisFull:Treatment_FTLMix 1.000
## Treatment_bisSmart:Treatment_FTLMix 0.994
## Treatment_bisMixt_smart:Treatment_FTLMix 1.000
## Treatment_bisFull:Treatment_FTLNight 1.000
## Treatment_bisSmart:Treatment_FTLNight 0.999
## Treatment_bisMixt_smart:Treatment_FTLNight 1.000
## SexMale:Light_orientationSouth 0.999
## RegionLuxembourg:Light_orientationSouth 1.000
## Treatment_bisFull:Light_orientationSouth 0.994
## Treatment_bisSmart:Light_orientationSouth 0.999
## Treatment_bisMixt_smart:Light_orientationSouth 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## optimizer (Nelder_Mead) convergence code: 4 (failure to converge in 10000 evaluations)
## unable to evaluate scaled gradient
## Model failed to converge: degenerate Hessian with 7 negative eigenvalues
## failure to converge in 10000 evaluations5.2.2 Simplification du modèle
Simplification par AIC/BIC
drop1(GLM_Did_move)## Single term deletions
##
## Model:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex +
## Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region +
## Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region +
## Light_orientation:Treatment_bis
## npar AIC
## <none> 82.840
## Treatment_bis:Sex 3 76.836
## Treatment_bis:Region 3 84.454
## Sex:Treatment_FTL 2 78.847
## Region:Treatment_FTL 2 78.842
## Treatment_bis:Treatment_FTL 6 75.965
## Sex:Light_orientation 1 80.851
## Region:Light_orientation 1 80.846
## Treatment_bis:Light_orientation 3 77.030GLM_Did_move2 <- update(GLM_Did_move, . ~ . - Treatment_bis:Treatment_FTL)
drop1(GLM_Did_move2)## Single term deletions
##
## Model:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex +
## Treatment_bis:Region + Sex:Treatment_FTL + Region:Treatment_FTL +
## Sex:Light_orientation + Region:Light_orientation + Treatment_bis:Light_orientation
## npar AIC
## <none> 75.965
## Treatment_bis:Sex 3 69.951
## Treatment_bis:Region 3 78.097
## Sex:Treatment_FTL 2 71.927
## Region:Treatment_FTL 2 71.961
## Sex:Light_orientation 1 73.979
## Region:Light_orientation 1 73.984
## Treatment_bis:Light_orientation 3 72.157GLM_Did_move3 <- update(GLM_Did_move2, . ~ . - Treatment_bis:Sex)
drop1(GLM_Did_move3)## Single term deletions
##
## Model:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Sex:Treatment_FTL + Region:Treatment_FTL + Sex:Light_orientation +
## Region:Light_orientation + Treatment_bis:Light_orientation
## npar AIC
## <none> 69.951
## Treatment_bis:Region 3 76.656
## Sex:Treatment_FTL 2 65.930
## Region:Treatment_FTL 2 70.348
## Sex:Light_orientation 1 67.958
## Region:Light_orientation 1 67.958
## Treatment_bis:Light_orientation 3 66.157GLM_Did_move4 <- update(GLM_Did_move3, . ~ . - Sex:Treatment_FTL)
drop1(GLM_Did_move4)## Single term deletions
##
## Model:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Region:Treatment_FTL + Sex:Light_orientation + Region:Light_orientation +
## Treatment_bis:Light_orientation
## npar AIC
## <none> 65.930
## Treatment_bis:Region 3 74.694
## Region:Treatment_FTL 2 66.715
## Sex:Light_orientation 1 63.942
## Region:Light_orientation 1 63.926
## Treatment_bis:Light_orientation 3 62.157GLM_Did_move5 <- update(GLM_Did_move4, . ~ . - Treatment_bis:Light_orientation)
drop1(GLM_Did_move5)## Single term deletions
##
## Model:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Region:Treatment_FTL + Sex:Light_orientation + Region:Light_orientation
## npar AIC
## <none> 62.157
## Treatment_bis:Region 3 71.755
## Region:Treatment_FTL 2 62.432
## Sex:Light_orientation 1 60.157
## Region:Light_orientation 1 63.258Est ce qu’il faut pas juste retirer toutes les interactions ?
BIC(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## [1] 100.0252BIC(GLM_Did_move5)## [1] 114.8BIC(GLM_Did_move4)## [1] 126.8855BIC(GLM_Did_move3)## [1] 136.4479BIC(GLM_Did_move2)## [1] 150.7731BIC(GLM_Did_move)## [1] 174.2725Si
GLM_Did_move <- glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial)5.2.3 Treatment VS Treatment_bis
AIC(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## [1] 66.77695AIC(glmer(Did_move ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## [1] 65.0217summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 66.8 100.0 -21.4 42.8 106
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.5255 0.1076 0.1483 0.2316 0.4602
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.231e-01 0.723250
## Site (Intercept) 1.574e-02 0.125457
## Room (Intercept) 5.221e-06 0.002285
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.3901 1.2336 1.937 0.0527 .
## Treatment_bisFull 0.7011 1.3140 0.534 0.5936
## Treatment_bisSmart 0.3476 1.3507 0.257 0.7969
## Treatment_bisMixt_smart -0.3041 1.1123 -0.273 0.7845
## SexMale 1.2964 1.1539 1.123 0.2612
## RegionLuxembourg 0.3085 1.1939 0.258 0.7961
## Treatment_FTLMix 0.4637 1.4721 0.315 0.7528
## Treatment_FTLNight 1.3724 1.5201 0.903 0.3666
## Light_orientationSouth -0.6529 0.9700 -0.673 0.5009
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## Trtmnt_bsFl -0.386
## Trtmnt_bsSm -0.348 0.350
## Trtmnt_bsM_ -0.358 0.416 0.412
## SexMale -0.210 -0.015 0.105 0.004
## ReginLxmbrg -0.261 -0.061 -0.132 -0.106 -0.047
## Trtmnt_FTLM -0.078 0.166 0.151 0.083 0.032 -0.448
## Trtmnt_FTLN -0.003 0.054 0.101 0.002 0.049 -0.323 0.602
## Lght_rnttnS -0.500 -0.023 -0.093 -0.147 0.056 0.215 -0.077 -0.131
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0048478 (tol = 0.002, component 1)summary(glmer(Did_move ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_move ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 65.0 95.5 -21.5 43.0 107
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.3716 0.1081 0.1500 0.2389 0.4639
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.400e-01 0.734872
## Site (Intercept) 2.445e-02 0.156362
## Room (Intercept) 4.613e-05 0.006792
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.43282 1.23907 1.963 0.0496 *
## TreatmentFull 0.69939 1.31477 0.532 0.5948
## TreatmentSmart -0.04876 1.01580 -0.048 0.9617
## SexMale 1.24235 1.14705 1.083 0.2788
## RegionLuxembourg 0.33512 1.15604 0.290 0.7719
## Treatment_FTLMix 0.42982 1.42766 0.301 0.7634
## Treatment_FTLNight 1.32599 1.48284 0.894 0.3712
## Light_orientationSouth -0.67145 0.97231 -0.691 0.4898
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnF TrtmnS SexMal RgnLxm T_FTLM T_FTLN
## TreatmntFll -0.377
## TretmntSmrt -0.426 0.460
## SexMale -0.213 -0.027 0.065
## ReginLxmbrg -0.247 -0.051 -0.152 -0.057
## Trtmnt_FTLM -0.098 0.169 0.141 0.000 -0.388
## Trtmnt_FTLN -0.026 0.054 0.055 0.022 -0.295 0.589
## Lght_rnttnS -0.500 -0.032 -0.148 0.051 0.238 -0.103 -0.135
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0182943 (tol = 0.002, component 1)Aucune grosse différence mais vu qu’on a utilisé treatment_bis dans les autres tests, nous allons continuer avec treatment.
5.2.4 Résultats
Analyse des p-val
summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0048478 (tol = 0.002, component 1)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 66.8 100.0 -21.4 42.8 106
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.5255 0.1076 0.1483 0.2316 0.4602
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.231e-01 0.723250
## Site (Intercept) 1.574e-02 0.125457
## Room (Intercept) 5.221e-06 0.002285
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.3901 1.2336 1.937 0.0527 .
## Treatment_bisFull 0.7011 1.3140 0.534 0.5936
## Treatment_bisSmart 0.3476 1.3507 0.257 0.7969
## Treatment_bisMixt_smart -0.3041 1.1123 -0.273 0.7845
## SexMale 1.2964 1.1539 1.123 0.2612
## RegionLuxembourg 0.3085 1.1939 0.258 0.7961
## Treatment_FTLMix 0.4637 1.4721 0.315 0.7528
## Treatment_FTLNight 1.3724 1.5201 0.903 0.3666
## Light_orientationSouth -0.6529 0.9700 -0.673 0.5009
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## Trtmnt_bsFl -0.386
## Trtmnt_bsSm -0.348 0.350
## Trtmnt_bsM_ -0.358 0.416 0.412
## SexMale -0.210 -0.015 0.105 0.004
## ReginLxmbrg -0.261 -0.061 -0.132 -0.106 -0.047
## Trtmnt_FTLM -0.078 0.166 0.151 0.083 0.032 -0.448
## Trtmnt_FTLN -0.003 0.054 0.101 0.002 0.049 -0.323 0.602
## Lght_rnttnS -0.500 -0.023 -0.093 -0.147 0.056 0.215 -0.077 -0.131
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0048478 (tol = 0.002, component 1)summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_full, family = binomial))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0707921 (tol = 0.002, component 1)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_ref_full
##
## AIC BIC logLik deviance df.resid
## 66.8 100.0 -21.4 42.8 106
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.4542 0.1148 0.1497 0.2430 0.5059
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.009e-01 0.5485201
## Site (Intercept) 1.399e-01 0.3740368
## Room (Intercept) 3.607e-07 0.0006006
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 3.0908 1.4171 2.181 0.0292 *
## Treatment_bisDark -0.7080 1.3126 -0.539 0.5896
## Treatment_bisSmart -0.3731 1.5083 -0.247 0.8046
## Treatment_bisMixt_smart -1.0085 1.3215 -0.763 0.4454
## SexMale 1.2829 1.1474 1.118 0.2635
## RegionLuxembourg 0.2861 1.1205 0.255 0.7984
## Treatment_FTLMix 0.4681 1.4047 0.333 0.7390
## Treatment_FTLNight 1.3641 1.5157 0.900 0.3681
## Light_orientationSouth -0.6667 0.9584 -0.696 0.4866
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## Trtmnt_bsDr -0.590
## Trtmnt_bsSm -0.495 0.559
## Trtmnt_bsM_ -0.533 0.647 0.560
## SexMale -0.198 0.018 0.103 0.025
## ReginLxmbrg -0.289 0.062 -0.060 -0.022 -0.059
## Trtmnt_FTLM 0.092 -0.172 -0.025 -0.106 0.040 -0.384
## Trtmnt_FTLN 0.062 -0.058 0.030 -0.054 0.049 -0.291 0.596
## Lght_rnttnS -0.452 0.021 -0.061 -0.101 0.052 0.189 -0.042 -0.111
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0707921 (tol = 0.002, component 1)summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_smart, family = binomial))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00344854 (tol = 0.002, component 1)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_ref_smart
##
## AIC BIC logLik deviance df.resid
## 66.8 100.0 -21.4 42.8 106
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.5288 0.1076 0.1482 0.2319 0.4606
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.201e-01 0.7211608
## Site (Intercept) 1.796e-02 0.1340225
## Room (Intercept) 4.601e-08 0.0002145
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.7363 1.4782 1.851 0.0642 .
## Treatment_bisDark -0.3477 1.3507 -0.257 0.7968
## Treatment_bisFull 0.3546 1.5193 0.233 0.8154
## Treatment_bisMixt_smart -0.6528 1.3502 -0.483 0.6288
## SexMale 1.2969 1.1541 1.124 0.2611
## RegionLuxembourg 0.3092 1.1833 0.261 0.7939
## Treatment_FTLMix 0.4653 1.4598 0.319 0.7499
## Treatment_FTLNight 1.3740 1.5162 0.906 0.3648
## Light_orientationSouth -0.6522 0.9688 -0.673 0.5008
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## Trtmnt_bsDr -0.623
## Trtmnt_bsFl -0.556 0.586
## Trtmnt_bsM_ -0.560 0.661 0.580
## SexMale -0.079 -0.105 -0.106 -0.102
## ReginLxmbrg -0.337 0.132 0.065 0.045 -0.049
## Trtmnt_FTLM 0.069 -0.151 0.009 -0.083 0.034 -0.437
## Trtmnt_FTLN 0.088 -0.100 -0.043 -0.100 0.050 -0.316 0.599
## Lght_rnttnS -0.501 0.093 0.063 -0.028 0.056 0.210 -0.071 -0.127
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.00344854 (tol = 0.002, component 1)summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_mixt_smart, family = binomial))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00443571 (tol = 0.002, component 1)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_ref_mixt_smart
##
## AIC BIC logLik deviance df.resid
## 66.8 100.0 -21.4 42.8 106
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.5214 0.1078 0.1479 0.2331 0.4604
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.037e-01 0.7097328
## Site (Intercept) 3.352e-02 0.1830893
## Room (Intercept) 8.342e-07 0.0009133
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.0874 1.3300 1.569 0.117
## Treatment_bisDark 0.3036 1.1117 0.273 0.785
## Treatment_bisFull 1.0084 1.3236 0.762 0.446
## Treatment_bisSmart 0.6503 1.3494 0.482 0.630
## SexMale 1.2954 1.1535 1.123 0.261
## RegionLuxembourg 0.3023 1.1421 0.265 0.791
## Treatment_FTLMix 0.4698 1.4074 0.334 0.739
## Treatment_FTLNight 1.3785 1.4984 0.920 0.358
## Light_orientationSouth -0.6549 0.9643 -0.679 0.497
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_FTLM T_FTLN
## Trtmnt_bsDr -0.502
## Trtmnt_bsFl -0.434 0.428
## Trtmnt_bsSm -0.392 0.412 0.354
## SexMale -0.190 -0.005 -0.018 0.101
## ReginLxmbrg -0.323 0.102 0.029 -0.049 -0.057
## Trtmnt_FTLM -0.026 -0.079 0.099 0.087 0.041 -0.397
## Trtmnt_FTLN -0.013 0.002 0.053 0.101 0.054 -0.291 0.586
## Lght_rnttnS -0.582 0.145 0.102 0.028 0.053 0.193 -0.048 -0.116
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.00443571 (tol = 0.002, component 1)summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_refFTL_Mix, family = binomial))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0153663 (tol = 0.002, component 1)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_refFTL_Mix
##
## AIC BIC logLik deviance df.resid
## 66.8 100.0 -21.4 42.8 106
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.4845 0.1078 0.1485 0.2368 0.4704
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.567e-01 0.6758202
## Site (Intercept) 6.981e-02 0.2642145
## Room (Intercept) 2.416e-08 0.0001555
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.8705 1.7675 1.624 0.104
## Treatment_bisFull 0.7036 1.3137 0.536 0.592
## Treatment_bisSmart 0.3510 1.3490 0.260 0.795
## Treatment_bisMixt_smart -0.3028 1.1113 -0.272 0.785
## SexMale 1.2957 1.1534 1.123 0.261
## RegionLuxembourg 0.2926 1.1309 0.259 0.796
## Treatment_FTLDay -0.4807 1.3925 -0.345 0.730
## Treatment_FTLNight 0.9030 1.3218 0.683 0.495
## Light_orientationSouth -0.6567 0.9627 -0.682 0.495
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLD T_FTLN
## Trtmnt_bsFl -0.138
## Trtmnt_bsSm -0.124 0.350
## Trtmnt_bsM_ -0.191 0.415 0.411
## SexMale -0.110 -0.015 0.103 0.005
## ReginLxmbrg -0.486 -0.057 -0.132 -0.099 -0.060
## Trtmnt_FTLD -0.718 -0.169 -0.151 -0.078 -0.044 0.384
## Trtmnt_FTLN -0.246 -0.119 -0.048 -0.084 0.016 0.082 0.395
## Lght_rnttnS -0.380 -0.021 -0.092 -0.146 0.052 0.189 0.043 -0.083
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0153663 (tol = 0.002, component 1)summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_refFTL_Night, family = binomial))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvalues## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_refFTL_Night
##
## AIC BIC logLik deviance df.resid
## 66.8 100.0 -21.4 42.8 106
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.5406 0.1075 0.1482 0.2310 0.4605
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.311e-01 0.728754
## Site (Intercept) 6.561e-03 0.081001
## Room (Intercept) 2.873e-07 0.000536
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 3.7597 1.8451 2.038 0.0416 *
## Treatment_bisFull 0.7019 1.3125 0.535 0.5928
## Treatment_bisSmart 0.3490 1.3507 0.258 0.7961
## Treatment_bisMixt_smart -0.3047 1.1102 -0.274 0.7837
## SexMale 1.2972 1.1530 1.125 0.2605
## RegionLuxembourg 0.3121 0.9685 0.322 0.7472
## Treatment_FTLDay -1.3715 1.4381 -0.954 0.3402
## Treatment_FTLMix -0.9108 1.2911 -0.705 0.4805
## Light_orientationSouth -0.6522 0.9465 -0.689 0.4908
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLD T_FTLM
## Trtmnt_bsFl -0.232
## Trtmnt_bsSm -0.161 0.349
## Trtmnt_bsM_ -0.259 0.414 0.411
## SexMale -0.084 -0.013 0.107 0.007
## ReginLxmbrg -0.287 -0.038 -0.139 -0.089 -0.091
## Trtmnt_FTLD -0.749 -0.039 -0.095 0.019 -0.068 0.170
## Trtmnt_FTLM -0.557 0.112 0.045 0.078 -0.009 0.031 0.613
## Lght_rnttnS -0.373 -0.012 -0.088 -0.137 0.048 0.109 0.063 0.128
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## unable to evaluate scaled gradient
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluestest1 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Day", as.data.frame(( summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0048478 (tol = 0.002, component 1)test2 <- data.frame(Reference_Treatment = "Smart", Reference_Timing = "Day", as.data.frame(( summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_smart, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00344854 (tol = 0.002, component 1)test3 <- data.frame(Reference_Treatment = "Full", Reference_Timing = "Day", as.data.frame(( summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_full, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0707921 (tol = 0.002, component 1)test4 <- data.frame(Reference_Treatment = "Mixt_smart", Reference_Timing = "Day", as.data.frame(( summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_mixt_smart, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00443571 (tol = 0.002, component 1)test5 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Mixt", as.data.frame(( summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_refFTL_Mix, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0153663 (tol = 0.002, component 1)test6 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Night", as.data.frame(( summary(glmer(Did_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_refFTL_Night, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluesResults_Did_move <- rbind(test1,test2,test3,test4,test5,test6)
colnames(Results_Did_move ) <- c("Reference_Treatment", "Reference_Timing" ,"Estimate", "Std. Error", "z value", "Pr(>|z|)")
write.csv2( Results_Did_move , file = "output/Results_Did_move.csv" )
kable(Results_Did_move , caption = " Probabilité de bouger ", padding = 1 )| Reference_Treatment | Reference_Timing | Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | Day | 2.3901238 | 1.2336420 | 1.9374534 | 0.0526899 |
| Treatment_bisFull | Dark | Day | 0.7011087 | 1.3140024 | 0.5335673 | 0.5936409 |
| Treatment_bisSmart | Dark | Day | 0.3475819 | 1.3507182 | 0.2573312 | 0.7969231 |
| Treatment_bisMixt_smart | Dark | Day | -0.3041434 | 1.1122814 | -0.2734411 | 0.7845142 |
| SexMale | Dark | Day | 1.2964030 | 1.1539143 | 1.1234829 | 0.2612325 |
| RegionLuxembourg | Dark | Day | 0.3085259 | 1.1939095 | 0.2584165 | 0.7960855 |
| Treatment_FTLMix | Dark | Day | 0.4636972 | 1.4721090 | 0.3149883 | 0.7527705 |
| Treatment_FTLNight | Dark | Day | 1.3724161 | 1.5200623 | 0.9028683 | 0.3665958 |
| Light_orientationSouth | Dark | Day | -0.6529492 | 0.9700257 | -0.6731257 | 0.5008673 |
| (Intercept)1 | Smart | Day | 2.7362811 | 1.4782375 | 1.8510429 | 0.0641634 |
| Treatment_bisDark | Smart | Day | -0.3477340 | 1.3507389 | -0.2574398 | 0.7968393 |
| Treatment_bisFull1 | Smart | Day | 0.3546464 | 1.5193135 | 0.2334254 | 0.8154311 |
| Treatment_bisMixt_smart1 | Smart | Day | -0.6527769 | 1.3502463 | -0.4834502 | 0.6287761 |
| SexMale1 | Smart | Day | 1.2968534 | 1.1540905 | 1.1237016 | 0.2611396 |
| RegionLuxembourg1 | Smart | Day | 0.3092047 | 1.1833336 | 0.2612997 | 0.7938614 |
| Treatment_FTLMix1 | Smart | Day | 0.4653352 | 1.4597812 | 0.3187705 | 0.7499006 |
| Treatment_FTLNight1 | Smart | Day | 1.3739814 | 1.5162392 | 0.9061772 | 0.3648421 |
| Light_orientationSouth1 | Smart | Day | -0.6521780 | 0.9688398 | -0.6731536 | 0.5008496 |
| (Intercept)2 | Full | Day | 3.0908225 | 1.4170550 | 2.1811591 | 0.0291716 |
| Treatment_bisDark1 | Full | Day | -0.7080212 | 1.3125690 | -0.5394163 | 0.5895996 |
| Treatment_bisSmart1 | Full | Day | -0.3730571 | 1.5082938 | -0.2473371 | 0.8046473 |
| Treatment_bisMixt_smart2 | Full | Day | -1.0084502 | 1.3214600 | -0.7631334 | 0.4453838 |
| SexMale2 | Full | Day | 1.2828972 | 1.1473734 | 1.1181166 | 0.2635172 |
| RegionLuxembourg2 | Full | Day | 0.2861447 | 1.1204720 | 0.2553787 | 0.7984306 |
| Treatment_FTLMix2 | Full | Day | 0.4680808 | 1.4047109 | 0.3332221 | 0.7389666 |
| Treatment_FTLNight2 | Full | Day | 1.3640888 | 1.5156706 | 0.8999902 | 0.3681254 |
| Light_orientationSouth2 | Full | Day | -0.6667241 | 0.9583846 | -0.6956748 | 0.4866325 |
| (Intercept)3 | Mixt_smart | Day | 2.0874162 | 1.3300254 | 1.5694559 | 0.1165418 |
| Treatment_bisDark2 | Mixt_smart | Day | 0.3036088 | 1.1117003 | 0.2731032 | 0.7847739 |
| Treatment_bisFull2 | Mixt_smart | Day | 1.0084434 | 1.3236045 | 0.7618917 | 0.4461246 |
| Treatment_bisSmart2 | Mixt_smart | Day | 0.6503214 | 1.3493855 | 0.4819389 | 0.6298493 |
| SexMale3 | Mixt_smart | Day | 1.2954164 | 1.1534816 | 1.1230490 | 0.2614167 |
| RegionLuxembourg3 | Mixt_smart | Day | 0.3022548 | 1.1421008 | 0.2646481 | 0.7912806 |
| Treatment_FTLMix3 | Mixt_smart | Day | 0.4698313 | 1.4074051 | 0.3338281 | 0.7385093 |
| Treatment_FTLNight3 | Mixt_smart | Day | 1.3784983 | 1.4983519 | 0.9200097 | 0.3575677 |
| Light_orientationSouth3 | Mixt_smart | Day | -0.6549420 | 0.9642647 | -0.6792139 | 0.4970024 |
| (Intercept)4 | Dark | Mixt | 2.8705459 | 1.7675156 | 1.6240569 | 0.1043637 |
| Treatment_bisFull3 | Dark | Mixt | 0.7036001 | 1.3136518 | 0.5356062 | 0.5922307 |
| Treatment_bisSmart3 | Dark | Mixt | 0.3510246 | 1.3489716 | 0.2602165 | 0.7946968 |
| Treatment_bisMixt_smart3 | Dark | Mixt | -0.3027501 | 1.1112692 | -0.2724363 | 0.7852866 |
| SexMale4 | Dark | Mixt | 1.2957495 | 1.1533782 | 1.1234385 | 0.2612513 |
| RegionLuxembourg4 | Dark | Mixt | 0.2926305 | 1.1309426 | 0.2587492 | 0.7958287 |
| Treatment_FTLDay | Dark | Mixt | -0.4806651 | 1.3924834 | -0.3451855 | 0.7299549 |
| Treatment_FTLNight4 | Dark | Mixt | 0.9029848 | 1.3218072 | 0.6831441 | 0.4945158 |
| Light_orientationSouth4 | Dark | Mixt | -0.6567263 | 0.9626599 | -0.6821997 | 0.4951127 |
| (Intercept)5 | Dark | Night | 3.7597409 | 1.8450793 | 2.0377124 | 0.0415787 |
| Treatment_bisFull4 | Dark | Night | 0.7019112 | 1.3125280 | 0.5347781 | 0.5928033 |
| Treatment_bisSmart4 | Dark | Night | 0.3489525 | 1.3506667 | 0.2583557 | 0.7961324 |
| Treatment_bisMixt_smart4 | Dark | Night | -0.3047051 | 1.1102495 | -0.2744474 | 0.7837409 |
| SexMale5 | Dark | Night | 1.2972109 | 1.1529738 | 1.1251001 | 0.2605466 |
| RegionLuxembourg5 | Dark | Night | 0.3121419 | 0.9685003 | 0.3222940 | 0.7472300 |
| Treatment_FTLDay1 | Dark | Night | -1.3714979 | 1.4380795 | -0.9537010 | 0.3402350 |
| Treatment_FTLMix4 | Dark | Night | -0.9108337 | 1.2911473 | -0.7054452 | 0.4805332 |
| Light_orientationSouth5 | Dark | Night | -0.6521568 | 0.9465170 | -0.6890070 | 0.4908189 |
Info_Did_move <- "
Aucun effet significatif
"5.2.5 Visualisation
ggplot(Data %>% filter(Did_move != "NA")) +
aes(x = Did_move, fill = Treatment_FTL) +
geom_bar(position = "dodge") +
scale_fill_hue(direction = 1) +
labs(title= "Probabilité de bouger", x = "A bougé", y = "Nombre d'individus", fill = "Timing") +
theme_minimal()
5.3 Did_FTL
5.3.1 Test
GLM_Did_FTL <- glmer(Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis, family = binomial, data = Data)
summary(GLM_Did_FTL)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex +
## Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region +
## Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region +
## Light_orientation:Treatment_bis
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 165.1 256.5 -49.5 99.1 85
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.74352 -0.35258 0.00733 0.23899 2.18663
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.260e-05 0.0065267
## Site (Intercept) 7.131e+00 2.6704276
## Room (Intercept) 1.976e-07 0.0004445
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value
## (Intercept) -0.3018 1.9216 -0.157
## Treatment_bisFull -1.7400 1.7252 -1.009
## Treatment_bisSmart 1.4081 2.2880 0.615
## Treatment_bisMixt_smart -5.3938 3.2691 -1.650
## SexMale -2.2853 1.5708 -1.455
## RegionLuxembourg -1.7960 2.5350 -0.708
## Treatment_FTLMix 3.1362 2.1441 1.463
## Treatment_FTLNight 2.9418 2.3338 1.260
## Light_orientationSouth -2.0254 1.3389 -1.513
## Treatment_bisFull:SexMale 0.3259 1.7972 0.181
## Treatment_bisSmart:SexMale 2.5960 2.6518 0.979
## Treatment_bisMixt_smart:SexMale 2.7817 2.7297 1.019
## Treatment_bisFull:RegionLuxembourg 5.9814 2.6704 2.240
## Treatment_bisSmart:RegionLuxembourg -0.6725 2.1744 -0.309
## Treatment_bisMixt_smart:RegionLuxembourg -3.9033 3.5521 -1.099
## SexMale:Treatment_FTLMix 0.2077 1.7634 0.118
## SexMale:Treatment_FTLNight 1.6124 1.9388 0.832
## RegionLuxembourg:Treatment_FTLMix -2.6025 2.4761 -1.051
## RegionLuxembourg:Treatment_FTLNight 3.7749 2.8212 1.338
## Treatment_bisFull:Treatment_FTLMix 0.7023 2.1248 0.331
## Treatment_bisSmart:Treatment_FTLMix 1.4699 2.0862 0.705
## Treatment_bisMixt_smart:Treatment_FTLMix 9.1656 4.6430 1.974
## Treatment_bisFull:Treatment_FTLNight 0.5079 2.1223 0.239
## Treatment_bisSmart:Treatment_FTLNight -3.3713 2.7167 -1.241
## Treatment_bisMixt_smart:Treatment_FTLNight 2.2935 3.2844 0.698
## SexMale:Light_orientationSouth 4.2483 1.6544 2.568
## RegionLuxembourg:Light_orientationSouth 1.0977 1.8499 0.593
## Treatment_bisFull:Light_orientationSouth -0.3587 1.8708 -0.192
## Treatment_bisSmart:Light_orientationSouth -1.3291 2.1743 -0.611
## Treatment_bisMixt_smart:Light_orientationSouth 5.3970 2.8328 1.905
## Pr(>|z|)
## (Intercept) 0.8752
## Treatment_bisFull 0.3132
## Treatment_bisSmart 0.5383
## Treatment_bisMixt_smart 0.0990 .
## SexMale 0.1457
## RegionLuxembourg 0.4786
## Treatment_FTLMix 0.1435
## Treatment_FTLNight 0.2075
## Light_orientationSouth 0.1303
## Treatment_bisFull:SexMale 0.8561
## Treatment_bisSmart:SexMale 0.3276
## Treatment_bisMixt_smart:SexMale 0.3082
## Treatment_bisFull:RegionLuxembourg 0.0251 *
## Treatment_bisSmart:RegionLuxembourg 0.7571
## Treatment_bisMixt_smart:RegionLuxembourg 0.2718
## SexMale:Treatment_FTLMix 0.9062
## SexMale:Treatment_FTLNight 0.4056
## RegionLuxembourg:Treatment_FTLMix 0.2932
## RegionLuxembourg:Treatment_FTLNight 0.1809
## Treatment_bisFull:Treatment_FTLMix 0.7410
## Treatment_bisSmart:Treatment_FTLMix 0.4811
## Treatment_bisMixt_smart:Treatment_FTLMix 0.0484 *
## Treatment_bisFull:Treatment_FTLNight 0.8109
## Treatment_bisSmart:Treatment_FTLNight 0.2146
## Treatment_bisMixt_smart:Treatment_FTLNight 0.4850
## SexMale:Light_orientationSouth 0.0102 *
## RegionLuxembourg:Light_orientationSouth 0.5529
## Treatment_bisFull:Light_orientationSouth 0.8479
## Treatment_bisSmart:Light_orientationSouth 0.5410
## Treatment_bisMixt_smart:Light_orientationSouth 0.0568 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## optimizer (Nelder_Mead) convergence code: 4 (failure to converge in 10000 evaluations)
## Model failed to converge with max|grad| = 0.0151932 (tol = 0.002, component 1)
## failure to converge in 10000 evaluations5.3.2 Simplification du modèle
Simplification par AIC/BIC
drop1(GLM_Did_FTL)## Single term deletions
##
## Model:
## Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex +
## Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region +
## Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region +
## Light_orientation:Treatment_bis
## npar AIC
## <none> 165.09
## Treatment_bis:Sex 3 160.96
## Treatment_bis:Region 3 172.07
## Sex:Treatment_FTL 2 161.94
## Region:Treatment_FTL 2 169.99
## Treatment_bis:Treatment_FTL 6 163.04
## Sex:Light_orientation 1 171.54
## Region:Light_orientation 1 163.49
## Treatment_bis:Light_orientation 3 166.26GLM_Did_FTL2 <- update(GLM_Did_FTL, . ~ . - Treatment_bis:Sex)
drop1(GLM_Did_FTL2)## Single term deletions
##
## Model:
## Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Sex:Treatment_FTL + Region:Treatment_FTL + Treatment_bis:Treatment_FTL +
## Sex:Light_orientation + Region:Light_orientation + Treatment_bis:Light_orientation
## npar AIC
## <none> 160.96
## Treatment_bis:Region 3 166.62
## Sex:Treatment_FTL 2 158.05
## Region:Treatment_FTL 2 166.70
## Treatment_bis:Treatment_FTL 6 159.33
## Sex:Light_orientation 1 167.90
## Region:Light_orientation 1 159.11
## Treatment_bis:Light_orientation 3 162.00GLM_Did_FTL3 <- update(GLM_Did_FTL2, . ~ . - Sex:Treatment_FTL)
drop1(GLM_Did_FTL3)## Single term deletions
##
## Model:
## Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Sex:Light_orientation +
## Region:Light_orientation + Treatment_bis:Light_orientation
## npar AIC
## <none> 158.05
## Treatment_bis:Region 3 163.59
## Region:Treatment_FTL 2 162.96
## Treatment_bis:Treatment_FTL 6 156.53
## Sex:Light_orientation 1 165.73
## Region:Light_orientation 1 156.12
## Treatment_bis:Light_orientation 3 159.12GLM_Did_FTL4 <- update(GLM_Did_FTL3, . ~ . - Treatment_bis:Treatment_FTL)
drop1(GLM_Did_FTL4)## Single term deletions
##
## Model:
## Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Region:Treatment_FTL + Sex:Light_orientation + Region:Light_orientation +
## Treatment_bis:Light_orientation
## npar AIC
## <none> 156.53
## Treatment_bis:Region 3 158.19
## Region:Treatment_FTL 2 156.47
## Sex:Light_orientation 1 163.31
## Region:Light_orientation 1 154.63
## Treatment_bis:Light_orientation 3 154.77GLM_Did_FTL5 <- update(GLM_Did_FTL4, . ~ . - Region:Light_orientation)
drop1(GLM_Did_FTL5)## Single term deletions
##
## Model:
## Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Region:Treatment_FTL + Sex:Light_orientation + Treatment_bis:Light_orientation
## npar AIC
## <none> 154.63
## Treatment_bis:Region 3 156.27
## Region:Treatment_FTL 2 154.49
## Sex:Light_orientation 1 161.32
## Treatment_bis:Light_orientation 3 152.80GLM_Did_FTL6 <- update(GLM_Did_FTL5, . ~ . - Treatment_bis:Light_orientation)
drop1(GLM_Did_FTL6)## Single term deletions
##
## Model:
## Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Region:Treatment_FTL + Sex:Light_orientation
## npar AIC
## <none> 152.80
## Treatment_bis:Region 3 155.06
## Region:Treatment_FTL 2 152.56
## Sex:Light_orientation 1 158.45GLM_Did_FTL7 <- update(GLM_Did_FTL6, . ~ . - Region:Treatment_FTL)
drop1(GLM_Did_FTL7)## Single term deletions
##
## Model:
## Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Sex:Light_orientation
## npar AIC
## <none> 152.56
## Treatment_FTL 2 161.50
## Treatment_bis:Region 3 154.61
## Sex:Light_orientation 1 158.98Est ce qu’il faut pas juste retirer toutes les interactions ?
BIC(glmer(Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## [1] 193.4505BIC(GLM_Did_FTL7)## [1] 196.8872Si
GLM_Did_FTL <- glmer(Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial)5.3.3 Treatment VS Treatment_bis
AIC(glmer(Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## [1] 160.2023AIC(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## [1] 158.3439summary(glmer(Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_FTL ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 160.2 193.5 -68.1 136.2 106
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.1596 -0.6899 0.2677 0.5302 2.0153
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.849e-01 0.6963779
## Site (Intercept) 6.223e-01 0.7888452
## Room (Intercept) 4.255e-07 0.0006523
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.7096 0.7721 -2.214 0.02681 *
## Treatment_bisFull 0.3596 0.5948 0.605 0.54546
## Treatment_bisSmart 0.5708 0.6804 0.839 0.40152
## Treatment_bisMixt_smart 0.2832 0.6529 0.434 0.66446
## SexMale 0.1707 0.4758 0.359 0.71984
## RegionLuxembourg 0.7777 0.7826 0.994 0.32035
## Treatment_FTLMix 1.2505 0.7526 1.662 0.09659 .
## Treatment_FTLNight 2.2091 0.7516 2.939 0.00329 **
## Light_orientationSouth 0.2275 0.4851 0.469 0.63904
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## Trtmnt_bsFl -0.350
## Trtmnt_bsSm -0.287 0.370
## Trtmnt_bsM_ -0.285 0.443 0.337
## SexMale -0.290 -0.056 0.053 -0.012
## ReginLxmbrg -0.450 0.015 -0.060 -0.001 0.042
## Trtmnt_FTLM -0.287 0.102 0.018 -0.002 -0.085 -0.277
## Trtmnt_FTLN -0.299 0.043 0.013 -0.027 0.014 -0.199 0.686
## Lght_rnttnS -0.315 -0.123 -0.039 -0.108 0.075 0.157 -0.099 -0.157
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0031881 (tol = 0.002, component 1)summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 158.3 188.8 -68.2 136.3 107
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3031 -0.6765 0.2807 0.5189 1.9056
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.495e-01 0.6704824
## Site (Intercept) 6.214e-01 0.7882978
## Room (Intercept) 8.679e-07 0.0009316
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.7082 0.7679 -2.225 0.0261 *
## TreatmentFull 0.3693 0.5925 0.623 0.5331
## TreatmentSmart 0.4182 0.5431 0.770 0.4413
## SexMale 0.1606 0.4732 0.339 0.7343
## RegionLuxembourg 0.7944 0.7766 1.023 0.3063
## Treatment_FTLMix 1.2481 0.7592 1.644 0.1002
## Treatment_FTLNight 2.2038 0.7592 2.903 0.0037 **
## Light_orientationSouth 0.2173 0.4846 0.448 0.6538
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnF TrtmnS SexMal RgnLxm T_FTLM T_FTLN
## TreatmntFll -0.352
## TretmntSmrt -0.354 0.499
## SexMale -0.288 -0.055 0.023
## ReginLxmbrg -0.448 0.010 -0.033 0.044
## Trtmnt_FTLM -0.286 0.106 0.007 -0.088 -0.282
## Trtmnt_FTLN -0.298 0.051 -0.012 0.011 -0.206 0.694
## Lght_rnttnS -0.315 -0.123 -0.085 0.070 0.165 -0.106 -0.164
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0048435 (tol = 0.002, component 1)Il faudrait muieux continuer avec Treatment
5.3.4 Résultats
Analyse des p-val
summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0048435 (tol = 0.002, component 1)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data
##
## AIC BIC logLik deviance df.resid
## 158.3 188.8 -68.2 136.3 107
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3031 -0.6765 0.2807 0.5189 1.9056
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.495e-01 0.6704824
## Site (Intercept) 6.214e-01 0.7882978
## Room (Intercept) 8.679e-07 0.0009316
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.7082 0.7679 -2.225 0.0261 *
## TreatmentFull 0.3693 0.5925 0.623 0.5331
## TreatmentSmart 0.4182 0.5431 0.770 0.4413
## SexMale 0.1606 0.4732 0.339 0.7343
## RegionLuxembourg 0.7944 0.7766 1.023 0.3063
## Treatment_FTLMix 1.2481 0.7592 1.644 0.1002
## Treatment_FTLNight 2.2038 0.7592 2.903 0.0037 **
## Light_orientationSouth 0.2173 0.4846 0.448 0.6538
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnF TrtmnS SexMal RgnLxm T_FTLM T_FTLN
## TreatmntFll -0.352
## TretmntSmrt -0.354 0.499
## SexMale -0.288 -0.055 0.023
## ReginLxmbrg -0.448 0.010 -0.033 0.044
## Trtmnt_FTLM -0.286 0.106 0.007 -0.088 -0.282
## Trtmnt_FTLN -0.298 0.051 -0.012 0.011 -0.206 0.694
## Lght_rnttnS -0.315 -0.123 -0.085 0.070 0.165 -0.106 -0.164
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0048435 (tol = 0.002, component 1)summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_full, family = binomial))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0370792 (tol = 0.002, component 1)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_ref_full
##
## AIC BIC logLik deviance df.resid
## 158.3 188.8 -68.2 136.3 107
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3040 -0.6777 0.2802 0.5191 1.9080
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.371e-01 0.661123
## Site (Intercept) 6.356e-01 0.797251
## Room (Intercept) 5.085e-05 0.007131
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.33401 0.78815 -1.693 0.09054 .
## TreatmentDark -0.37250 0.59236 -0.629 0.52946
## TreatmentSmart 0.04595 0.57019 0.081 0.93576
## SexMale 0.16021 0.47307 0.339 0.73487
## RegionLuxembourg 0.79106 0.77776 1.017 0.30910
## Treatment_FTLMix 1.25125 0.75762 1.652 0.09862 .
## Treatment_FTLNight 2.20844 0.75847 2.912 0.00359 **
## Light_orientationSouth 0.21517 0.48437 0.444 0.65688
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnS SexMal RgnLxm T_FTLM T_FTLN
## TreatmntDrk -0.408
## TretmntSmrt -0.395 0.564
## SexMale -0.323 0.055 0.079
## ReginLxmbrg -0.430 -0.011 -0.043 0.044
## Trtmnt_FTLM -0.200 -0.106 -0.104 -0.088 -0.281
## Trtmnt_FTLN -0.253 -0.051 -0.064 0.011 -0.205 0.694
## Lght_rnttnS -0.399 0.123 0.047 0.070 0.164 -0.105 -0.163
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0370792 (tol = 0.002, component 1)summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_smart, family = binomial))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00826885 (tol = 0.002, component 1)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_ref_smart
##
## AIC BIC logLik deviance df.resid
## 158.3 188.8 -68.2 136.3 107
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3019 -0.6767 0.2807 0.5188 1.9059
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.489e-01 0.67001
## Site (Intercept) 6.219e-01 0.78861
## Room (Intercept) 2.530e-06 0.00159
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.28982 0.76787 -1.680 0.09301 .
## TreatmentDark -0.41758 0.54309 -0.769 0.44196
## TreatmentFull -0.04827 0.57012 -0.085 0.93253
## SexMale 0.15992 0.47315 0.338 0.73537
## RegionLuxembourg 0.79304 0.77669 1.021 0.30723
## Treatment_FTLMix 1.24860 0.75916 1.645 0.10003
## Treatment_FTLNight 2.20405 0.75919 2.903 0.00369 **
## Light_orientationSouth 0.21777 0.48463 0.449 0.65318
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnF SexMal RgnLxm T_FTLM T_FTLN
## TreatmntDrk -0.354
## TreatmntFll -0.336 0.434
## SexMale -0.272 -0.023 -0.079
## ReginLxmbrg -0.471 0.033 0.042 0.044
## Trtmnt_FTLM -0.281 -0.007 0.104 -0.088 -0.283
## Trtmnt_FTLN -0.306 0.012 0.064 0.011 -0.207 0.694
## Lght_rnttnS -0.376 0.085 -0.047 0.070 0.165 -0.106 -0.164
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.00826885 (tol = 0.002, component 1)summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_refFTL_Mix, family = binomial))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0150819 (tol = 0.002, component 1)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_refFTL_Mix
##
## AIC BIC logLik deviance df.resid
## 158.3 188.8 -68.2 136.3 107
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3022 -0.6767 0.2804 0.5189 1.9073
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.457e-01 0.667623
## Site (Intercept) 6.255e-01 0.790899
## Room (Intercept) 8.415e-06 0.002901
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.4588 0.9125 -0.503 0.6152
## TreatmentFull 0.3705 0.5925 0.625 0.5318
## TreatmentSmart 0.4177 0.5431 0.769 0.4419
## SexMale 0.1604 0.4732 0.339 0.7346
## RegionLuxembourg 0.7927 0.7770 1.020 0.3076
## Treatment_FTLDay -1.2499 0.7591 -1.647 0.0996 .
## Treatment_FTLNight 0.9569 0.5937 1.612 0.1070
## Light_orientationSouth 0.2171 0.4846 0.448 0.6542
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnF TrtmnS SexMal RgnLxm T_FTLD T_FTLN
## TreatmntFll -0.208
## TretmntSmrt -0.292 0.499
## SexMale -0.316 -0.055 0.023
## ReginLxmbrg -0.612 0.010 -0.033 0.044
## Trtmnt_FTLD -0.591 -0.106 -0.007 0.088 0.282
## Trtmnt_FTLN -0.338 -0.071 -0.024 0.127 0.097 0.391
## Lght_rnttnS -0.354 -0.123 -0.085 0.070 0.165 0.106 -0.074
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0150819 (tol = 0.002, component 1)summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_refFTL_Night, family = binomial))## boundary (singular) fit: see help('isSingular')## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula:
## Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_refFTL_Night
##
## AIC BIC logLik deviance df.resid
## 158.3 188.8 -68.2 136.3 107
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3030 -0.6765 0.2807 0.5189 1.9053
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.506e-01 6.713e-01
## Site (Intercept) 6.203e-01 7.876e-01
## Room (Intercept) 7.767e-10 2.787e-05
## Number of obs: 118, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.4953 0.9049 0.547 0.5841
## TreatmentFull 0.3695 0.5925 0.624 0.5329
## TreatmentSmart 0.4185 0.5431 0.771 0.4410
## SexMale 0.1605 0.4732 0.339 0.7345
## RegionLuxembourg 0.7945 0.7765 1.023 0.3063
## Treatment_FTLDay -2.2036 0.7592 -2.902 0.0037 **
## Treatment_FTLMix -0.9559 0.5938 -1.610 0.1074
## Light_orientationSouth 0.2175 0.4846 0.449 0.6536
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnF TrtmnS SexMal RgnLxm T_FTLD T_FTLM
## TreatmntFll -0.256
## TretmntSmrt -0.310 0.499
## SexMale -0.235 -0.055 0.023
## ReginLxmbrg -0.553 0.010 -0.033 0.044
## Trtmnt_FTLD -0.586 -0.051 0.012 -0.011 0.207
## Trtmnt_FTLM -0.315 0.071 0.024 -0.127 -0.097 0.391
## Lght_rnttnS -0.405 -0.123 -0.085 0.070 0.165 0.164 0.074
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Day", as.data.frame(( summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0048435 (tol = 0.002, component 1)test2 <- data.frame(Reference_Treatment = "Smart", Reference_Timing = "Day", as.data.frame(( summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_smart, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00826885 (tol = 0.002, component 1)test3 <- data.frame(Reference_Treatment = "Full", Reference_Timing = "Day", as.data.frame(( summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_ref_full, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0370792 (tol = 0.002, component 1)test4 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Mixt", as.data.frame(( summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_refFTL_Mix, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0150819 (tol = 0.002, component 1)test5 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Night", as.data.frame(( summary(glmer(Did_FTL ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_refFTL_Night, family = binomial))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Did_FTL <- rbind(test1,test2,test3,test4,test5)
colnames(Results_Did_FTL ) <- c("Reference_Treatment", "Reference_Timing" ,"Estimate", "Std. Error", "z value", "Pr(>|z|)")
write.csv2( Results_Did_FTL , file = "output/Results_Did_FTL.csv" )
kable(Results_Did_FTL , caption = " Probabilité de voler à la lumière ", padding = 1 )| Reference_Treatment | Reference_Timing | Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | Day | -1.7081688 | 0.7678707 | -2.2245527 | 0.0261113 |
| TreatmentFull | Dark | Day | 0.3692970 | 0.5924814 | 0.6233057 | 0.5330837 |
| TreatmentSmart | Dark | Day | 0.4181749 | 0.5431189 | 0.7699509 | 0.4413290 |
| SexMale | Dark | Day | 0.1606063 | 0.4731734 | 0.3394237 | 0.7342906 |
| RegionLuxembourg | Dark | Day | 0.7943784 | 0.7765694 | 1.0229330 | 0.3063395 |
| Treatment_FTLMix | Dark | Day | 1.2481417 | 0.7591940 | 1.6440352 | 0.1001689 |
| Treatment_FTLNight | Dark | Day | 2.2038279 | 0.7591823 | 2.9028968 | 0.0036973 |
| Light_orientationSouth | Dark | Day | 0.2173402 | 0.4846258 | 0.4484702 | 0.6538139 |
| (Intercept)1 | Smart | Day | -1.2898222 | 0.7678653 | -1.6797507 | 0.0930058 |
| TreatmentDark | Smart | Day | -0.4175789 | 0.5430945 | -0.7688881 | 0.4419597 |
| TreatmentFull1 | Smart | Day | -0.0482672 | 0.5701190 | -0.0846617 | 0.9325304 |
| SexMale1 | Smart | Day | 0.1599194 | 0.4731498 | 0.3379890 | 0.7353715 |
| RegionLuxembourg1 | Smart | Day | 0.7930412 | 0.7766902 | 1.0210523 | 0.3072297 |
| Treatment_FTLMix1 | Smart | Day | 1.2486025 | 0.7591617 | 1.6447122 | 0.1000292 |
| Treatment_FTLNight1 | Smart | Day | 2.2040502 | 0.7591942 | 2.9031441 | 0.0036944 |
| Light_orientationSouth1 | Smart | Day | 0.2177711 | 0.4846307 | 0.4493548 | 0.6531758 |
| (Intercept)2 | Full | Day | -1.3340058 | 0.7881515 | -1.6925753 | 0.0905363 |
| TreatmentDark1 | Full | Day | -0.3725007 | 0.5923637 | -0.6288378 | 0.5294553 |
| TreatmentSmart1 | Full | Day | 0.0459538 | 0.5701884 | 0.0805941 | 0.9357648 |
| SexMale2 | Full | Day | 0.1602076 | 0.4730727 | 0.3386532 | 0.7348710 |
| RegionLuxembourg2 | Full | Day | 0.7910603 | 0.7777554 | 1.0171069 | 0.3091026 |
| Treatment_FTLMix2 | Full | Day | 1.2512528 | 0.7576178 | 1.6515621 | 0.0986239 |
| Treatment_FTLNight2 | Full | Day | 2.2084372 | 0.7584730 | 2.9116888 | 0.0035948 |
| Light_orientationSouth2 | Full | Day | 0.2151654 | 0.4843673 | 0.4442195 | 0.6568839 |
| (Intercept)3 | Dark | Mixt | -0.4587509 | 0.9125183 | -0.5027306 | 0.6151537 |
| TreatmentFull2 | Dark | Mixt | 0.3704720 | 0.5924966 | 0.6252727 | 0.5317921 |
| TreatmentSmart2 | Dark | Mixt | 0.4176852 | 0.5431032 | 0.7690716 | 0.4418508 |
| SexMale3 | Dark | Mixt | 0.1603856 | 0.4731678 | 0.3389613 | 0.7346389 |
| RegionLuxembourg3 | Dark | Mixt | 0.7927231 | 0.7770149 | 1.0202160 | 0.3076260 |
| Treatment_FTLDay | Dark | Mixt | -1.2498978 | 0.7590747 | -1.6466070 | 0.0996388 |
| Treatment_FTLNight3 | Dark | Mixt | 0.9569163 | 0.5936644 | 1.6118808 | 0.1069879 |
| Light_orientationSouth3 | Dark | Mixt | 0.2170862 | 0.4846294 | 0.4479427 | 0.6541946 |
| (Intercept)4 | Dark | Night | 0.4953280 | 0.9048637 | 0.5474062 | 0.5840997 |
| TreatmentFull3 | Dark | Night | 0.3694517 | 0.5924917 | 0.6235560 | 0.5329192 |
| TreatmentSmart3 | Dark | Night | 0.4185338 | 0.5431387 | 0.7705837 | 0.4409537 |
| SexMale4 | Dark | Night | 0.1604751 | 0.4731869 | 0.3391367 | 0.7345067 |
| RegionLuxembourg4 | Dark | Night | 0.7944654 | 0.7765149 | 1.0231168 | 0.3062526 |
| Treatment_FTLDay1 | Dark | Night | -2.2036136 | 0.7592487 | -2.9023607 | 0.0037036 |
| Treatment_FTLMix3 | Dark | Night | -0.9558769 | 0.5937535 | -1.6098885 | 0.1074222 |
| Light_orientationSouth4 | Dark | Night | 0.2174625 | 0.4846481 | 0.4487019 | 0.6536467 |
Info_Did_FTL <- "
Les individus expérimentés durant la nuit volent significativement plus que ceux expérimentés durant le jour. Les individus expérimentés avec la méthode (timing de l'expérience) Mixte ne sont pas significativement différent ni de ceux expérimentés pendant la nuit ni de ceux expérimentés pendant le jour.
"5.3.5 Visualisation
ggplot(Data %>% filter(Did_FTL != "NA")) +
aes(x = Did_FTL, fill = Treatment_FTL) +
geom_bar(position = "dodge") +
scale_fill_hue(direction = 1) +
labs(title= "Probabilité de voler à la lumière", x = "A volé à la lumière", y = "Nombre d'individus", fill = "Timing") +
theme_minimal()
5.4 First_move
5.4.1 Test
LM_First_move <- lmer(First_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis, data = Data)## boundary (singular) fit: see help('isSingular')summary(LM_First_move)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## First_move ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex +
## Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region +
## Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region +
## Light_orientation:Treatment_bis
## Data: Data
##
## REML criterion at convergence: 1214.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.9244 -0.4845 -0.1087 0.3113 2.6388
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0 0.0
## Site (Intercept) 16861 129.9
## Room (Intercept) 0 0.0
## Residual 104999 324.0
## Number of obs: 110, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 829.80 190.23 58.20
## Treatment_bisFull -266.23 184.92 76.98
## Treatment_bisSmart -216.32 235.83 75.70
## Treatment_bisMixt_smart -148.29 240.58 77.49
## SexMale -380.44 166.40 77.74
## RegionLuxembourg -345.13 202.27 47.24
## Treatment_FTLMix -198.87 206.79 70.43
## Treatment_FTLNight -528.78 208.10 76.96
## Light_orientationSouth -275.81 147.84 74.84
## Treatment_bisFull:SexMale 265.36 176.56 76.58
## Treatment_bisSmart:SexMale 158.63 212.13 77.62
## Treatment_bisMixt_smart:SexMale 124.15 206.95 79.98
## Treatment_bisFull:RegionLuxembourg 43.09 181.96 78.94
## Treatment_bisSmart:RegionLuxembourg 116.45 206.25 77.08
## Treatment_bisMixt_smart:RegionLuxembourg -475.67 261.97 78.80
## SexMale:Treatment_FTLMix 395.55 174.60 79.37
## SexMale:Treatment_FTLNight 261.46 172.80 79.32
## RegionLuxembourg:Treatment_FTLMix -80.44 210.22 73.79
## RegionLuxembourg:Treatment_FTLNight 383.92 201.32 79.42
## Treatment_bisFull:Treatment_FTLMix -254.14 227.40 78.12
## Treatment_bisSmart:Treatment_FTLMix 111.69 248.13 75.56
## Treatment_bisMixt_smart:Treatment_FTLMix 373.01 321.18 77.57
## Treatment_bisFull:Treatment_FTLNight -116.86 208.71 75.57
## Treatment_bisSmart:Treatment_FTLNight -117.89 245.11 75.44
## Treatment_bisMixt_smart:Treatment_FTLNight 47.29 264.99 79.93
## SexMale:Light_orientationSouth -10.58 150.85 76.45
## RegionLuxembourg:Light_orientationSouth 170.86 144.60 76.34
## Treatment_bisFull:Light_orientationSouth 249.55 177.39 78.48
## Treatment_bisSmart:Light_orientationSouth -8.84 208.22 78.96
## Treatment_bisMixt_smart:Light_orientationSouth 324.77 219.53 79.91
## t value Pr(>|t|)
## (Intercept) 4.362 5.33e-05 ***
## Treatment_bisFull -1.440 0.1540
## Treatment_bisSmart -0.917 0.3619
## Treatment_bisMixt_smart -0.616 0.5394
## SexMale -2.286 0.0250 *
## RegionLuxembourg -1.706 0.0945 .
## Treatment_FTLMix -0.962 0.3395
## Treatment_FTLNight -2.541 0.0131 *
## Light_orientationSouth -1.866 0.0660 .
## Treatment_bisFull:SexMale 1.503 0.1370
## Treatment_bisSmart:SexMale 0.748 0.4568
## Treatment_bisMixt_smart:SexMale 0.600 0.5503
## Treatment_bisFull:RegionLuxembourg 0.237 0.8134
## Treatment_bisSmart:RegionLuxembourg 0.565 0.5740
## Treatment_bisMixt_smart:RegionLuxembourg -1.816 0.0732 .
## SexMale:Treatment_FTLMix 2.265 0.0262 *
## SexMale:Treatment_FTLNight 1.513 0.1342
## RegionLuxembourg:Treatment_FTLMix -0.383 0.7031
## RegionLuxembourg:Treatment_FTLNight 1.907 0.0601 .
## Treatment_bisFull:Treatment_FTLMix -1.118 0.2672
## Treatment_bisSmart:Treatment_FTLMix 0.450 0.6539
## Treatment_bisMixt_smart:Treatment_FTLMix 1.161 0.2490
## Treatment_bisFull:Treatment_FTLNight -0.560 0.5772
## Treatment_bisSmart:Treatment_FTLNight -0.481 0.6319
## Treatment_bisMixt_smart:Treatment_FTLNight 0.178 0.8588
## SexMale:Light_orientationSouth -0.070 0.9443
## RegionLuxembourg:Light_orientationSouth 1.182 0.2410
## Treatment_bisFull:Light_orientationSouth 1.407 0.1634
## Treatment_bisSmart:Light_orientationSouth -0.042 0.9662
## Treatment_bisMixt_smart:Light_orientationSouth 1.479 0.1430
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 30 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
Normalité
qqnorm(resid(LM_First_move))
qqline(resid(LM_First_move))
Il faudrait modifier les données
LM_First_move <- lmer(log(First_move+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis, data = Data )## boundary (singular) fit: see help('isSingular')summary(LM_First_move)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log(First_move + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL +
## Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) +
## Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex +
## Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex +
## Light_orientation:Region + Light_orientation:Treatment_bis
## Data: Data
##
## REML criterion at convergence: 412.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4888 -0.3715 0.1588 0.5251 1.6406
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.339e-01 6.587e-01
## Site (Intercept) 5.221e-01 7.226e-01
## Room (Intercept) 1.182e-09 3.438e-05
## Residual 4.506e+00 2.123e+00
## Number of obs: 110, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 7.0093 1.2658 58.2166
## Treatment_bisFull -0.8821 1.2254 71.2361
## Treatment_bisSmart -0.8169 1.5713 73.9684
## Treatment_bisMixt_smart -1.2066 1.5980 73.0403
## SexMale -2.5582 1.1050 73.9849
## RegionLuxembourg -0.4689 1.3430 46.9051
## Treatment_FTLMix -2.6393 1.3760 65.5602
## Treatment_FTLNight -4.1603 1.4028 73.8812
## Light_orientationSouth 0.1262 0.9779 67.8600
## Treatment_bisFull:SexMale 2.1444 1.1716 72.3734
## Treatment_bisSmart:SexMale 0.6633 1.4241 77.9840
## Treatment_bisMixt_smart:SexMale 2.6338 1.3761 77.7271
## Treatment_bisFull:RegionLuxembourg -2.1795 1.2055 73.9313
## Treatment_bisSmart:RegionLuxembourg -0.2561 1.3775 76.4981
## Treatment_bisMixt_smart:RegionLuxembourg -4.5323 1.7410 75.6100
## SexMale:Treatment_FTLMix 2.5951 1.1606 76.6476
## SexMale:Treatment_FTLNight 1.1313 1.1640 78.8548
## RegionLuxembourg:Treatment_FTLMix 0.2617 1.4057 72.0367
## RegionLuxembourg:Treatment_FTLNight 0.1334 1.3392 77.6288
## Treatment_bisFull:Treatment_FTLMix -1.4817 1.5160 76.8144
## Treatment_bisSmart:Treatment_FTLMix 1.4552 1.6502 72.5063
## Treatment_bisMixt_smart:Treatment_FTLMix 2.0905 2.1532 77.5942
## Treatment_bisFull:Treatment_FTLNight 0.6639 1.4012 76.3098
## Treatment_bisSmart:Treatment_FTLNight 2.1800 1.6319 73.9299
## Treatment_bisMixt_smart:Treatment_FTLNight 2.5614 1.7628 77.6015
## SexMale:Light_orientationSouth 0.0626 1.0080 75.9717
## RegionLuxembourg:Light_orientationSouth 1.7505 0.9583 70.6591
## Treatment_bisFull:Light_orientationSouth -0.2312 1.1797 74.6924
## Treatment_bisSmart:Light_orientationSouth -1.2774 1.3818 76.1052
## Treatment_bisMixt_smart:Light_orientationSouth -0.1748 1.4546 75.4273
## t value Pr(>|t|)
## (Intercept) 5.537 7.71e-07 ***
## Treatment_bisFull -0.720 0.47397
## Treatment_bisSmart -0.520 0.60469
## Treatment_bisMixt_smart -0.755 0.45264
## SexMale -2.315 0.02339 *
## RegionLuxembourg -0.349 0.72852
## Treatment_FTLMix -1.918 0.05945 .
## Treatment_FTLNight -2.966 0.00406 **
## Light_orientationSouth 0.129 0.89772
## Treatment_bisFull:SexMale 1.830 0.07133 .
## Treatment_bisSmart:SexMale 0.466 0.64268
## Treatment_bisMixt_smart:SexMale 1.914 0.05931 .
## Treatment_bisFull:RegionLuxembourg -1.808 0.07469 .
## Treatment_bisSmart:RegionLuxembourg -0.186 0.85298
## Treatment_bisMixt_smart:RegionLuxembourg -2.603 0.01111 *
## SexMale:Treatment_FTLMix 2.236 0.02826 *
## SexMale:Treatment_FTLNight 0.972 0.33408
## RegionLuxembourg:Treatment_FTLMix 0.186 0.85282
## RegionLuxembourg:Treatment_FTLNight 0.100 0.92094
## Treatment_bisFull:Treatment_FTLMix -0.977 0.33144
## Treatment_bisSmart:Treatment_FTLMix 0.882 0.38080
## Treatment_bisMixt_smart:Treatment_FTLMix 0.971 0.33462
## Treatment_bisFull:Treatment_FTLNight 0.474 0.63698
## Treatment_bisSmart:Treatment_FTLNight 1.336 0.18569
## Treatment_bisMixt_smart:Treatment_FTLNight 1.453 0.15025
## SexMale:Light_orientationSouth 0.062 0.95064
## RegionLuxembourg:Light_orientationSouth 1.827 0.07196 .
## Treatment_bisFull:Light_orientationSouth -0.196 0.84514
## Treatment_bisSmart:Light_orientationSouth -0.924 0.35819
## Treatment_bisMixt_smart:Light_orientationSouth -0.120 0.90468
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 30 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')qqnorm(resid(LM_First_move))
qqline(resid(LM_First_move))
Homogénité des variances
plot(LM_First_move)
Distance de cook
plot(cooks.distance(LM_First_move))
5.4.2 Simplification du modèle
drop1(LM_First_move)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(First_move + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 22.660 7.5535 3 76.888 1.6764 0.17906
## Treatment_bis:Region 37.137 12.3790 3 75.715 2.7473 0.04868 *
## Sex:Treatment_FTL 22.572 11.2859 2 71.505 2.5047 0.08884 .
## Region:Treatment_FTL 0.159 0.0796 2 74.993 0.0177 0.98249
## Treatment_bis:Treatment_FTL 29.184 4.8639 6 75.409 1.0795 0.38243
## Sex:Light_orientation 0.017 0.0174 1 75.972 0.0039 0.95064
## Region:Light_orientation 15.037 15.0366 1 70.659 3.3371 0.07196 .
## Treatment_bis:Light_orientation 4.068 1.3561 3 75.275 0.3010 0.82460
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_First_move1 <- update(LM_First_move, . ~ . - Region:Treatment_FTL)## boundary (singular) fit: see help('isSingular')drop1(LM_First_move1)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(First_move + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Treatment_FTL + Treatment_bis:Treatment_FTL + Sex:Light_orientation + Region:Light_orientation + Treatment_bis:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 23.224 7.7413 3 78.707 1.7698 0.15974
## Treatment_bis:Region 38.601 12.8670 3 77.447 2.9417 0.03824 *
## Sex:Treatment_FTL 22.889 11.4444 2 76.052 2.6165 0.07963 .
## Treatment_bis:Treatment_FTL 29.183 4.8638 6 76.491 1.1120 0.36330
## Sex:Light_orientation 0.011 0.0106 1 77.518 0.0024 0.96090
## Region:Light_orientation 15.062 15.0621 1 72.914 3.4436 0.06754 .
## Treatment_bis:Light_orientation 4.224 1.4081 3 76.754 0.3219 0.80948
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_First_move2 <- update(LM_First_move1, . ~ . - Sex:Light_orientation)## boundary (singular) fit: see help('isSingular')drop1(LM_First_move2)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(First_move + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Treatment_FTL + Treatment_bis:Treatment_FTL + Region:Light_orientation + Treatment_bis:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 23.959 7.9864 3 79.415 1.8520 0.14451
## Treatment_bis:Region 41.926 13.9753 3 78.400 3.2408 0.02647 *
## Sex:Treatment_FTL 22.933 11.4665 2 76.613 2.6590 0.07647 .
## Treatment_bis:Treatment_FTL 29.073 4.8455 6 77.078 1.1237 0.35659
## Region:Light_orientation 15.332 15.3324 1 73.526 3.5555 0.06330 .
## Treatment_bis:Light_orientation 4.251 1.4169 3 77.792 0.3286 0.80469
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_First_move3 <- update(LM_First_move2, . ~ . - Treatment_bis:Light_orientation)## boundary (singular) fit: see help('isSingular')drop1(LM_First_move3)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(First_move + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Treatment_FTL + Treatment_bis:Treatment_FTL + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 23.805 7.9351 3 81.374 1.9038 0.13548
## Treatment_bis:Region 45.456 15.1519 3 80.047 3.6352 0.01628 *
## Sex:Treatment_FTL 23.558 11.7789 2 79.331 2.8259 0.06523 .
## Treatment_bis:Treatment_FTL 28.802 4.8004 6 79.747 1.1517 0.34064
## Region:Light_orientation 13.051 13.0506 1 78.725 3.1310 0.08069 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_First_move4 <- update(LM_First_move3, . ~ . - Treatment_bis:Treatment_FTL)## boundary (singular) fit: see help('isSingular')drop1(LM_First_move4)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(First_move + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Treatment_FTL + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 15.606 5.2019 3 85.993 1.2522 0.29596
## Treatment_bis:Region 47.956 15.9853 3 83.084 3.8480 0.01243 *
## Sex:Treatment_FTL 18.350 9.1748 2 84.366 2.2086 0.11617
## Region:Light_orientation 12.109 12.1086 1 81.931 2.9148 0.09156 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_First_move5 <- update(LM_First_move4, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_First_move5)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(First_move + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Treatment_FTL + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Region 50.735 16.9117 3 86.466 3.9706 0.01058 *
## Sex:Treatment_FTL 16.393 8.1964 2 81.997 1.9244 0.15250
## Region:Light_orientation 7.255 7.2547 1 84.995 1.7033 0.19538
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_First_move6 <- update(LM_First_move5, . ~ . - Region:Light_orientation)## boundary (singular) fit: see help('isSingular')drop1(LM_First_move6)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(First_move + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Treatment_FTL
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Light_orientation 9.249 9.2491 1 87.893 2.1637 0.1449
## Treatment_bis:Region 46.640 15.5467 3 87.199 3.6369 0.0159 *
## Sex:Treatment_FTL 14.555 7.2776 2 83.571 1.7025 0.1885
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_First_move7 <- update(LM_First_move6, . ~ . - Sex:Treatment_FTL)## boundary (singular) fit: see help('isSingular')drop1(LM_First_move7)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(First_move + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 0.387 0.387 1 87.951 0.0882 0.7672263
## Treatment_FTL 76.880 38.440 2 91.904 8.7512 0.0003319 ***
## Light_orientation 8.768 8.768 1 87.578 1.9960 0.1612546
## Treatment_bis:Region 46.540 15.513 3 89.420 3.5318 0.0179941 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Le modèle ne sait pas être plus simplifié. Au vu de la complexité du modèle initial (nombre de paramètres), nous choisissons d’utiliser le BIC et non le AIC.
BIC(LM_First_move7)## [1] 543.0197BIC(LM_First_move)## [1] 572.6645La simplification fu utile
LM_First_move <- LM_First_move75.4.3 Treatment VS Teatment_bis
AIC(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data))## boundary (singular) fit: see help('isSingular')## [1] 507.9532AIC(lmer(log(First_move+0.1) ~ Treatment + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region + Treatment:Treatment_FTL, data = Data))## boundary (singular) fit: see help('isSingular')## [1] 509.7186summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 5.2089785 0.7070051 35.25734
## Treatment_bisFull 0.2318253 0.7397706 98.96286
## Treatment_bisSmart 0.2418912 0.9949686 98.11955
## Treatment_bisMixt_smart 1.1429676 0.8171949 96.35274
## RegionLuxembourg 0.3409024 0.9237476 36.19606
## Treatment_FTLMix -0.7839194 0.6269590 91.45414
## Treatment_FTLNight -2.2068127 0.5749287 98.40990
## Treatment_bisFull:RegionLuxembourg -2.1083257 1.1350375 100.28573
## Treatment_bisSmart:RegionLuxembourg -0.1494290 1.3088747 97.84767
## Treatment_bisMixt_smart:RegionLuxembourg -3.2354127 1.2835300 99.19832
## t value Pr(>|t|)
## (Intercept) 7.3676671 1.233474e-08
## Treatment_bisFull 0.3133746 7.546556e-01
## Treatment_bisSmart 0.2431144 8.084243e-01
## Treatment_bisMixt_smart 1.3986475 1.651293e-01
## RegionLuxembourg 0.3690428 7.142459e-01
## Treatment_FTLMix -1.2503519 2.143608e-01
## Treatment_FTLNight -3.8384113 2.189820e-04
## Treatment_bisFull:RegionLuxembourg -1.8574943 6.617505e-02
## Treatment_bisSmart:RegionLuxembourg -0.1141660 9.093401e-01
## Treatment_bisMixt_smart:RegionLuxembourg -2.5207145 1.330579e-02summary(lmer(log(First_move+0.1) ~ Treatment + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region + Treatment:Treatment_FTL, data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 5.4386296 0.8232656 49.76561 6.60616609
## TreatmentFull 0.3972479 1.0178796 97.86447 0.39027006
## TreatmentSmart 0.2396492 1.0072096 94.92062 0.23793381
## RegionLuxembourg 0.3700720 0.9097715 35.59608 0.40677465
## Treatment_FTLMix -0.8235021 1.0107187 93.97098 -0.81476877
## Treatment_FTLNight -2.9587374 1.0395292 98.96126 -2.84622836
## TreatmentFull:RegionLuxembourg -1.8543897 1.2050088 98.76695 -1.53890139
## TreatmentSmart:RegionLuxembourg -1.8460948 1.1344830 95.55353 -1.62725652
## TreatmentFull:Treatment_FTLMix -0.9284983 1.4436577 98.16350 -0.64315684
## TreatmentSmart:Treatment_FTLMix 0.3459947 1.3760586 94.88229 0.25143893
## TreatmentFull:Treatment_FTLNight 0.1089596 1.3981629 94.34781 0.07793054
## TreatmentSmart:Treatment_FTLNight 1.7810445 1.3614548 96.56456 1.30819221
## Pr(>|t|)
## (Intercept) 2.530559e-08
## TreatmentFull 6.971850e-01
## TreatmentSmart 8.124453e-01
## RegionLuxembourg 6.866091e-01
## Treatment_FTLMix 4.172648e-01
## Treatment_FTLNight 5.378669e-03
## TreatmentFull:RegionLuxembourg 1.270261e-01
## TreatmentSmart:RegionLuxembourg 1.069759e-01
## TreatmentFull:Treatment_FTLMix 5.216219e-01
## TreatmentSmart:Treatment_FTLMix 8.020185e-01
## TreatmentFull:Treatment_FTLNight 9.380483e-01
## TreatmentSmart:Treatment_FTLNight 1.939136e-01Le modèle avec treatment_bis est mieux
5.4.4 Résultats
Analyse des pval
summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(First_move + 0.1) ~ Treatment_bis + Region + Treatment_FTL +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data
##
## REML criterion at convergence: 480
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.8092 -0.3300 0.1791 0.5134 2.1774
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0000 0.0000
## Site (Intercept) 0.5351 0.7315
## Room (Intercept) 0.0000 0.0000
## Residual 4.9097 2.2158
## Number of obs: 111, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 5.2090 0.7070 35.2573 7.368
## Treatment_bisFull 0.2318 0.7398 98.9629 0.313
## Treatment_bisSmart 0.2419 0.9950 98.1195 0.243
## Treatment_bisMixt_smart 1.1430 0.8172 96.3527 1.399
## RegionLuxembourg 0.3409 0.9237 36.1961 0.369
## Treatment_FTLMix -0.7839 0.6270 91.4541 -1.250
## Treatment_FTLNight -2.2068 0.5749 98.4099 -3.838
## Treatment_bisFull:RegionLuxembourg -2.1083 1.1350 100.2857 -1.857
## Treatment_bisSmart:RegionLuxembourg -0.1494 1.3089 97.8477 -0.114
## Treatment_bisMixt_smart:RegionLuxembourg -3.2354 1.2835 99.1983 -2.521
## Pr(>|t|)
## (Intercept) 1.23e-08 ***
## Treatment_bisFull 0.754656
## Treatment_bisSmart 0.808424
## Treatment_bisMixt_smart 0.165129
## RegionLuxembourg 0.714246
## Treatment_FTLMix 0.214361
## Treatment_FTLNight 0.000219 ***
## Treatment_bisFull:RegionLuxembourg 0.066175 .
## Treatment_bisSmart:RegionLuxembourg 0.909340
## Treatment_bisMixt_smart:RegionLuxembourg 0.013306 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ RgnLxm T_FTLM T_FTLN T_F:RL T_S:RL
## Trtmnt_bsFl -0.594
## Trtmnt_bsSm -0.384 0.368
## Trtmnt_bsM_ -0.535 0.471 0.324
## ReginLxmbrg -0.581 0.415 0.294 0.359
## Trtmnt_FTLM -0.416 0.125 0.013 0.170 -0.055
## Trtmnt_FTLN -0.380 0.038 -0.013 0.043 -0.072 0.592
## Trtmnt_F:RL 0.409 -0.659 -0.241 -0.316 -0.627 -0.136 -0.056
## Trtmnt_S:RL 0.304 -0.280 -0.760 -0.246 -0.525 -0.026 -0.025 0.438
## Trtmn_M_:RL 0.403 -0.321 -0.209 -0.665 -0.526 -0.266 -0.106 0.478 0.370
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(First_move + 0.1) ~ Treatment_bis + Region + Treatment_FTL +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_ref_full
##
## REML criterion at convergence: 480
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.8092 -0.3300 0.1791 0.5134 2.1774
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0000 0.0000
## Site (Intercept) 0.5351 0.7315
## Room (Intercept) 0.0000 0.0000
## Residual 4.9097 2.2158
## Number of obs: 111, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 5.44080 0.65277 36.54084 8.335
## Treatment_bisDark -0.23183 0.73977 98.96286 -0.313
## Treatment_bisSmart 0.01007 0.99762 98.26004 0.010
## Treatment_bisMixt_smart 0.91114 0.80336 95.52516 1.134
## RegionLuxembourg -1.76742 0.90895 39.74323 -1.944
## Treatment_FTLMix -0.78392 0.62696 91.45414 -1.250
## Treatment_FTLNight -2.20681 0.57493 98.40990 -3.838
## Treatment_bisDark:RegionLuxembourg 2.10833 1.13504 100.28573 1.857
## Treatment_bisSmart:RegionLuxembourg 1.95890 1.30343 97.87396 1.503
## Treatment_bisMixt_smart:RegionLuxembourg -1.12709 1.24215 99.02967 -0.907
## Pr(>|t|)
## (Intercept) 5.65e-10 ***
## Treatment_bisDark 0.754656
## Treatment_bisSmart 0.991970
## Treatment_bisMixt_smart 0.259562
## RegionLuxembourg 0.058941 .
## Treatment_FTLMix 0.214361
## Treatment_FTLNight 0.000219 ***
## Treatment_bisDark:RegionLuxembourg 0.066175 .
## Treatment_bisSmart:RegionLuxembourg 0.136090
## Treatment_bisMixt_smart:RegionLuxembourg 0.366416
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ RgnLxm T_FTLM T_FTLN T_D:RL T_S:RL
## Trtmnt_bsDr -0.490
## Trtmnt_bsSm -0.363 0.374
## Trtmnt_bsM_ -0.498 0.442 0.318
## ReginLxmbrg -0.539 0.400 0.295 0.337
## Trtmnt_FTLM -0.309 -0.125 -0.080 0.058 -0.225
## Trtmnt_FTLN -0.368 -0.038 -0.041 0.009 -0.143 0.592
## Trtmnt_D:RL 0.303 -0.659 -0.248 -0.285 -0.611 0.136 0.056
## Trtmnt_S:RL 0.275 -0.292 -0.768 -0.240 -0.518 0.092 0.024 0.431
## Trtmn_M_:RL 0.353 -0.271 -0.196 -0.654 -0.494 -0.151 -0.058 0.420 0.347
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(First_move + 0.1) ~ Treatment_bis + Region + Treatment_FTL +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_ref_smart
##
## REML criterion at convergence: 480
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.8092 -0.3300 0.1791 0.5134 2.1774
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000e+00 0.000e+00
## Site (Intercept) 5.351e-01 7.315e-01
## Room (Intercept) 1.373e-09 3.705e-05
## Residual 4.910e+00 2.216e+00
## Number of obs: 111, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 5.45087 0.97418 72.13485 5.595
## Treatment_bisDark -0.24189 0.99497 98.11955 -0.243
## Treatment_bisFull -0.01007 0.99762 98.26005 -0.010
## Treatment_bisMixt_smart 0.90108 1.06369 99.13439 0.847
## RegionLuxembourg 0.19147 1.13875 65.94407 0.168
## Treatment_FTLMix -0.78392 0.62696 91.45416 -1.250
## Treatment_FTLNight -2.20681 0.57493 98.40991 -3.838
## Treatment_bisDark:RegionLuxembourg 0.14943 1.30887 97.84767 0.114
## Treatment_bisFull:RegionLuxembourg -1.95890 1.30343 97.87397 -1.503
## Treatment_bisMixt_smart:RegionLuxembourg -3.08598 1.45517 100.53028 -2.121
## Pr(>|t|)
## (Intercept) 3.73e-07 ***
## Treatment_bisDark 0.808424
## Treatment_bisFull 0.991970
## Treatment_bisMixt_smart 0.398968
## RegionLuxembourg 0.866984
## Treatment_FTLMix 0.214361
## Treatment_FTLNight 0.000219 ***
## Treatment_bisDark:RegionLuxembourg 0.909340
## Treatment_bisFull:RegionLuxembourg 0.136090
## Treatment_bisMixt_smart:RegionLuxembourg 0.036407 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ RgnLxm T_FTLM T_FTLN T_D:RL T_F:RL
## Trtmnt_bsDr -0.742
## Trtmnt_bsFl -0.781 0.724
## Trtmnt_bsM_ -0.739 0.687 0.698
## ReginLxmbrg -0.737 0.635 0.644 0.600
## Trtmnt_FTLM -0.288 -0.013 0.080 0.118 -0.075
## Trtmnt_FTLN -0.289 0.013 0.041 0.046 -0.087 0.592
## Trtmnt_D:RL 0.555 -0.760 -0.550 -0.521 -0.723 0.026 0.025
## Trtmnt_F:RL 0.602 -0.553 -0.768 -0.539 -0.731 -0.092 -0.024 0.622
## Trtmn_M_:RL 0.570 -0.499 -0.520 -0.747 -0.652 -0.211 -0.071 0.573 0.599
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_ref_mixt_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(First_move + 0.1) ~ Treatment_bis + Region + Treatment_FTL +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_ref_mixt_smart
##
## REML criterion at convergence: 480
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.8092 -0.3300 0.1791 0.5134 2.1774
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.293e-14 1.137e-07
## Site (Intercept) 5.351e-01 7.315e-01
## Room (Intercept) 0.000e+00 0.000e+00
## Residual 4.910e+00 2.216e+00
## Number of obs: 111, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 6.3519 0.7409 50.0093 8.573
## Treatment_bisDark -1.1430 0.8172 96.3527 -1.399
## Treatment_bisFull -0.9111 0.8034 95.5252 -1.134
## Treatment_bisSmart -0.9011 1.0637 99.1344 -0.847
## RegionLuxembourg -2.8945 1.1194 54.9316 -2.586
## Treatment_FTLMix -0.7839 0.6270 91.4541 -1.250
## Treatment_FTLNight -2.2068 0.5749 98.4099 -3.838
## Treatment_bisDark:RegionLuxembourg 3.2354 1.2835 99.1983 2.521
## Treatment_bisFull:RegionLuxembourg 1.1271 1.2422 99.0297 0.907
## Treatment_bisSmart:RegionLuxembourg 3.0860 1.4552 100.5303 2.121
## Pr(>|t|)
## (Intercept) 2.18e-11 ***
## Treatment_bisDark 0.165129
## Treatment_bisFull 0.259562
## Treatment_bisSmart 0.398968
## RegionLuxembourg 0.012398 *
## Treatment_FTLMix 0.214361
## Treatment_FTLNight 0.000219 ***
## Treatment_bisDark:RegionLuxembourg 0.013306 *
## Treatment_bisFull:RegionLuxembourg 0.366416
## Treatment_bisSmart:RegionLuxembourg 0.036407 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trtm_S RgnLxm T_FTLM T_FTLN T_D:RL T_F:RL
## Trtmnt_bsDr -0.592
## Trtmnt_bsFl -0.645 0.583
## Trtmnt_bsSm -0.464 0.466 0.457
## ReginLxmbrg -0.530 0.466 0.452 0.361
## Trtmnt_FTLM -0.209 -0.170 -0.058 -0.118 -0.350
## Trtmnt_FTLN -0.315 -0.043 -0.009 -0.046 -0.181 0.592
## Trtmnt_D:RL 0.348 -0.665 -0.381 -0.316 -0.712 0.266 0.106
## Trtmnt_F:RL 0.398 -0.398 -0.654 -0.310 -0.708 0.151 0.058 0.597
## Trtmnt_S:RL 0.324 -0.365 -0.343 -0.747 -0.637 0.211 0.071 0.549 0.543
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_refFTL_Night))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(First_move + 0.1) ~ Treatment_bis + Region + Treatment_FTL +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_refFTL_Night
##
## REML criterion at convergence: 480
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.8092 -0.3300 0.1791 0.5134 2.1774
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0000 0.0000
## Site (Intercept) 0.5352 0.7315
## Room (Intercept) 0.0000 0.0000
## Residual 4.9097 2.2158
## Number of obs: 111, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.0022 0.7223 37.8438 4.156
## Treatment_bisFull 0.2318 0.7398 98.9629 0.313
## Treatment_bisSmart 0.2419 0.9950 98.1196 0.243
## Treatment_bisMixt_smart 1.1430 0.8172 96.3528 1.399
## RegionLuxembourg 0.3409 0.9238 36.1954 0.369
## Treatment_FTLDay 2.2068 0.5749 98.4100 3.838
## Treatment_FTLMix 1.4229 0.5450 100.0072 2.611
## Treatment_bisFull:RegionLuxembourg -2.1083 1.1350 100.2858 -1.857
## Treatment_bisSmart:RegionLuxembourg -0.1494 1.3089 97.8477 -0.114
## Treatment_bisMixt_smart:RegionLuxembourg -3.2354 1.2835 99.1984 -2.521
## Pr(>|t|)
## (Intercept) 0.000178 ***
## Treatment_bisFull 0.754657
## Treatment_bisSmart 0.808426
## Treatment_bisMixt_smart 0.165130
## RegionLuxembourg 0.714244
## Treatment_FTLDay 0.000219 ***
## Treatment_FTLMix 0.010426 *
## Treatment_bisFull:RegionLuxembourg 0.066175 .
## Treatment_bisSmart:RegionLuxembourg 0.909342
## Treatment_bisMixt_smart:RegionLuxembourg 0.013306 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ RgnLxm T_FTLD T_FTLM T_F:RL T_S:RL
## Trtmnt_bsFl -0.551
## Trtmnt_bsSm -0.387 0.368
## Trtmnt_bsM_ -0.490 0.471 0.324
## ReginLxmbrg -0.626 0.415 0.294 0.359
## Trtmnt_FTLD -0.424 -0.038 0.013 -0.043 0.072
## Trtmnt_FTLM -0.375 0.104 0.029 0.150 0.012 0.374
## Trtmnt_F:RL 0.356 -0.659 -0.241 -0.316 -0.627 0.056 -0.097
## Trtmnt_S:RL 0.278 -0.280 -0.760 -0.246 -0.525 0.025 -0.004 0.438
## Trtmn_M_:RL 0.311 -0.321 -0.209 -0.665 -0.526 0.106 -0.194 0.478 0.370
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_refFTL_Mix))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(First_move + 0.1) ~ Treatment_bis + Region + Treatment_FTL +
## (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_refFTL_Mix
##
## REML criterion at convergence: 480
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.8094 -0.3299 0.1791 0.5134 2.1771
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.775e-08 0.0001332
## Site (Intercept) 5.346e-01 0.7311879
## Room (Intercept) 3.925e-07 0.0006265
## Residual 4.910e+00 2.2158406
## Number of obs: 111, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 4.4251 0.7237 33.8659 6.115
## Treatment_bisFull 0.2319 0.7398 98.9610 0.313
## Treatment_bisSmart 0.2420 0.9950 98.1165 0.243
## Treatment_bisMixt_smart 1.1430 0.8172 96.3498 1.399
## RegionLuxembourg 0.3408 0.9237 36.2166 0.369
## Treatment_FTLDay 0.7838 0.6269 91.4462 1.250
## Treatment_FTLNight -1.4229 0.5450 100.0065 -2.611
## Treatment_bisFull:RegionLuxembourg -2.1083 1.1350 100.2848 -1.857
## Treatment_bisSmart:RegionLuxembourg -0.1495 1.3089 97.8454 -0.114
## Treatment_bisMixt_smart:RegionLuxembourg -3.2354 1.2835 99.1970 -2.521
## Pr(>|t|)
## (Intercept) 6.21e-07 ***
## Treatment_bisFull 0.7546
## Treatment_bisSmart 0.8084
## Treatment_bisMixt_smart 0.1651
## RegionLuxembourg 0.7143
## Treatment_FTLDay 0.2144
## Treatment_FTLNight 0.0104 *
## Treatment_bisFull:RegionLuxembourg 0.0662 .
## Treatment_bisSmart:RegionLuxembourg 0.9093
## Treatment_bisMixt_smart:RegionLuxembourg 0.0133 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ RgnLxm T_FTLD T_FTLN T_F:RL T_S:RL
## Trtmnt_bsFl -0.471
## Trtmnt_bsSm -0.364 0.368
## Trtmnt_bsM_ -0.375 0.471 0.324
## ReginLxmbrg -0.615 0.415 0.294 0.359
## Trtmnt_FTLD -0.460 -0.125 -0.013 -0.170 0.055
## Trtmnt_FTLN -0.379 -0.104 -0.029 -0.150 -0.012 0.526
## Trtmnt_F:RL 0.282 -0.659 -0.241 -0.316 -0.627 0.136 0.097
## Trtmnt_S:RL 0.274 -0.280 -0.760 -0.246 -0.525 0.026 0.004 0.438
## Trtmn_M_:RL 0.164 -0.321 -0.209 -0.665 -0.526 0.266 0.194 0.478 0.370
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference_Treatment = "Smart", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference_Treatment = "Full", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test4 <- data.frame(Reference_Treatment = "Mixt_smart", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_ref_mixt_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test5 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Mixt", as.data.frame(( summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_refFTL_Mix))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test6 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Night", as.data.frame(( summary(lmer(log(First_move+0.1) ~ Treatment_bis + Region + Treatment_FTL + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region , data = Data_refFTL_Night))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_First_move <- rbind(test1,test2,test3,test4,test5,test6)
colnames(Results_First_move ) <- c("Reference_Treatment", "Reference_Timing" ,"Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_First_move , file = "output/Results_First_move.csv" )
kable(Results_First_move , caption = " Temps mis pour faire le premier mouvement ", padding = 1 )| Reference_Treatment | Reference_Timing | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|---|
| (Intercept) | Dark | Day | 5.2089785 | 0.7070051 | 35.25734 | 7.3676671 | 0.0000000 |
| Treatment_bisFull | Dark | Day | 0.2318253 | 0.7397706 | 98.96286 | 0.3133746 | 0.7546556 |
| Treatment_bisSmart | Dark | Day | 0.2418912 | 0.9949686 | 98.11955 | 0.2431144 | 0.8084243 |
| Treatment_bisMixt_smart | Dark | Day | 1.1429676 | 0.8171949 | 96.35274 | 1.3986475 | 0.1651293 |
| RegionLuxembourg | Dark | Day | 0.3409024 | 0.9237476 | 36.19606 | 0.3690428 | 0.7142459 |
| Treatment_FTLMix | Dark | Day | -0.7839194 | 0.6269590 | 91.45414 | -1.2503519 | 0.2143608 |
| Treatment_FTLNight | Dark | Day | -2.2068127 | 0.5749287 | 98.40990 | -3.8384113 | 0.0002190 |
| Treatment_bisFull:RegionLuxembourg | Dark | Day | -2.1083257 | 1.1350375 | 100.28573 | -1.8574943 | 0.0661750 |
| Treatment_bisSmart:RegionLuxembourg | Dark | Day | -0.1494290 | 1.3088747 | 97.84767 | -0.1141660 | 0.9093401 |
| Treatment_bisMixt_smart:RegionLuxembourg | Dark | Day | -3.2354127 | 1.2835300 | 99.19832 | -2.5207145 | 0.0133058 |
| (Intercept)1 | Smart | Day | 5.4508696 | 0.9741807 | 72.13485 | 5.5953372 | 0.0000004 |
| Treatment_bisDark | Smart | Day | -0.2418909 | 0.9949685 | 98.11955 | -0.2431141 | 0.8084245 |
| Treatment_bisFull1 | Smart | Day | -0.0100658 | 0.9976191 | 98.26005 | -0.0100898 | 0.9919701 |
| Treatment_bisMixt_smart1 | Smart | Day | 0.9010765 | 1.0636926 | 99.13439 | 0.8471212 | 0.3989680 |
| RegionLuxembourg1 | Smart | Day | 0.1914740 | 1.1387462 | 65.94407 | 0.1681445 | 0.8669842 |
| Treatment_FTLMix1 | Smart | Day | -0.7839198 | 0.6269590 | 91.45416 | -1.2503526 | 0.2143606 |
| Treatment_FTLNight1 | Smart | Day | -2.2068130 | 0.5749287 | 98.40991 | -3.8384117 | 0.0002190 |
| Treatment_bisDark:RegionLuxembourg | Smart | Day | 0.1494288 | 1.3088746 | 97.84767 | 0.1141659 | 0.9093402 |
| Treatment_bisFull:RegionLuxembourg1 | Smart | Day | -1.9588970 | 1.3034300 | 97.87397 | -1.5028785 | 0.1360902 |
| Treatment_bisMixt_smart:RegionLuxembourg1 | Smart | Day | -3.0859841 | 1.4551718 | 100.53028 | -2.1207009 | 0.0364072 |
| (Intercept)2 | Full | Day | 5.4408039 | 0.6527680 | 36.54084 | 8.3349737 | 0.0000000 |
| Treatment_bisDark1 | Full | Day | -0.2318253 | 0.7397706 | 98.96286 | -0.3133746 | 0.7546556 |
| Treatment_bisSmart1 | Full | Day | 0.0100658 | 0.9976191 | 98.26004 | 0.0100899 | 0.9919701 |
| Treatment_bisMixt_smart2 | Full | Day | 0.9111423 | 0.8033576 | 95.52516 | 1.1341677 | 0.2595624 |
| RegionLuxembourg2 | Full | Day | -1.7674233 | 0.9089518 | 39.74323 | -1.9444632 | 0.0589410 |
| Treatment_FTLMix2 | Full | Day | -0.7839194 | 0.6269590 | 91.45414 | -1.2503519 | 0.2143608 |
| Treatment_FTLNight2 | Full | Day | -2.2068127 | 0.5749287 | 98.40990 | -3.8384113 | 0.0002190 |
| Treatment_bisDark:RegionLuxembourg1 | Full | Day | 2.1083257 | 1.1350375 | 100.28573 | 1.8574943 | 0.0661750 |
| Treatment_bisSmart:RegionLuxembourg1 | Full | Day | 1.9588967 | 1.3034301 | 97.87396 | 1.5028782 | 0.1360903 |
| Treatment_bisMixt_smart:RegionLuxembourg2 | Full | Day | -1.1270870 | 1.2421520 | 99.02967 | -0.9073664 | 0.3664157 |
| (Intercept)3 | Mixt_smart | Day | 6.3519461 | 0.7409082 | 50.00933 | 8.5731890 | 0.0000000 |
| Treatment_bisDark2 | Mixt_smart | Day | -1.1429676 | 0.8171949 | 96.35274 | -1.3986475 | 0.1651293 |
| Treatment_bisFull2 | Mixt_smart | Day | -0.9111423 | 0.8033576 | 95.52516 | -1.1341677 | 0.2595624 |
| Treatment_bisSmart2 | Mixt_smart | Day | -0.9010764 | 1.0636926 | 99.13440 | -0.8471211 | 0.3989681 |
| RegionLuxembourg3 | Mixt_smart | Day | -2.8945103 | 1.1193934 | 54.93158 | -2.5857847 | 0.0123982 |
| Treatment_FTLMix3 | Mixt_smart | Day | -0.7839194 | 0.6269590 | 91.45414 | -1.2503520 | 0.2143608 |
| Treatment_FTLNight3 | Mixt_smart | Day | -2.2068127 | 0.5749287 | 98.40990 | -3.8384113 | 0.0002190 |
| Treatment_bisDark:RegionLuxembourg2 | Mixt_smart | Day | 3.2354127 | 1.2835300 | 99.19832 | 2.5207145 | 0.0133058 |
| Treatment_bisFull:RegionLuxembourg2 | Mixt_smart | Day | 1.1270870 | 1.2421520 | 99.02967 | 0.9073664 | 0.3664157 |
| Treatment_bisSmart:RegionLuxembourg2 | Mixt_smart | Day | 3.0859837 | 1.4551718 | 100.53028 | 2.1207006 | 0.0364072 |
| (Intercept)4 | Dark | Mixt | 4.4251476 | 0.7237020 | 33.86586 | 6.1145994 | 0.0000006 |
| Treatment_bisFull3 | Dark | Mixt | 0.2318759 | 0.7397786 | 98.96096 | 0.3134396 | 0.7546064 |
| Treatment_bisSmart3 | Dark | Mixt | 0.2419635 | 0.9949815 | 98.11650 | 0.2431840 | 0.8083706 |
| Treatment_bisMixt_smart3 | Dark | Mixt | 1.1430066 | 0.8172084 | 96.34984 | 1.3986721 | 0.1651220 |
| RegionLuxembourg4 | Dark | Mixt | 0.3407876 | 0.9236550 | 36.21661 | 0.3689555 | 0.7143092 |
| Treatment_FTLDay | Dark | Mixt | 0.7837835 | 0.6269438 | 91.44620 | 1.2501654 | 0.2144289 |
| Treatment_FTLNight4 | Dark | Mixt | -1.4229351 | 0.5450349 | 100.00655 | -2.6107231 | 0.0104241 |
| Treatment_bisFull:RegionLuxembourg3 | Dark | Mixt | -2.1082937 | 1.1350447 | 100.28483 | -1.8574543 | 0.0661808 |
| Treatment_bisSmart:RegionLuxembourg3 | Dark | Mixt | -0.1495026 | 1.3088923 | 97.84540 | -0.1142207 | 0.9092969 |
| Treatment_bisMixt_smart:RegionLuxembourg3 | Dark | Mixt | -3.2353629 | 1.2835430 | 99.19703 | -2.5206502 | 0.0133081 |
| (Intercept)5 | Dark | Night | 3.0021643 | 0.7223312 | 37.84380 | 4.1562156 | 0.0001781 |
| Treatment_bisFull4 | Dark | Night | 0.2318236 | 0.7397703 | 98.96292 | 0.3133724 | 0.7546572 |
| Treatment_bisSmart4 | Dark | Night | 0.2418887 | 0.9949681 | 98.11963 | 0.2431120 | 0.8084261 |
| Treatment_bisMixt_smart4 | Dark | Night | 1.1429663 | 0.8171944 | 96.35283 | 1.3986467 | 0.1651295 |
| RegionLuxembourg5 | Dark | Night | 0.3409062 | 0.9237507 | 36.19537 | 0.3690457 | 0.7142438 |
| Treatment_FTLDay1 | Dark | Night | 2.2068158 | 0.5749289 | 98.41001 | 3.8384152 | 0.0002190 |
| Treatment_FTLMix4 | Dark | Night | 1.4228919 | 0.5450307 | 100.00724 | 2.6106639 | 0.0104258 |
| Treatment_bisFull:RegionLuxembourg4 | Dark | Night | -2.1083268 | 1.1350373 | 100.28576 | -1.8574956 | 0.0661749 |
| Treatment_bisSmart:RegionLuxembourg4 | Dark | Night | -0.1494266 | 1.3088741 | 97.84774 | -0.1141642 | 0.9093415 |
| Treatment_bisMixt_smart:RegionLuxembourg4 | Dark | Night | -3.2354144 | 1.2835296 | 99.19836 | -2.5207167 | 0.0133057 |
Info_First_move <- "
Le traitement Night diminue le temps mis avant le premier mouvement. Day et Mix ne sont pas significativement différent.
L'impacte du traitement Mixt_smart est différent (plus rapide dans le luxembourg) en fonction de la région d'ou provient la mère de la chenille qui passe le test. (Il est toujours significatif sauf quand comparé avec Full mais là la p val est de 0.06634)
"
Info_First_move## [1] "\nLe traitement Night diminue le temps mis avant le premier mouvement. Day et Mix ne sont pas significativement différent.\nL'impacte du traitement Mixt_smart est différent (plus rapide dans le luxembourg) en fonction de la région d'ou provient la mère de la chenille qui passe le test. (Il est toujours significatif sauf quand comparé avec Full mais là la p val est de 0.06634)\n"5.4.5 Visualisation
Summary_First_move <- Data %>%
filter(Treatment_FTL != "NA") %>%
group_by(Region, Treatment_FTL, Treatment_bis) %>%
summarise(Mean=mean(log(First_move+0.1)),
Var=var(log(First_move+0.1)),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))## Warning: There were 4 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `CI_S = Mean + qt(0.975, N - 1) * sqrt(Var/N)`.
## ℹ In group 2: `Region = Brabant`, `Treatment_FTL = Mix`.
## Caused by warning in `qt()`:
## ! Production de NaN
## ℹ Run ]8;;ide:run:dplyr::last_dplyr_warnings()dplyr::last_dplyr_warnings()]8;; to see the 3 remaining warnings.ggplot(Summary_First_move, aes(x=Treatment_bis, y=Mean, color = Treatment_FTL))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5, position = "dodge") +
geom_point(alpha = 1) +
facet_wrap(~Region) +
labs(title = "First move", x = "Treatment", y = "log(Time to have the first move)") +
theme_bw()## Warning: Removed 8 rows containing missing values (`geom_point()`).
ggplot(data = Data %>% filter(Treatment_FTL != "NA"), aes(x = Treatment_bis, y = log(First_move+0.1), color = Treatment_FTL)) +
geom_boxplot() +
geom_point(position = position_dodge(width = 1), alpha = 0.75, data = Data %>% filter(Treatment_FTL == "Day" | Treatment_FTL == "Night")) +
geom_point(alpha = 0.75, data = Data %>% filter(Treatment_FTL == "Mix")) +
labs(title = "Temps pour faire le premier mouvement", x = "Tratiement", y = "log(Temps pour faire le premier mouvement (s))", color = "Timing" ) +
theme_bw()## Warning: Removed 9 rows containing non-finite values (`stat_boxplot()`).## Warning: Removed 6 rows containing missing values (`geom_point()`).## Warning: Removed 3 rows containing missing values (`geom_point()`).
5.5 Flight_to_light
5.5.1 Test
LM_Flight_to_light <- lmer(Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis, data = Data)## boundary (singular) fit: see help('isSingular')summary(LM_Flight_to_light)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL +
## Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) +
## Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex +
## Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex +
## Light_orientation:Region + Light_orientation:Treatment_bis
## Data: Data
##
## REML criterion at convergence: 486.7
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.4162 -0.4591 -0.0566 0.4457 1.7175
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000e+00 0.00000
## Site (Intercept) 3.745e+04 193.51786
## Room (Intercept) 1.555e-04 0.01247
## Residual 2.097e+05 457.89263
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 933.11 453.86 22.66
## Treatment_bisFull 109.90 480.16 23.32
## Treatment_bisSmart 1109.56 782.78 26.35
## Treatment_bisMixt_smart -585.49 896.25 29.97
## SexMale -280.25 531.70 29.92
## RegionLuxembourg -343.88 514.54 24.61
## Treatment_FTLMix 574.90 569.23 25.34
## Treatment_FTLNight 163.53 606.05 29.75
## Light_orientationSouth -956.89 426.65 23.65
## Treatment_bisFull:SexMale -146.48 495.83 29.03
## Treatment_bisSmart:SexMale 46.93 546.88 28.32
## Treatment_bisMixt_smart:SexMale 764.34 537.98 29.90
## Treatment_bisFull:RegionLuxembourg 484.93 498.36 23.82
## Treatment_bisSmart:RegionLuxembourg 420.91 619.22 27.37
## Treatment_bisMixt_smart:RegionLuxembourg -619.04 540.08 23.28
## SexMale:Treatment_FTLMix 196.37 565.71 29.68
## SexMale:Treatment_FTLNight 260.03 529.73 29.96
## RegionLuxembourg:Treatment_FTLMix -762.66 554.75 27.16
## RegionLuxembourg:Treatment_FTLNight -438.99 522.17 29.86
## Treatment_bisFull:Treatment_FTLMix -630.28 561.74 27.61
## Treatment_bisSmart:Treatment_FTLMix -1382.99 1058.20 26.10
## Treatment_bisMixt_smart:Treatment_FTLMix 427.78 922.39 29.88
## Treatment_bisFull:Treatment_FTLNight -639.18 478.33 26.71
## Treatment_bisSmart:Treatment_FTLNight -1659.99 1048.85 27.91
## Treatment_bisMixt_smart:Treatment_FTLNight 268.56 793.97 29.66
## SexMale:Light_orientationSouth -48.11 378.69 24.05
## RegionLuxembourg:Light_orientationSouth 1030.20 400.28 28.25
## Treatment_bisFull:Light_orientationSouth 383.78 466.87 26.77
## Treatment_bisSmart:Light_orientationSouth -97.14 560.02 29.06
## Treatment_bisMixt_smart:Light_orientationSouth 539.27 476.18 27.90
## t value Pr(>|t|)
## (Intercept) 2.056 0.0515 .
## Treatment_bisFull 0.229 0.8210
## Treatment_bisSmart 1.417 0.1681
## Treatment_bisMixt_smart -0.653 0.5186
## SexMale -0.527 0.6020
## RegionLuxembourg -0.668 0.5101
## Treatment_FTLMix 1.010 0.3221
## Treatment_FTLNight 0.270 0.7892
## Light_orientationSouth -2.243 0.0346 *
## Treatment_bisFull:SexMale -0.295 0.7698
## Treatment_bisSmart:SexMale 0.086 0.9322
## Treatment_bisMixt_smart:SexMale 1.421 0.1657
## Treatment_bisFull:RegionLuxembourg 0.973 0.3403
## Treatment_bisSmart:RegionLuxembourg 0.680 0.5024
## Treatment_bisMixt_smart:RegionLuxembourg -1.146 0.2634
## SexMale:Treatment_FTLMix 0.347 0.7309
## SexMale:Treatment_FTLNight 0.491 0.6271
## RegionLuxembourg:Treatment_FTLMix -1.375 0.1804
## RegionLuxembourg:Treatment_FTLNight -0.841 0.4072
## Treatment_bisFull:Treatment_FTLMix -1.122 0.2715
## Treatment_bisSmart:Treatment_FTLMix -1.307 0.2026
## Treatment_bisMixt_smart:Treatment_FTLMix 0.464 0.6462
## Treatment_bisFull:Treatment_FTLNight -1.336 0.1927
## Treatment_bisSmart:Treatment_FTLNight -1.583 0.1248
## Treatment_bisMixt_smart:Treatment_FTLNight 0.338 0.7376
## SexMale:Light_orientationSouth -0.127 0.9000
## RegionLuxembourg:Light_orientationSouth 2.574 0.0156 *
## Treatment_bisFull:Light_orientationSouth 0.822 0.4183
## Treatment_bisSmart:Light_orientationSouth -0.173 0.8635
## Treatment_bisMixt_smart:Light_orientationSouth 1.132 0.2671
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 30 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Normalité des résidus
qqnorm(resid(LM_Flight_to_light))
qqline(resid(LM_Flight_to_light))
Homogénité des variances
plot(LM_Flight_to_light)
légère forme d’entonnoir mais c’est passable
Distance de cook
plot(cooks.distance(LM_Flight_to_light))
(cooks.distance(LM_Flight_to_light))## 204 207 214 215 226 227
## 4.420913e-03 1.554063e-02 1.791769e-01 2.822961e-01 6.240720e-02 1.939528e-01
## 242 247 248 249 252 258
## 1.973436e-01 1.236786e-02 2.989103e-02 2.749752e-02 8.168596e+00 2.385110e-03
## 262 266 271 272 274 275
## 2.303683e-03 1.244502e-03 3.049857e-04 8.899909e-02 2.865108e-03 7.886870e-03
## 276 278 299 300 302 303
## 2.349206e-01 3.001285e-02 7.657401e-02 5.148891e-02 1.494078e-02 1.147430e-01
## 305 310 315 316 319 327
## 1.554063e-02 9.959095e-03 2.973313e-02 8.530616e-02 3.779978e-02 3.584821e-02
## 332 342 356 358 359 360
## 5.157073e-04 7.482208e-03 2.663550e-03 5.616472e-02 2.504243e-02 1.169165e-01
## 366 367 369 372 383 384
## 7.109003e-03 2.351681e-03 5.139800e-02 2.351681e-03 1.587105e-04 2.793514e-05
## 389 393 395 398 399 400
## 1.274773e-01 1.067810e-01 1.274773e-01 5.058466e-04 5.139800e-02 6.415542e-03
## 407 408 412 414 415 421
## 1.067810e-01 2.301799e-04 1.606555e-01 2.951929e-04 1.212960e-01 5.972077e-03
## 426 439 440 441 442 445
## 2.605002e-02 2.410862e-06 1.030623e-02 2.109382e-02 4.921083e-06 6.183630e-03Nous avons un problème avec le point de la ligne 252 sans trop savoir pourquoi honnètement. On va juste le retirer
LM_Flight_to_light <- lmer(Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis, data = Data[-252,])## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## boundary (singular) fit: see help('isSingular')summary(LM_Flight_to_light)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL +
## Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) +
## Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex +
## Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex +
## Light_orientation:Region + Light_orientation:Treatment_bis
## Data: Data[-252, ]
##
## REML criterion at convergence: 486.7
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.41618 -0.46115 -0.07309 0.45227 1.71754
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0 0.0
## Site (Intercept) 37448 193.5
## Room (Intercept) 0 0.0
## Residual 209666 457.9
## Number of obs: 59, groups: Mother, 20; Site, 12; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 933.11 453.86 22.66
## Treatment_bisFull 109.90 480.16 23.32
## Treatment_bisSmart 1109.56 782.78 26.35
## Treatment_bisMixt_smart -316.93 589.81 29.72
## SexMale -280.24 531.70 29.92
## RegionLuxembourg -343.88 514.54 24.61
## Treatment_FTLMix 574.90 569.23 25.34
## Treatment_FTLNight 163.53 606.05 29.75
## Light_orientationSouth -956.89 426.65 23.65
## Treatment_bisFull:SexMale -146.48 495.83 29.03
## Treatment_bisSmart:SexMale 46.93 546.88 28.32
## Treatment_bisMixt_smart:SexMale 764.34 537.98 29.90
## Treatment_bisFull:RegionLuxembourg 484.93 498.36 23.82
## Treatment_bisSmart:RegionLuxembourg 420.91 619.22 27.37
## Treatment_bisMixt_smart:RegionLuxembourg -619.04 540.08 23.28
## SexMale:Treatment_FTLMix 196.37 565.71 29.68
## SexMale:Treatment_FTLNight 260.03 529.73 29.96
## RegionLuxembourg:Treatment_FTLMix -762.66 554.75 27.16
## RegionLuxembourg:Treatment_FTLNight -438.99 522.17 29.86
## Treatment_bisFull:Treatment_FTLMix -630.27 561.74 27.61
## Treatment_bisSmart:Treatment_FTLMix -1382.98 1058.20 26.10
## Treatment_bisMixt_smart:Treatment_FTLMix 159.22 577.10 29.43
## Treatment_bisFull:Treatment_FTLNight -639.18 478.33 26.71
## Treatment_bisSmart:Treatment_FTLNight -1659.98 1048.85 27.91
## SexMale:Light_orientationSouth -48.11 378.69 24.05
## RegionLuxembourg:Light_orientationSouth 1030.19 400.28 28.25
## Treatment_bisFull:Light_orientationSouth 383.78 466.87 26.77
## Treatment_bisSmart:Light_orientationSouth -97.13 560.02 29.06
## Treatment_bisMixt_smart:Light_orientationSouth 539.27 476.18 27.90
## t value Pr(>|t|)
## (Intercept) 2.056 0.0515 .
## Treatment_bisFull 0.229 0.8210
## Treatment_bisSmart 1.417 0.1681
## Treatment_bisMixt_smart -0.537 0.5950
## SexMale -0.527 0.6020
## RegionLuxembourg -0.668 0.5101
## Treatment_FTLMix 1.010 0.3221
## Treatment_FTLNight 0.270 0.7892
## Light_orientationSouth -2.243 0.0346 *
## Treatment_bisFull:SexMale -0.295 0.7698
## Treatment_bisSmart:SexMale 0.086 0.9322
## Treatment_bisMixt_smart:SexMale 1.421 0.1657
## Treatment_bisFull:RegionLuxembourg 0.973 0.3403
## Treatment_bisSmart:RegionLuxembourg 0.680 0.5024
## Treatment_bisMixt_smart:RegionLuxembourg -1.146 0.2634
## SexMale:Treatment_FTLMix 0.347 0.7309
## SexMale:Treatment_FTLNight 0.491 0.6271
## RegionLuxembourg:Treatment_FTLMix -1.375 0.1804
## RegionLuxembourg:Treatment_FTLNight -0.841 0.4072
## Treatment_bisFull:Treatment_FTLMix -1.122 0.2715
## Treatment_bisSmart:Treatment_FTLMix -1.307 0.2026
## Treatment_bisMixt_smart:Treatment_FTLMix 0.276 0.7846
## Treatment_bisFull:Treatment_FTLNight -1.336 0.1927
## Treatment_bisSmart:Treatment_FTLNight -1.583 0.1248
## SexMale:Light_orientationSouth -0.127 0.9000
## RegionLuxembourg:Light_orientationSouth 2.574 0.0156 *
## Treatment_bisFull:Light_orientationSouth 0.822 0.4183
## Treatment_bisSmart:Light_orientationSouth -0.173 0.8635
## Treatment_bisMixt_smart:Light_orientationSouth 1.132 0.2671
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 29 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Normalité des résidus
qqnorm(resid(LM_Flight_to_light))
qqline(resid(LM_Flight_to_light))
Homogénité des variances
plot(LM_Flight_to_light)
légère forme d’entonnoir mais c’est passable
Distance de cook
plot(cooks.distance(LM_Flight_to_light))
5.5.2 Simplification du modèle
drop1(LM_Flight_to_light)## Single term deletions using Satterthwaite's method:
##
## Model:
## Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 1032054 344018 3 26.889 1.6408 0.20339
## Treatment_bis:Region 1436744 478915 3 26.647 2.2842 0.10188
## Sex:Treatment_FTL 50802 25401 2 28.940 0.1211 0.88635
## Region:Treatment_FTL 442881 221441 2 27.172 1.0562 0.36164
## Treatment_bis:Treatment_FTL 756215 151243 5 27.410 0.7214 0.61310
## Sex:Light_orientation 3384 3384 1 24.049 0.0161 0.89997
## Region:Light_orientation 1388805 1388805 1 28.245 6.6239 0.01559 *
## Treatment_bis:Light_orientation 467224 155741 3 27.949 0.7428 0.53558
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Flight_to_light1 <- update(LM_Flight_to_light, . ~ . - Treatment_bis:Treatment_FTL)## boundary (singular) fit: see help('isSingular')drop1(LM_Flight_to_light1)## Single term deletions using Satterthwaite's method:
##
## Model:
## Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Treatment_FTL + Region:Treatment_FTL + Sex:Light_orientation + Region:Light_orientation + Treatment_bis:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 1167873 389291 3 34.518 1.7969 0.16604
## Treatment_bis:Region 1333349 444450 3 32.977 2.0515 0.12571
## Sex:Treatment_FTL 268172 134086 2 31.559 0.6189 0.54493
## Region:Treatment_FTL 289666 144833 2 31.752 0.6685 0.51953
## Sex:Light_orientation 34236 34236 1 33.071 0.1580 0.69353
## Region:Light_orientation 942283 942283 1 33.450 4.3495 0.04472 *
## Treatment_bis:Light_orientation 337123 112374 3 34.536 0.5187 0.67220
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Flight_to_light2 <- update(LM_Flight_to_light1, . ~ . - Sex:Light_orientation)## boundary (singular) fit: see help('isSingular')drop1(LM_Flight_to_light2)## Single term deletions using Satterthwaite's method:
##
## Model:
## Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Treatment_FTL + Region:Treatment_FTL + Region:Light_orientation + Treatment_bis:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 1139070 379690 3 35.708 1.7833 0.1679
## Treatment_bis:Region 1308846 436282 3 34.088 2.0491 0.1254
## Sex:Treatment_FTL 249143 124572 2 32.104 0.5851 0.5629
## Region:Treatment_FTL 263422 131711 2 33.034 0.6186 0.5448
## Region:Light_orientation 905198 905198 1 34.135 4.2514 0.0469 *
## Treatment_bis:Light_orientation 314518 104839 3 35.637 0.4924 0.6898
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Flight_to_light3 <- update(LM_Flight_to_light2, . ~ . - Treatment_bis:Light_orientation)## boundary (singular) fit: see help('isSingular')drop1(LM_Flight_to_light3)## Single term deletions using Satterthwaite's method:
##
## Model:
## Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Treatment_FTL + Region:Treatment_FTL + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 1024957 341652 3 38.798 1.6833 0.18647
## Treatment_bis:Region 1234816 411605 3 36.639 2.0280 0.12695
## Sex:Treatment_FTL 255420 127710 2 34.161 0.6292 0.53906
## Region:Treatment_FTL 241094 120547 2 32.685 0.5939 0.55800
## Region:Light_orientation 916542 916542 1 36.237 4.5159 0.04047 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Flight_to_light4 <- update(LM_Flight_to_light3, . ~ . - Region:Treatment_FTL)## boundary (singular) fit: see help('isSingular')drop1(LM_Flight_to_light4)## Single term deletions using Satterthwaite's method:
##
## Model:
## Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Treatment_FTL + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 1055211 351737 3 41 1.7315 0.17554
## Treatment_bis:Region 1301461 433820 3 41 2.1356 0.11045
## Sex:Treatment_FTL 223075 111537 2 41 0.5491 0.58167
## Region:Light_orientation 843518 843518 1 41 4.1525 0.04806 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Flight_to_light5 <- update(LM_Flight_to_light4, . ~ . - Sex:Treatment_FTL)## boundary (singular) fit: see help('isSingular')drop1(LM_Flight_to_light5)## Single term deletions using Satterthwaite's method:
##
## Model:
## Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_FTL 897179 448589 2 43 2.2556 0.11707
## Treatment_bis:Sex 1212300 404100 3 43 2.0319 0.12359
## Treatment_bis:Region 1456693 485564 3 43 2.4416 0.07716 .
## Region:Light_orientation 812870 812870 1 43 4.0873 0.04946 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Flight_to_light6 <- update(LM_Flight_to_light5, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_Flight_to_light6)## Single term deletions using Satterthwaite's method:
##
## Model:
## Flight_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 62844 62844 1 45.725 0.2961 0.58896
## Treatment_FTL 980069 490034 2 44.229 2.3092 0.11120
## Treatment_bis:Region 2085105 695035 3 43.542 3.2752 0.02984 *
## Region:Light_orientation 910704 910704 1 43.839 4.2915 0.04422 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Les seules interactions qui restent sont significatives donc on les laisse.
LM_Flight_to_light <- LM_Flight_to_light65.5.3 Treatment VS Teatment_bis
AIC(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data))## boundary (singular) fit: see help('isSingular')## [1] 222.9282AIC(lmer(log(Flight_to_light+0.1) ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region + Region:Light_orientation , data = Data))## boundary (singular) fit: see help('isSingular')## [1] 228.2195summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 7.5371419 0.7578269 43.39270
## Treatment_bisFull -0.8894182 0.8175556 43.65873
## Treatment_bisSmart 0.9772394 0.8960778 42.04335
## Treatment_bisMixt_smart 0.8872505 0.8369004 42.39478
## SexMale 0.1549360 0.3816299 45.07619
## RegionLuxembourg -1.7455601 0.8448226 43.99869
## Treatment_FTLMix -1.4984334 0.5997217 44.82190
## Treatment_FTLNight -1.4710087 0.5557108 46.55908
## Light_orientationSouth -1.7221106 0.6291575 39.96183
## Treatment_bisFull:RegionLuxembourg 1.0369952 1.0220248 40.37219
## Treatment_bisSmart:RegionLuxembourg -0.1789724 1.1503728 40.75477
## Treatment_bisMixt_smart:RegionLuxembourg -2.0686921 1.0923982 39.74051
## RegionLuxembourg:Light_orientationSouth 2.8082442 0.7981288 43.48096
## t value Pr(>|t|)
## (Intercept) 9.9457300 9.208866e-13
## Treatment_bisFull -1.0878993 2.826090e-01
## Treatment_bisSmart 1.0905743 2.816712e-01
## Treatment_bisMixt_smart 1.0601626 2.950734e-01
## SexMale 0.4059849 6.866746e-01
## RegionLuxembourg -2.0661854 4.472916e-02
## Treatment_FTLMix -2.4985479 1.620539e-02
## Treatment_FTLNight -2.6470760 1.104281e-02
## Light_orientationSouth -2.7371695 9.204666e-03
## Treatment_bisFull:RegionLuxembourg 1.0146478 3.163162e-01
## Treatment_bisSmart:RegionLuxembourg -0.1555777 8.771339e-01
## Treatment_bisMixt_smart:RegionLuxembourg -1.8937162 6.555869e-02
## RegionLuxembourg:Light_orientationSouth 3.5185351 1.030487e-03summary(lmer(log(Flight_to_light+0.1) ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region + Region:Light_orientation , data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 7.5448061 0.8233584 21.90040
## TreatmentFull -0.9857974 0.8537022 45.70729
## TreatmentSmart 0.8441239 0.7746380 43.25969
## SexMale 0.2860856 0.3946037 47.73426
## RegionLuxembourg -1.6398141 0.8797691 46.68934
## Treatment_FTLMix -1.5432569 0.6167422 45.41727
## Treatment_FTLNight -1.4067140 0.5640784 47.17294
## Light_orientationSouth -1.6643066 0.6554100 42.65889
## TreatmentFull:RegionLuxembourg 1.1285450 1.0767938 43.48971
## TreatmentSmart:RegionLuxembourg -0.9269634 1.0133546 42.54166
## RegionLuxembourg:Light_orientationSouth 2.3001945 0.8027440 44.45446
## t value Pr(>|t|)
## (Intercept) 9.1634527 6.012290e-09
## TreatmentFull -1.1547321 2.542017e-01
## TreatmentSmart 1.0897011 2.818779e-01
## SexMale 0.7249947 4.719944e-01
## RegionLuxembourg -1.8639142 6.862879e-02
## Treatment_FTLMix -2.5022723 1.600603e-02
## Treatment_FTLNight -2.4938273 1.619967e-02
## Light_orientationSouth -2.5393365 1.483567e-02
## TreatmentFull:RegionLuxembourg 1.0480605 3.004006e-01
## TreatmentSmart:RegionLuxembourg -0.9147473 3.654803e-01
## RegionLuxembourg:Light_orientationSouth 2.8654148 6.338759e-03On garde Treatment_bis
5.5.4 Résultats
Analyse des p-val
summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log(Flight_to_light + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL +
## Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) +
## Treatment_bis:Region + Region:Light_orientation
## Data: Data
##
## REML criterion at convergence: 188.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.77230 -0.55949 0.05376 0.62568 1.74354
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.331e-01 5.771e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 1.431e-09 3.783e-05
## Residual 1.613e+00 1.270e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 7.5371 0.7578 43.3927 9.946
## Treatment_bisFull -0.8894 0.8176 43.6587 -1.088
## Treatment_bisSmart 0.9772 0.8961 42.0433 1.091
## Treatment_bisMixt_smart 0.8873 0.8369 42.3948 1.060
## SexMale 0.1549 0.3816 45.0762 0.406
## RegionLuxembourg -1.7456 0.8448 43.9987 -2.066
## Treatment_FTLMix -1.4984 0.5997 44.8219 -2.499
## Treatment_FTLNight -1.4710 0.5557 46.5591 -2.647
## Light_orientationSouth -1.7221 0.6292 39.9618 -2.737
## Treatment_bisFull:RegionLuxembourg 1.0370 1.0220 40.3722 1.015
## Treatment_bisSmart:RegionLuxembourg -0.1790 1.1504 40.7548 -0.156
## Treatment_bisMixt_smart:RegionLuxembourg -2.0687 1.0924 39.7405 -1.894
## RegionLuxembourg:Light_orientationSouth 2.8082 0.7981 43.4810 3.519
## Pr(>|t|)
## (Intercept) 9.21e-13 ***
## Treatment_bisFull 0.28261
## Treatment_bisSmart 0.28167
## Treatment_bisMixt_smart 0.29507
## SexMale 0.68667
## RegionLuxembourg 0.04473 *
## Treatment_FTLMix 0.01621 *
## Treatment_FTLNight 0.01104 *
## Light_orientationSouth 0.00920 **
## Treatment_bisFull:RegionLuxembourg 0.31632
## Treatment_bisSmart:RegionLuxembourg 0.87713
## Treatment_bisMixt_smart:RegionLuxembourg 0.06556 .
## RegionLuxembourg:Light_orientationSouth 0.00103 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 13 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log(Flight_to_light + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL +
## Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) +
## Treatment_bis:Region + Region:Light_orientation
## Data: Data_ref_full
##
## REML criterion at convergence: 188.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.77230 -0.55949 0.05376 0.62568 1.74354
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.331e-01 5.771e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 1.431e-09 3.783e-05
## Residual 1.613e+00 1.270e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 6.6477 0.8297 46.5214 8.013
## Treatment_bisDark 0.8894 0.8176 43.6587 1.088
## Treatment_bisSmart 1.8667 0.8614 43.1593 2.167
## Treatment_bisMixt_smart 1.7767 0.7614 45.9641 2.334
## SexMale 0.1549 0.3816 45.0762 0.406
## RegionLuxembourg -0.7086 0.8425 45.1167 -0.841
## Treatment_FTLMix -1.4984 0.5997 44.8219 -2.499
## Treatment_FTLNight -1.4710 0.5557 46.5591 -2.647
## Light_orientationSouth -1.7221 0.6292 39.9618 -2.737
## Treatment_bisDark:RegionLuxembourg -1.0370 1.0220 40.3722 -1.015
## Treatment_bisSmart:RegionLuxembourg -1.2160 1.0595 42.2494 -1.148
## Treatment_bisMixt_smart:RegionLuxembourg -3.1057 0.9869 44.0551 -3.147
## RegionLuxembourg:Light_orientationSouth 2.8082 0.7981 43.4810 3.519
## Pr(>|t|)
## (Intercept) 2.62e-10 ***
## Treatment_bisDark 0.28261
## Treatment_bisSmart 0.03580 *
## Treatment_bisMixt_smart 0.02405 *
## SexMale 0.68667
## RegionLuxembourg 0.40479
## Treatment_FTLMix 0.01621 *
## Treatment_FTLNight 0.01104 *
## Light_orientationSouth 0.00920 **
## Treatment_bisDark:RegionLuxembourg 0.31632
## Treatment_bisSmart:RegionLuxembourg 0.25757
## Treatment_bisMixt_smart:RegionLuxembourg 0.00296 **
## RegionLuxembourg:Light_orientationSouth 0.00103 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 13 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log(Flight_to_light + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL +
## Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) +
## Treatment_bis:Region + Region:Light_orientation
## Data: Data_ref_smart
##
## REML criterion at convergence: 188.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.77230 -0.55949 0.05376 0.62568 1.74354
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.331e-01 5.771e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 1.431e-09 3.783e-05
## Residual 1.613e+00 1.270e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 8.51438 0.83974 42.75772 10.139
## Treatment_bisDark -0.97724 0.89608 42.04335 -1.091
## Treatment_bisFull -1.86666 0.86139 43.15933 -2.167
## Treatment_bisMixt_smart -0.08999 0.89928 45.15476 -0.100
## SexMale 0.15494 0.38163 45.07619 0.406
## RegionLuxembourg -1.92453 0.91578 46.91737 -2.102
## Treatment_FTLMix -1.49843 0.59972 44.82190 -2.499
## Treatment_FTLNight -1.47101 0.55571 46.55908 -2.647
## Light_orientationSouth -1.72211 0.62916 39.96183 -2.737
## Treatment_bisDark:RegionLuxembourg 0.17897 1.15037 40.75477 0.156
## Treatment_bisFull:RegionLuxembourg 1.21597 1.05952 42.24940 1.148
## Treatment_bisMixt_smart:RegionLuxembourg -1.88972 1.16430 43.84133 -1.623
## RegionLuxembourg:Light_orientationSouth 2.80824 0.79813 43.48096 3.519
## Pr(>|t|)
## (Intercept) 6.04e-13 ***
## Treatment_bisDark 0.28167
## Treatment_bisFull 0.03580 *
## Treatment_bisMixt_smart 0.92073
## SexMale 0.68667
## RegionLuxembourg 0.04099 *
## Treatment_FTLMix 0.01621 *
## Treatment_FTLNight 0.01104 *
## Light_orientationSouth 0.00920 **
## Treatment_bisDark:RegionLuxembourg 0.87713
## Treatment_bisFull:RegionLuxembourg 0.25757
## Treatment_bisMixt_smart:RegionLuxembourg 0.11175
## RegionLuxembourg:Light_orientationSouth 0.00103 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 13 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data_ref_mixt_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log(Flight_to_light + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL +
## Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) +
## Treatment_bis:Region + Region:Light_orientation
## Data: Data_ref_mixt_smart
##
## REML criterion at convergence: 188.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.77230 -0.55949 0.05376 0.62568 1.74354
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.331e-01 5.771e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 1.431e-09 3.783e-05
## Residual 1.613e+00 1.270e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 8.42439 0.87690 45.45552 9.607
## Treatment_bisDark -0.88725 0.83690 42.39478 -1.060
## Treatment_bisFull -1.77667 0.76135 45.96407 -2.334
## Treatment_bisSmart 0.08999 0.89928 45.15476 0.100
## SexMale 0.15494 0.38163 45.07619 0.406
## RegionLuxembourg -3.81425 0.96809 46.40804 -3.940
## Treatment_FTLMix -1.49843 0.59972 44.82190 -2.499
## Treatment_FTLNight -1.47101 0.55571 46.55908 -2.647
## Light_orientationSouth -1.72211 0.62916 39.96183 -2.737
## Treatment_bisDark:RegionLuxembourg 2.06869 1.09240 39.74051 1.894
## Treatment_bisFull:RegionLuxembourg 3.10569 0.98691 44.05509 3.147
## Treatment_bisSmart:RegionLuxembourg 1.88972 1.16430 43.84133 1.623
## RegionLuxembourg:Light_orientationSouth 2.80824 0.79813 43.48096 3.519
## Pr(>|t|)
## (Intercept) 1.62e-12 ***
## Treatment_bisDark 0.295073
## Treatment_bisFull 0.024047 *
## Treatment_bisSmart 0.920733
## SexMale 0.686675
## RegionLuxembourg 0.000272 ***
## Treatment_FTLMix 0.016205 *
## Treatment_FTLNight 0.011043 *
## Light_orientationSouth 0.009205 **
## Treatment_bisDark:RegionLuxembourg 0.065559 .
## Treatment_bisFull:RegionLuxembourg 0.002957 **
## Treatment_bisSmart:RegionLuxembourg 0.111749
## RegionLuxembourg:Light_orientationSouth 0.001030 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 13 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data_refFTL_Night))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log(Flight_to_light + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL +
## Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) +
## Treatment_bis:Region + Region:Light_orientation
## Data: Data_refFTL_Night
##
## REML criterion at convergence: 188.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.77230 -0.55949 0.05376 0.62568 1.74354
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.331e-01 5.771e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 1.431e-09 3.783e-05
## Residual 1.613e+00 1.270e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 6.06613 0.64973 46.00047 9.336
## Treatment_bisFull -0.88942 0.81756 43.65873 -1.088
## Treatment_bisSmart 0.97724 0.89608 42.04335 1.091
## Treatment_bisMixt_smart 0.88725 0.83690 42.39478 1.060
## SexMale 0.15494 0.38163 45.07619 0.406
## RegionLuxembourg -1.74556 0.84482 43.99869 -2.066
## Treatment_FTLDay 1.47101 0.55571 46.55908 2.647
## Treatment_FTLMix -0.02742 0.41244 46.56432 -0.066
## Light_orientationSouth -1.72211 0.62916 39.96183 -2.737
## Treatment_bisFull:RegionLuxembourg 1.03700 1.02202 40.37219 1.015
## Treatment_bisSmart:RegionLuxembourg -0.17897 1.15037 40.75477 -0.156
## Treatment_bisMixt_smart:RegionLuxembourg -2.06869 1.09240 39.74051 -1.894
## RegionLuxembourg:Light_orientationSouth 2.80824 0.79813 43.48096 3.519
## Pr(>|t|)
## (Intercept) 3.45e-12 ***
## Treatment_bisFull 0.28261
## Treatment_bisSmart 0.28167
## Treatment_bisMixt_smart 0.29507
## SexMale 0.68667
## RegionLuxembourg 0.04473 *
## Treatment_FTLDay 0.01104 *
## Treatment_FTLMix 0.94727
## Light_orientationSouth 0.00920 **
## Treatment_bisFull:RegionLuxembourg 0.31632
## Treatment_bisSmart:RegionLuxembourg 0.87713
## Treatment_bisMixt_smart:RegionLuxembourg 0.06556 .
## RegionLuxembourg:Light_orientationSouth 0.00103 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 13 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data_refFTL_Mix))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log(Flight_to_light + 0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL +
## Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) +
## Treatment_bis:Region + Region:Light_orientation
## Data: Data_refFTL_Mix
##
## REML criterion at convergence: 188.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.77230 -0.55949 0.05376 0.62568 1.74354
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.331e-01 5.771e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 1.431e-09 3.783e-05
## Residual 1.613e+00 1.270e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 6.03871 0.65494 43.62492 9.220
## Treatment_bisFull -0.88942 0.81756 43.65873 -1.088
## Treatment_bisSmart 0.97724 0.89608 42.04335 1.091
## Treatment_bisMixt_smart 0.88725 0.83690 42.39478 1.060
## SexMale 0.15494 0.38163 45.07619 0.406
## RegionLuxembourg -1.74556 0.84482 43.99869 -2.066
## Treatment_FTLDay 1.49843 0.59972 44.82190 2.499
## Treatment_FTLNight 0.02742 0.41244 46.56432 0.066
## Light_orientationSouth -1.72211 0.62916 39.96183 -2.737
## Treatment_bisFull:RegionLuxembourg 1.03700 1.02202 40.37219 1.015
## Treatment_bisSmart:RegionLuxembourg -0.17897 1.15037 40.75477 -0.156
## Treatment_bisMixt_smart:RegionLuxembourg -2.06869 1.09240 39.74051 -1.894
## RegionLuxembourg:Light_orientationSouth 2.80824 0.79813 43.48096 3.519
## Pr(>|t|)
## (Intercept) 8.34e-12 ***
## Treatment_bisFull 0.28261
## Treatment_bisSmart 0.28167
## Treatment_bisMixt_smart 0.29507
## SexMale 0.68667
## RegionLuxembourg 0.04473 *
## Treatment_FTLDay 0.01621 *
## Treatment_FTLNight 0.94727
## Light_orientationSouth 0.00920 **
## Treatment_bisFull:RegionLuxembourg 0.31632
## Treatment_bisSmart:RegionLuxembourg 0.87713
## Treatment_bisMixt_smart:RegionLuxembourg 0.06556 .
## RegionLuxembourg:Light_orientationSouth 0.00103 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 13 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference_Treatment = "Smart", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference_Treatment = "Full", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test4 <- data.frame(Reference_Treatment = "Mixt_smart", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data_ref_mixt_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test5 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Mixt", as.data.frame(( summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data_refFTL_Mix))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test6 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Night", as.data.frame(( summary(lmer(log(Flight_to_light+0.1) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Light_orientation , data = Data_refFTL_Night))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_FTL <- rbind(test1,test2,test3,test4,test5,test6)
colnames(Results_FTL ) <- c("Reference_Treatment", "Reference_Timing" ,"Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_FTL , file = "output/Results_FTL.csv" )
kable(Results_FTL , caption = " Temps mis pour voler à la lumière ", padding = 1 )| Reference_Treatment | Reference_Timing | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|---|
| (Intercept) | Dark | Day | 7.5371419 | 0.7578269 | 43.39270 | 9.9457300 | 0.0000000 |
| Treatment_bisFull | Dark | Day | -0.8894182 | 0.8175556 | 43.65873 | -1.0878993 | 0.2826090 |
| Treatment_bisSmart | Dark | Day | 0.9772394 | 0.8960778 | 42.04335 | 1.0905743 | 0.2816712 |
| Treatment_bisMixt_smart | Dark | Day | 0.8872505 | 0.8369004 | 42.39478 | 1.0601626 | 0.2950734 |
| SexMale | Dark | Day | 0.1549360 | 0.3816299 | 45.07619 | 0.4059849 | 0.6866746 |
| RegionLuxembourg | Dark | Day | -1.7455601 | 0.8448226 | 43.99869 | -2.0661854 | 0.0447292 |
| Treatment_FTLMix | Dark | Day | -1.4984334 | 0.5997217 | 44.82190 | -2.4985479 | 0.0162054 |
| Treatment_FTLNight | Dark | Day | -1.4710087 | 0.5557108 | 46.55908 | -2.6470760 | 0.0110428 |
| Light_orientationSouth | Dark | Day | -1.7221106 | 0.6291575 | 39.96183 | -2.7371695 | 0.0092047 |
| Treatment_bisFull:RegionLuxembourg | Dark | Day | 1.0369952 | 1.0220248 | 40.37219 | 1.0146478 | 0.3163162 |
| Treatment_bisSmart:RegionLuxembourg | Dark | Day | -0.1789724 | 1.1503728 | 40.75477 | -0.1555777 | 0.8771339 |
| Treatment_bisMixt_smart:RegionLuxembourg | Dark | Day | -2.0686921 | 1.0923982 | 39.74051 | -1.8937162 | 0.0655587 |
| RegionLuxembourg:Light_orientationSouth | Dark | Day | 2.8082442 | 0.7981288 | 43.48096 | 3.5185351 | 0.0010305 |
| (Intercept)1 | Smart | Day | 8.5143813 | 0.8397396 | 42.75772 | 10.1393115 | 0.0000000 |
| Treatment_bisDark | Smart | Day | -0.9772394 | 0.8960778 | 42.04335 | -1.0905743 | 0.2816712 |
| Treatment_bisFull1 | Smart | Day | -1.8666576 | 0.8613917 | 43.15933 | -2.1670254 | 0.0357966 |
| Treatment_bisMixt_smart1 | Smart | Day | -0.0899889 | 0.8992770 | 45.15476 | -0.1000680 | 0.9207333 |
| SexMale1 | Smart | Day | 0.1549360 | 0.3816299 | 45.07619 | 0.4059849 | 0.6866746 |
| RegionLuxembourg1 | Smart | Day | -1.9245325 | 0.9157843 | 46.91737 | -2.1015130 | 0.0409934 |
| Treatment_FTLMix1 | Smart | Day | -1.4984334 | 0.5997217 | 44.82190 | -2.4985479 | 0.0162054 |
| Treatment_FTLNight1 | Smart | Day | -1.4710087 | 0.5557108 | 46.55908 | -2.6470760 | 0.0110428 |
| Light_orientationSouth1 | Smart | Day | -1.7221106 | 0.6291575 | 39.96183 | -2.7371695 | 0.0092047 |
| Treatment_bisDark:RegionLuxembourg | Smart | Day | 0.1789724 | 1.1503728 | 40.75477 | 0.1555777 | 0.8771339 |
| Treatment_bisFull:RegionLuxembourg1 | Smart | Day | 1.2159675 | 1.0595188 | 42.24940 | 1.1476602 | 0.2575661 |
| Treatment_bisMixt_smart:RegionLuxembourg1 | Smart | Day | -1.8897198 | 1.1643045 | 43.84133 | -1.6230460 | 0.1117495 |
| RegionLuxembourg:Light_orientationSouth1 | Smart | Day | 2.8082442 | 0.7981288 | 43.48096 | 3.5185351 | 0.0010305 |
| (Intercept)2 | Full | Day | 6.6477237 | 0.8296690 | 46.52137 | 8.0125011 | 0.0000000 |
| Treatment_bisDark1 | Full | Day | 0.8894182 | 0.8175556 | 43.65873 | 1.0878993 | 0.2826090 |
| Treatment_bisSmart1 | Full | Day | 1.8666576 | 0.8613917 | 43.15933 | 2.1670254 | 0.0357966 |
| Treatment_bisMixt_smart2 | Full | Day | 1.7766688 | 0.7613513 | 45.96407 | 2.3335728 | 0.0240470 |
| SexMale2 | Full | Day | 0.1549360 | 0.3816299 | 45.07619 | 0.4059849 | 0.6866746 |
| RegionLuxembourg2 | Full | Day | -0.7085650 | 0.8425465 | 45.11672 | -0.8409803 | 0.4047942 |
| Treatment_FTLMix2 | Full | Day | -1.4984334 | 0.5997217 | 44.82190 | -2.4985479 | 0.0162054 |
| Treatment_FTLNight2 | Full | Day | -1.4710087 | 0.5557108 | 46.55908 | -2.6470760 | 0.0110428 |
| Light_orientationSouth2 | Full | Day | -1.7221106 | 0.6291575 | 39.96183 | -2.7371695 | 0.0092047 |
| Treatment_bisDark:RegionLuxembourg1 | Full | Day | -1.0369952 | 1.0220248 | 40.37219 | -1.0146478 | 0.3163162 |
| Treatment_bisSmart:RegionLuxembourg1 | Full | Day | -1.2159675 | 1.0595188 | 42.24940 | -1.1476602 | 0.2575661 |
| Treatment_bisMixt_smart:RegionLuxembourg2 | Full | Day | -3.1056873 | 0.9869123 | 44.05509 | -3.1468725 | 0.0029572 |
| RegionLuxembourg:Light_orientationSouth2 | Full | Day | 2.8082442 | 0.7981288 | 43.48096 | 3.5185351 | 0.0010305 |
| (Intercept)3 | Mixt_smart | Day | 8.4243925 | 0.8769003 | 45.45552 | 9.6070130 | 0.0000000 |
| Treatment_bisDark2 | Mixt_smart | Day | -0.8872505 | 0.8369004 | 42.39478 | -1.0601626 | 0.2950734 |
| Treatment_bisFull2 | Mixt_smart | Day | -1.7766688 | 0.7613513 | 45.96407 | -2.3335728 | 0.0240470 |
| Treatment_bisSmart2 | Mixt_smart | Day | 0.0899889 | 0.8992770 | 45.15476 | 0.1000680 | 0.9207333 |
| SexMale3 | Mixt_smart | Day | 0.1549360 | 0.3816299 | 45.07619 | 0.4059849 | 0.6866746 |
| RegionLuxembourg3 | Mixt_smart | Day | -3.8142523 | 0.9680899 | 46.40804 | -3.9399773 | 0.0002724 |
| Treatment_FTLMix3 | Mixt_smart | Day | -1.4984334 | 0.5997217 | 44.82190 | -2.4985479 | 0.0162054 |
| Treatment_FTLNight3 | Mixt_smart | Day | -1.4710087 | 0.5557108 | 46.55908 | -2.6470760 | 0.0110428 |
| Light_orientationSouth3 | Mixt_smart | Day | -1.7221106 | 0.6291575 | 39.96183 | -2.7371695 | 0.0092047 |
| Treatment_bisDark:RegionLuxembourg2 | Mixt_smart | Day | 2.0686921 | 1.0923982 | 39.74051 | 1.8937162 | 0.0655587 |
| Treatment_bisFull:RegionLuxembourg2 | Mixt_smart | Day | 3.1056873 | 0.9869123 | 44.05509 | 3.1468725 | 0.0029572 |
| Treatment_bisSmart:RegionLuxembourg2 | Mixt_smart | Day | 1.8897198 | 1.1643045 | 43.84133 | 1.6230460 | 0.1117495 |
| RegionLuxembourg:Light_orientationSouth3 | Mixt_smart | Day | 2.8082442 | 0.7981288 | 43.48096 | 3.5185351 | 0.0010305 |
| (Intercept)4 | Dark | Mixt | 6.0387085 | 0.6549434 | 43.62492 | 9.2201994 | 0.0000000 |
| Treatment_bisFull3 | Dark | Mixt | -0.8894182 | 0.8175556 | 43.65873 | -1.0878993 | 0.2826090 |
| Treatment_bisSmart3 | Dark | Mixt | 0.9772394 | 0.8960778 | 42.04335 | 1.0905743 | 0.2816712 |
| Treatment_bisMixt_smart3 | Dark | Mixt | 0.8872505 | 0.8369004 | 42.39478 | 1.0601626 | 0.2950734 |
| SexMale4 | Dark | Mixt | 0.1549360 | 0.3816299 | 45.07619 | 0.4059849 | 0.6866746 |
| RegionLuxembourg4 | Dark | Mixt | -1.7455601 | 0.8448226 | 43.99869 | -2.0661854 | 0.0447292 |
| Treatment_FTLDay | Dark | Mixt | 1.4984334 | 0.5997217 | 44.82190 | 2.4985479 | 0.0162054 |
| Treatment_FTLNight4 | Dark | Mixt | 0.0274247 | 0.4124351 | 46.56432 | 0.0664946 | 0.9472688 |
| Light_orientationSouth4 | Dark | Mixt | -1.7221106 | 0.6291575 | 39.96183 | -2.7371695 | 0.0092047 |
| Treatment_bisFull:RegionLuxembourg3 | Dark | Mixt | 1.0369952 | 1.0220248 | 40.37219 | 1.0146478 | 0.3163162 |
| Treatment_bisSmart:RegionLuxembourg3 | Dark | Mixt | -0.1789724 | 1.1503728 | 40.75477 | -0.1555777 | 0.8771339 |
| Treatment_bisMixt_smart:RegionLuxembourg3 | Dark | Mixt | -2.0686921 | 1.0923982 | 39.74051 | -1.8937162 | 0.0655587 |
| RegionLuxembourg:Light_orientationSouth4 | Dark | Mixt | 2.8082442 | 0.7981288 | 43.48096 | 3.5185351 | 0.0010305 |
| (Intercept)5 | Dark | Night | 6.0661332 | 0.6497262 | 46.00047 | 9.3364448 | 0.0000000 |
| Treatment_bisFull4 | Dark | Night | -0.8894182 | 0.8175556 | 43.65873 | -1.0878993 | 0.2826090 |
| Treatment_bisSmart4 | Dark | Night | 0.9772394 | 0.8960778 | 42.04335 | 1.0905743 | 0.2816712 |
| Treatment_bisMixt_smart4 | Dark | Night | 0.8872505 | 0.8369004 | 42.39478 | 1.0601626 | 0.2950734 |
| SexMale5 | Dark | Night | 0.1549360 | 0.3816299 | 45.07619 | 0.4059849 | 0.6866746 |
| RegionLuxembourg5 | Dark | Night | -1.7455601 | 0.8448226 | 43.99869 | -2.0661854 | 0.0447292 |
| Treatment_FTLDay1 | Dark | Night | 1.4710087 | 0.5557108 | 46.55908 | 2.6470760 | 0.0110428 |
| Treatment_FTLMix4 | Dark | Night | -0.0274247 | 0.4124351 | 46.56432 | -0.0664946 | 0.9472688 |
| Light_orientationSouth5 | Dark | Night | -1.7221106 | 0.6291575 | 39.96183 | -2.7371695 | 0.0092047 |
| Treatment_bisFull:RegionLuxembourg4 | Dark | Night | 1.0369952 | 1.0220248 | 40.37219 | 1.0146478 | 0.3163162 |
| Treatment_bisSmart:RegionLuxembourg4 | Dark | Night | -0.1789724 | 1.1503728 | 40.75477 | -0.1555777 | 0.8771339 |
| Treatment_bisMixt_smart:RegionLuxembourg4 | Dark | Night | -2.0686921 | 1.0923982 | 39.74051 | -1.8937162 | 0.0655587 |
| RegionLuxembourg:Light_orientationSouth5 | Dark | Night | 2.8082442 | 0.7981288 | 43.48096 | 3.5185351 | 0.0010305 |
Info_Flight_to_light <- "
Les individus du expérimentés la nuit mettent significativement plus de temps que le traitement jour.
Le fait que la lampe soit orientée au Sud a impacte différent en fonction du sex expérimenté (les mâle sont plus lent)
"
Info_Flight_to_light## [1] "\nLes individus du expérimentés la nuit mettent significativement plus de temps que le traitement jour.\nLe fait que la lampe soit orientée au Sud a impacte différent en fonction du sex expérimenté (les mâle sont plus lent)\n"5.5.5 Visualisation
Summary_Flight_to_light <- Data %>%
filter(Treatment_FTL != "NA") %>%
group_by(Treatment_FTL, Treatment_bis) %>%
summarise(Mean=mean(log(Flight_to_light)),
Var=var(log(Flight_to_light)),
N=n()) %>%
mutate(CI_S=Mean+qt(0.975, N-1)*sqrt(Var/N),
CI_I=Mean-qt(0.975, N-1)*sqrt(Var/N))ggplot(Summary_Flight_to_light, aes(x=Treatment_bis, y=Mean, color = Treatment_FTL))+
geom_errorbar(aes(ymin=CI_I, ymax=CI_S),width=0.2,size = 1.2, alpha = 0.5, position = "dodge") +
geom_point(alpha = 1) +
labs(title = "Fly to light", x = "Treatment", y = "log(Time to have the first move)") +
theme_bw()## Warning: Removed 12 rows containing missing values (`geom_point()`).
ggplot(data = Data, aes(x = Treatment_bis, y = Flight_to_light, color = Treatment_FTL)) +
geom_boxplot() +
geom_point(position = position_dodge(width = 1), alpha = 0.75, data = Data %>% filter(Treatment_FTL == "Day" | Treatment_FTL == "Night")) +
geom_point(alpha = 0.75, data = Data %>% filter(Treatment_FTL == "Mix")) +
labs(title = "Temps pour voler à la lumière", x = "Tratiement", y = "Temps pour voler à la lumière (s)", color = "Timing" ) +
theme_bw()## Warning: Removed 390 rows containing non-finite values (`stat_boxplot()`).## Warning: Removed 42 rows containing missing values (`geom_point()`).## Warning: Removed 18 rows containing missing values (`geom_point()`).
5.6 Speed to light
5.6.1 Test
LM_Speed_to_light <- lmer(Speed_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis, data = Data)## boundary (singular) fit: see help('isSingular')summary(LM_Speed_to_light)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Speed_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL +
## Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) +
## Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex +
## Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex +
## Light_orientation:Region + Light_orientation:Treatment_bis
## Data: Data
##
## REML criterion at convergence: 691.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8376 -0.2980 -0.1061 0.1279 4.7052
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000e+00 0.0000000
## Site (Intercept) 3.317e-01 0.5758942
## Room (Intercept) 1.076e-08 0.0001037
## Residual 7.190e+01 8.4794774
## Number of obs: 119, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -0.6684 3.8476 61.7266
## Treatment_bisFull -0.6908 4.4362 86.7149
## Treatment_bisSmart -1.7895 5.7997 87.0917
## Treatment_bisMixt_smart -4.3715 5.7253 87.8189
## SexMale -0.8618 4.0410 88.5751
## RegionLuxembourg 1.3797 4.3133 54.4803
## Treatment_FTLMix 2.7056 4.2753 25.2134
## Treatment_FTLNight -0.2497 4.5397 53.0555
## Light_orientationSouth 3.1452 3.5320 86.6599
## Treatment_bisFull:SexMale 4.3769 4.3226 87.6676
## Treatment_bisSmart:SexMale 0.1742 5.3295 88.9601
## Treatment_bisMixt_smart:SexMale 2.9481 4.8289 77.6151
## Treatment_bisFull:RegionLuxembourg 1.8814 4.3474 88.9703
## Treatment_bisSmart:RegionLuxembourg 0.8324 5.1736 86.8273
## Treatment_bisMixt_smart:RegionLuxembourg 3.2665 5.7707 87.8793
## SexMale:Treatment_FTLMix 1.5762 4.2372 88.8126
## SexMale:Treatment_FTLNight -0.3888 4.2092 88.9353
## RegionLuxembourg:Treatment_FTLMix -2.7629 4.5199 46.0199
## RegionLuxembourg:Treatment_FTLNight 4.6347 4.4332 74.1899
## Treatment_bisFull:Treatment_FTLMix 0.7858 5.4630 88.8322
## Treatment_bisSmart:Treatment_FTLMix 0.2737 6.2240 87.2224
## Treatment_bisMixt_smart:Treatment_FTLMix 12.4439 7.2575 88.8583
## Treatment_bisFull:Treatment_FTLNight 3.2611 5.1365 86.2318
## Treatment_bisSmart:Treatment_FTLNight 0.1599 6.1174 87.7029
## Treatment_bisMixt_smart:Treatment_FTLNight -1.0548 5.8983 86.3624
## SexMale:Light_orientationSouth -0.7659 3.6449 85.9739
## RegionLuxembourg:Light_orientationSouth -4.8097 3.5028 87.5783
## Treatment_bisFull:Light_orientationSouth -2.5172 4.2665 88.8827
## Treatment_bisSmart:Light_orientationSouth -0.2800 5.0975 88.5928
## Treatment_bisMixt_smart:Light_orientationSouth 3.6937 5.1515 81.9001
## t value Pr(>|t|)
## (Intercept) -0.174 0.8627
## Treatment_bisFull -0.156 0.8766
## Treatment_bisSmart -0.309 0.7584
## Treatment_bisMixt_smart -0.764 0.4472
## SexMale -0.213 0.8316
## RegionLuxembourg 0.320 0.7503
## Treatment_FTLMix 0.633 0.5325
## Treatment_FTLNight -0.055 0.9564
## Light_orientationSouth 0.891 0.3757
## Treatment_bisFull:SexMale 1.013 0.3141
## Treatment_bisSmart:SexMale 0.033 0.9740
## Treatment_bisMixt_smart:SexMale 0.611 0.5433
## Treatment_bisFull:RegionLuxembourg 0.433 0.6662
## Treatment_bisSmart:RegionLuxembourg 0.161 0.8726
## Treatment_bisMixt_smart:RegionLuxembourg 0.566 0.5728
## SexMale:Treatment_FTLMix 0.372 0.7108
## SexMale:Treatment_FTLNight -0.092 0.9266
## RegionLuxembourg:Treatment_FTLMix -0.611 0.5440
## RegionLuxembourg:Treatment_FTLNight 1.045 0.2992
## Treatment_bisFull:Treatment_FTLMix 0.144 0.8860
## Treatment_bisSmart:Treatment_FTLMix 0.044 0.9650
## Treatment_bisMixt_smart:Treatment_FTLMix 1.715 0.0899 .
## Treatment_bisFull:Treatment_FTLNight 0.635 0.5272
## Treatment_bisSmart:Treatment_FTLNight 0.026 0.9792
## Treatment_bisMixt_smart:Treatment_FTLNight -0.179 0.8585
## SexMale:Light_orientationSouth -0.210 0.8341
## RegionLuxembourg:Light_orientationSouth -1.373 0.1732
## Treatment_bisFull:Light_orientationSouth -0.590 0.5567
## Treatment_bisSmart:Light_orientationSouth -0.055 0.9563
## Treatment_bisMixt_smart:Light_orientationSouth 0.717 0.4754
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 30 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Normalité des résidus
qqnorm(resid(LM_Speed_to_light))
qqline(resid(LM_Speed_to_light))
LM_Speed_to_light <- lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis, data = Data)## boundary (singular) fit: see help('isSingular')Normalité des résidus
qqnorm(resid(LM_Speed_to_light))
qqline(resid(LM_Speed_to_light))
Homogénité des variances
plot(LM_Speed_to_light)
La forme est due au grand nombre de 0
Distance de cook
plot(cooks.distance(LM_Speed_to_light))
On a un léger outlier mais je pense que cela passe sans trop de problème vu les valeurs de cook lui étant associées
5.6.2 Simplification du modèle
drop1(LM_Speed_to_light)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 24.990 8.330 3 85.645 0.2505 0.86080
## Treatment_bis:Region 232.055 77.352 3 83.642 2.3259 0.08061 .
## Sex:Treatment_FTL 0.182 0.091 2 84.099 0.0027 0.99726
## Region:Treatment_FTL 235.794 117.897 2 86.332 3.5450 0.03314 *
## Treatment_bis:Treatment_FTL 227.207 37.868 6 83.783 1.1386 0.34731
## Sex:Light_orientation 174.945 174.945 1 81.792 5.2604 0.02438 *
## Region:Light_orientation 0.009 0.009 1 82.446 0.0003 0.98681
## Treatment_bis:Light_orientation 175.382 58.461 3 84.925 1.7578 0.16141
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Speed_to_light1 <- update(LM_Speed_to_light, . ~ . - Sex:Treatment_FTL)## boundary (singular) fit: see help('isSingular')drop1(LM_Speed_to_light1)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Sex:Light_orientation + Region:Light_orientation + Treatment_bis:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 26.206 8.735 3 87.249 0.2691 0.84749
## Treatment_bis:Region 235.989 78.663 3 85.411 2.4237 0.07131 .
## Region:Treatment_FTL 239.080 119.540 2 88.049 3.6831 0.02910 *
## Treatment_bis:Treatment_FTL 240.590 40.098 6 85.587 1.2355 0.29635
## Sex:Light_orientation 191.717 191.717 1 83.647 5.9069 0.01722 *
## Region:Light_orientation 0.010 0.010 1 84.599 0.0003 0.98637
## Treatment_bis:Light_orientation 181.777 60.592 3 86.805 1.8669 0.14115
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Speed_to_light2 <- update(LM_Speed_to_light1, . ~ . - Region:Light_orientation)## boundary (singular) fit: see help('isSingular')drop1(LM_Speed_to_light2)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Sex:Light_orientation + Treatment_bis:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 26.735 8.912 3 88.220 0.2779 0.84121
## Treatment_bis:Region 236.797 78.932 3 86.500 2.4614 0.06798 .
## Region:Treatment_FTL 241.662 120.831 2 89.046 3.7679 0.02687 *
## Treatment_bis:Treatment_FTL 245.312 40.885 6 86.461 1.2749 0.27732
## Sex:Light_orientation 192.772 192.772 1 84.424 6.0112 0.01628 *
## Treatment_bis:Light_orientation 182.210 60.737 3 87.887 1.8940 0.13646
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Speed_to_light3 <- update(LM_Speed_to_light2, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_Speed_to_light3)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Sex:Light_orientation + Treatment_bis:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Region 233.40 77.799 3 89.447 2.4677 0.06721 .
## Region:Treatment_FTL 254.59 127.295 2 92.257 4.0377 0.02084 *
## Treatment_bis:Treatment_FTL 275.05 45.841 6 89.643 1.4541 0.20317
## Sex:Light_orientation 200.17 200.170 1 87.235 6.3492 0.01356 *
## Treatment_bis:Light_orientation 189.49 63.163 3 91.090 2.0035 0.11903
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Speed_to_light4 <- update(LM_Speed_to_light3, . ~ . - Treatment_bis:Treatment_FTL)## boundary (singular) fit: see help('isSingular')drop1(LM_Speed_to_light4)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Treatment_FTL + Sex:Light_orientation + Treatment_bis:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Region 92.998 30.999 3 90.928 0.9585 0.41590
## Region:Treatment_FTL 124.083 62.042 2 94.724 1.9184 0.15250
## Sex:Light_orientation 177.221 177.221 1 93.829 5.4799 0.02135 *
## Treatment_bis:Light_orientation 97.252 32.417 3 96.969 1.0024 0.39524
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Speed_to_light5 <- update(LM_Speed_to_light4, . ~ . - Treatment_bis:Region)
drop1(LM_Speed_to_light5)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL + Sex:Light_orientation + Treatment_bis:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Region:Treatment_FTL 118.75 59.378 2 100.428 1.8688 0.15964
## Sex:Light_orientation 171.09 171.093 1 96.461 5.3848 0.02242 *
## Treatment_bis:Light_orientation 103.02 34.339 3 97.183 1.0807 0.36099
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Speed_to_light6 <- update(LM_Speed_to_light5, . ~ . - Treatment_bis:Light_orientation)## boundary (singular) fit: see help('isSingular')drop1(LM_Speed_to_light6)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL + Sex:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 167.06 55.685 3 95.654 1.7265 0.1667
## Region:Treatment_FTL 134.37 67.186 2 101.944 2.0831 0.1298
## Sex:Light_orientation 159.35 159.351 1 99.407 4.9406 0.0285 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Speed_to_light7 <- update(LM_Speed_to_light6, . ~ . - Region:Treatment_FTL)
drop1(LM_Speed_to_light7)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 94.61 31.538 3 16.084 0.9827 0.4255149
## Region 70.04 70.042 1 6.549 2.1824 0.1859947
## Treatment_FTL 547.45 273.726 2 95.774 8.5289 0.0003901 ***
## Sex:Light_orientation 178.48 178.480 1 101.529 5.5612 0.0202789 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Simplification utile ? A nouveau, vu la complexité du modèle de base on tetse en utilisant le BIC
BIC(LM_Speed_to_light)## [1] 796.4812BIC(LM_Speed_to_light1)## [1] 794.7019BIC(LM_Speed_to_light2)## [1] 793.5115BIC(LM_Speed_to_light3)## [1] 792.3056BIC(LM_Speed_to_light4)## [1] 798.1384BIC(LM_Speed_to_light5)## [1] 798.4924BIC(LM_Speed_to_light6)## [1] 799.237BIC(LM_Speed_to_light7)## [1] 801.0452LM_Speed_to_light <- LM_Speed_to_light35.6.3 Treatment VS Teatment_bis
BIC(lmer(Speed_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Sex:Light_orientation + Treatment_bis:Light_orientation, data = Data))## boundary (singular) fit: see help('isSingular')## [1] 857.2907BIC(lmer(Speed_to_light ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region + Region:Treatment_FTL + Treatment:Treatment_FTL + Sex:Light_orientation + Treatment:Light_orientation, data = Data))## boundary (singular) fit: see help('isSingular')## [1] 867.9605summary(lmer(Speed_to_light ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Sex:Light_orientation + Treatment_bis:Light_orientation, data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) -0.5623216 3.303113 58.72162
## Treatment_bisFull 0.9399401 4.040219 94.08781
## Treatment_bisSmart 0.7791469 5.463922 94.23074
## Treatment_bisMixt_smart -2.5874488 4.808528 88.48338
## SexMale 1.1390076 2.300725 92.62686
## RegionLuxembourg -0.6691391 4.036261 55.54039
## Treatment_FTLMix 3.1826883 3.840637 28.24138
## Treatment_FTLNight -0.3892073 4.072936 61.24076
## Light_orientationSouth 1.1403175 3.167537 93.48623
## Treatment_bisFull:RegionLuxembourg 0.8003086 4.231638 94.82045
## Treatment_bisSmart:RegionLuxembourg 0.1828504 4.970358 92.50078
## Treatment_bisMixt_smart:RegionLuxembourg 2.3822536 5.456243 92.46709
## RegionLuxembourg:Treatment_FTLMix -2.3098937 4.468951 56.69889
## RegionLuxembourg:Treatment_FTLNight 4.3828561 4.367706 84.72517
## Treatment_bisFull:Treatment_FTLMix 2.2709666 5.191562 94.25902
## Treatment_bisSmart:Treatment_FTLMix -1.3211757 5.852684 92.75102
## Treatment_bisMixt_smart:Treatment_FTLMix 12.3996733 6.825662 93.91148
## Treatment_bisFull:Treatment_FTLNight 3.7774415 4.995103 92.38591
## Treatment_bisSmart:Treatment_FTLNight -1.1464974 5.932516 94.32723
## Treatment_bisMixt_smart:Treatment_FTLNight -0.6730816 5.743953 94.27765
## SexMale:Light_orientationSouth -0.8334761 3.401932 90.86562
## Treatment_bisFull:Light_orientationSouth -1.8298961 4.080678 94.92247
## Treatment_bisSmart:Light_orientationSouth -1.4208932 4.899039 94.93379
## Treatment_bisMixt_smart:Light_orientationSouth 3.0309144 4.935343 90.16797
## t value Pr(>|t|)
## (Intercept) -0.17023989 0.86540667
## Treatment_bisFull 0.23264582 0.81654177
## Treatment_bisSmart 0.14259846 0.88691178
## Treatment_bisMixt_smart -0.53809580 0.59186189
## SexMale 0.49506471 0.62172679
## RegionLuxembourg -0.16578191 0.86893058
## Treatment_FTLMix 0.82868764 0.41423025
## Treatment_FTLNight -0.09555939 0.92418253
## Light_orientationSouth 0.36000128 0.71965820
## Treatment_bisFull:RegionLuxembourg 0.18912500 0.85039907
## Treatment_bisSmart:RegionLuxembourg 0.03678817 0.97073318
## Treatment_bisMixt_smart:RegionLuxembourg 0.43661057 0.66341162
## RegionLuxembourg:Treatment_FTLMix -0.51687602 0.60725314
## RegionLuxembourg:Treatment_FTLNight 1.00346856 0.31849218
## Treatment_bisFull:Treatment_FTLMix 0.43743417 0.66279714
## Treatment_bisSmart:Treatment_FTLMix -0.22573843 0.82190154
## Treatment_bisMixt_smart:Treatment_FTLMix 1.81662569 0.07246446
## Treatment_bisFull:Treatment_FTLNight 0.75622887 0.45143603
## Treatment_bisSmart:Treatment_FTLNight -0.19325654 0.84717359
## Treatment_bisMixt_smart:Treatment_FTLNight -0.11718090 0.90696598
## SexMale:Light_orientationSouth -0.24500083 0.80700824
## Treatment_bisFull:Light_orientationSouth -0.44842941 0.65486527
## Treatment_bisSmart:Light_orientationSouth -0.29003509 0.77242196
## Treatment_bisMixt_smart:Light_orientationSouth 0.61412431 0.54067960summary(lmer(Speed_to_light ~ Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region + Region:Treatment_FTL + Treatment:Treatment_FTL + Sex:Light_orientation + Treatment:Light_orientation, data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) -0.74645972 3.670413 21.53659
## TreatmentFull 1.60912028 4.090328 97.14306
## TreatmentSmart -1.09760525 4.038514 94.52913
## SexMale 0.74458870 2.298441 96.36699
## RegionLuxembourg -0.36300969 4.094070 57.09026
## Treatment_FTLMix 3.31630826 4.025021 47.97469
## Treatment_FTLNight -0.17919563 4.159790 78.61690
## Light_orientationSouth 1.90659728 3.212126 98.02320
## TreatmentFull:RegionLuxembourg 0.24261371 4.286264 98.25319
## TreatmentSmart:RegionLuxembourg 2.56126675 4.034510 93.10151
## RegionLuxembourg:Treatment_FTLMix -1.35538964 4.507088 74.73790
## RegionLuxembourg:Treatment_FTLNight 3.94316660 4.228819 93.53565
## TreatmentFull:Treatment_FTLMix 2.23583733 5.239333 96.88374
## TreatmentSmart:Treatment_FTLMix 4.75976090 4.962365 95.27687
## TreatmentFull:Treatment_FTLNight 3.43564109 5.038358 95.41540
## TreatmentSmart:Treatment_FTLNight -0.53722043 4.822679 98.70254
## SexMale:Light_orientationSouth -1.17604269 3.408897 94.06381
## TreatmentFull:Light_orientationSouth -2.33010004 4.139674 99.03175
## TreatmentSmart:Light_orientationSouth -0.08337596 3.880339 99.99425
## t value Pr(>|t|)
## (Intercept) -0.20337214 0.8407535
## TreatmentFull 0.39339638 0.6948888
## TreatmentSmart -0.27178442 0.7863805
## SexMale 0.32395387 0.7466750
## RegionLuxembourg -0.08866718 0.9296567
## Treatment_FTLMix 0.82392319 0.4140606
## Treatment_FTLNight -0.04307804 0.9657485
## Light_orientationSouth 0.59356238 0.5541721
## TreatmentFull:RegionLuxembourg 0.05660260 0.9549767
## TreatmentSmart:RegionLuxembourg 0.63483964 0.5270901
## RegionLuxembourg:Treatment_FTLMix -0.30072401 0.7644599
## RegionLuxembourg:Treatment_FTLNight 0.93245113 0.3535041
## TreatmentFull:Treatment_FTLMix 0.42674079 0.6705149
## TreatmentSmart:Treatment_FTLMix 0.95917187 0.3398999
## TreatmentFull:Treatment_FTLNight 0.68189702 0.4969560
## TreatmentSmart:Treatment_FTLNight -0.11139461 0.9115296
## SexMale:Light_orientationSouth -0.34499213 0.7308705
## TreatmentFull:Light_orientationSouth -0.56287043 0.5747952
## TreatmentSmart:Light_orientationSouth -0.02148677 0.9829002Le meilleur est treatment_bis
Au final, au vu du nombre d’échantillons présent dans chaque termes d’interactions et les p-val associées à ces mêmes interactions, nous décidons de partir sur le modèle le plus simplifié.
5.6.4 Résultats
Analyse des p-val
summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room)
## Data: Data
##
## REML criterion at convergence: 742.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.08392 -0.66911 -0.06035 0.64322 2.21103
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.23538 1.7987
## Site (Intercept) 4.42014 2.1024
## Room (Intercept) 0.08175 0.2859
## Residual 34.04042 5.8344
## Number of obs: 119, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -12.84959 1.88770 15.56386 -6.807 4.88e-06 ***
## Treatment_bisFull 2.57721 1.42897 96.99756 1.804 0.0744 .
## Treatment_bisSmart 1.60590 1.63584 36.48376 0.982 0.3327
## Treatment_bisMixt_smart 2.18386 1.57164 9.43522 1.390 0.1966
## SexMale 0.23867 1.14970 95.18672 0.208 0.8360
## RegionLuxembourg 2.70646 1.92365 6.62081 1.407 0.2046
## Treatment_FTLMix 4.17538 1.59939 105.95477 2.611 0.0103 *
## Treatment_FTLNight 6.39674 1.49943 108.75968 4.266 4.26e-05 ***
## Light_orientationSouth -0.06976 1.12242 98.32173 -0.062 0.9506
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## Trtmnt_bsFl -0.356
## Trtmnt_bsSm -0.307 0.408
## Trtmnt_bsM_ -0.298 0.447 0.351
## SexMale -0.262 -0.061 0.081 0.012
## ReginLxmbrg -0.440 0.026 -0.086 -0.016 0.016
## Trtmnt_FTLM -0.313 0.056 0.037 0.007 -0.105 -0.224
## Trtmnt_FTLN -0.320 0.023 0.001 0.023 -0.019 -0.173 0.594
## Lght_rnttnS -0.279 -0.101 0.000 -0.127 0.028 0.060 0.024 -0.086summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_full))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room)
## Data: Data_ref_full
##
## REML criterion at convergence: 742.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.08392 -0.66911 -0.06035 0.64322 2.21103
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.23538 1.7987
## Site (Intercept) 4.42014 2.1024
## Room (Intercept) 0.08175 0.2859
## Residual 34.04042 5.8344
## Number of obs: 119, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -10.27238 1.91961 17.48049 -5.351 4.82e-05 ***
## Treatment_bisDark -2.57721 1.42897 96.99756 -1.804 0.0744 .
## Treatment_bisSmart -0.97131 1.67629 44.48007 -0.579 0.5652
## Treatment_bisMixt_smart -0.39335 1.58216 8.81767 -0.249 0.8094
## SexMale 0.23867 1.14970 95.18672 0.208 0.8360
## RegionLuxembourg 2.70646 1.92365 6.62081 1.407 0.2046
## Treatment_FTLMix 4.17538 1.59939 105.95477 2.611 0.0103 *
## Treatment_FTLNight 6.39674 1.49943 108.75968 4.266 4.26e-05 ***
## Light_orientationSouth -0.06976 1.12242 98.32173 -0.062 0.9506
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## Trtmnt_bsDr -0.394
## Trtmnt_bsSm -0.334 0.454
## Trtmnt_bsM_ -0.316 0.459 0.371
## SexMale -0.303 0.061 0.131 0.067
## ReginLxmbrg -0.413 -0.026 -0.106 -0.039 0.016
## Trtmnt_FTLM -0.266 -0.056 -0.012 -0.044 -0.105 -0.224
## Trtmnt_FTLN -0.297 -0.023 -0.018 0.002 -0.019 -0.173 0.594
## Lght_rnttnS -0.350 0.101 0.086 -0.035 0.028 0.060 0.024 -0.086summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room)
## Data: Data_ref_smart
##
## REML criterion at convergence: 742.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.08392 -0.66911 -0.06035 0.64322 2.21103
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.23538 1.7987
## Site (Intercept) 4.42014 2.1024
## Room (Intercept) 0.08175 0.2859
## Residual 34.04042 5.8344
## Number of obs: 119, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -11.24369 2.08452 17.01021 -5.394 4.84e-05 ***
## Treatment_bisDark -1.60590 1.63584 36.48376 -0.982 0.3327
## Treatment_bisFull 0.97131 1.67629 44.48007 0.579 0.5652
## Treatment_bisMixt_smart 0.57796 1.82838 2.11320 0.316 0.7804
## SexMale 0.23867 1.14970 95.18672 0.208 0.8360
## RegionLuxembourg 2.70646 1.92365 6.62081 1.407 0.2046
## Treatment_FTLMix 4.17538 1.59939 105.95477 2.611 0.0103 *
## Treatment_FTLNight 6.39674 1.49943 108.75968 4.266 4.26e-05 ***
## Light_orientationSouth -0.06976 1.12242 98.32173 -0.062 0.9506
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## Trtmnt_bsDr -0.507
## Trtmnt_bsFl -0.497 0.628
## Trtmnt_bsM_ -0.449 0.593 0.595
## SexMale -0.174 -0.081 -0.131 -0.062
## ReginLxmbrg -0.466 0.086 0.106 0.063 0.016
## Trtmnt_FTLM -0.254 -0.037 0.012 -0.027 -0.105 -0.224
## Trtmnt_FTLN -0.289 -0.001 0.018 0.019 -0.019 -0.173 0.594
## Lght_rnttnS -0.252 0.000 -0.086 -0.110 0.028 0.060 0.024 -0.086summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_mixt_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room)
## Data: Data_ref_mixt_smart
##
## REML criterion at convergence: 742.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.08392 -0.66911 -0.06035 0.64322 2.21103
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.23538 1.7987
## Site (Intercept) 4.42014 2.1024
## Room (Intercept) 0.08175 0.2859
## Residual 34.04042 5.8344
## Number of obs: 119, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -10.66573 2.06590 7.61296 -5.163 0.00101 **
## Treatment_bisDark -2.18386 1.57164 9.43522 -1.390 0.19658
## Treatment_bisFull 0.39335 1.58216 8.81767 0.249 0.80935
## Treatment_bisSmart -0.57796 1.82838 2.11320 -0.316 0.78043
## SexMale 0.23867 1.14970 95.18672 0.208 0.83599
## RegionLuxembourg 2.70646 1.92365 6.62081 1.407 0.20461
## Treatment_FTLMix 4.17538 1.59939 105.95477 2.611 0.01035 *
## Treatment_FTLNight 6.39674 1.49943 108.75968 4.266 4.26e-05 ***
## Light_orientationSouth -0.06976 1.12242 98.32173 -0.062 0.95057
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_FTLM T_FTLN
## Trtmnt_bsDr -0.489
## Trtmnt_bsFl -0.472 0.589
## Trtmnt_bsSm -0.432 0.546 0.525
## SexMale -0.231 -0.012 -0.067 0.062
## ReginLxmbrg -0.414 0.016 0.039 -0.063 0.016
## Trtmnt_FTLM -0.281 -0.007 0.044 0.027 -0.105 -0.224
## Trtmnt_FTLN -0.275 -0.023 -0.002 -0.019 -0.019 -0.173 0.594
## Lght_rnttnS -0.352 0.127 0.035 0.110 0.028 0.060 0.024 -0.086summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_refFTL_Night))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room)
## Data: Data_refFTL_Night
##
## REML criterion at convergence: 742.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.08392 -0.66911 -0.06035 0.64322 2.21103
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.23538 1.7987
## Site (Intercept) 4.42014 2.1024
## Room (Intercept) 0.08175 0.2859
## Residual 34.04042 5.8344
## Number of obs: 119, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -6.45285 2.00062 17.11998 -3.225 0.00493 **
## Treatment_bisFull 2.57721 1.42897 96.99756 1.804 0.07441 .
## Treatment_bisSmart 1.60590 1.63584 36.48376 0.982 0.33271
## Treatment_bisMixt_smart 2.18386 1.57164 9.43522 1.390 0.19658
## SexMale 0.23867 1.14970 95.18672 0.208 0.83599
## RegionLuxembourg 2.70646 1.92365 6.62081 1.407 0.20461
## Treatment_FTLDay -6.39674 1.49943 108.75968 -4.266 4.26e-05 ***
## Treatment_FTLMix -2.22136 1.39932 104.90285 -1.587 0.11542
## Light_orientationSouth -0.06976 1.12242 98.32173 -0.062 0.95057
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLD T_FTLM
## Trtmnt_bsFl -0.319
## Trtmnt_bsSm -0.289 0.408
## Trtmnt_bsM_ -0.264 0.447 0.351
## SexMale -0.262 -0.061 0.081 0.012
## ReginLxmbrg -0.545 0.026 -0.086 -0.016 0.016
## Trtmnt_FTLD -0.448 -0.023 -0.001 -0.023 0.019 0.173
## Trtmnt_FTLM -0.309 0.040 0.041 -0.017 -0.099 -0.071 0.393
## Lght_rnttnS -0.328 -0.101 0.000 -0.127 0.028 0.060 0.086 0.119summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_refFTL_Mix))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ Treatment_bis + Sex + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room)
## Data: Data_refFTL_Mix
##
## REML criterion at convergence: 742.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.08392 -0.66911 -0.06035 0.64322 2.21103
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.23538 1.7987
## Site (Intercept) 4.42014 2.1024
## Room (Intercept) 0.08175 0.2859
## Residual 34.04042 5.8344
## Number of obs: 119, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -8.67421 2.05705 17.23126 -4.217 0.000565 ***
## Treatment_bisFull 2.57721 1.42897 96.99756 1.804 0.074407 .
## Treatment_bisSmart 1.60590 1.63584 36.48377 0.982 0.332714
## Treatment_bisMixt_smart 2.18386 1.57164 9.43523 1.390 0.196580
## SexMale 0.23867 1.14970 95.18672 0.208 0.835988
## RegionLuxembourg 2.70646 1.92365 6.62081 1.407 0.204612
## Treatment_FTLDay -4.17538 1.59939 105.95477 -2.611 0.010347 *
## Treatment_FTLNight 2.22136 1.39932 104.90285 1.587 0.115419
## Light_orientationSouth -0.06976 1.12242 98.32173 -0.062 0.950569
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLD T_FTLN
## Trtmnt_bsFl -0.283
## Trtmnt_bsSm -0.253 0.408
## Trtmnt_bsM_ -0.268 0.447 0.351
## SexMale -0.322 -0.061 0.081 0.012
## ReginLxmbrg -0.578 0.026 -0.086 -0.016 0.016
## Trtmnt_FTLD -0.490 -0.056 -0.037 -0.007 0.105 0.224
## Trtmnt_FTLN -0.380 -0.040 -0.041 0.017 0.099 0.071 0.507
## Lght_rnttnS -0.237 -0.101 0.000 -0.127 0.028 0.060 -0.024 -0.119test1 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))$coeff)[,]))
test2 <- data.frame(Reference_Treatment = "Smart", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Flight_to_light) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference_Treatment = "Full", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_smart))$coeff)[,]))
test4 <- data.frame(Reference_Treatment = "Mixt_smart", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_mixt_smart))$coeff)[,]))
test5 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Mixt", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_refFTL_Mix))$coeff)[,]))
test6 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Night", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_refFTL_Night))$coeff)[,]))
Results_Speed_to_light <- rbind(test1,test2,test3,test4,test5,test6)
colnames(Results_Speed_to_light ) <- c("Reference_Treatment", "Reference_Timing" ,"Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Speed_to_light , file = "output/Results_Speed_to_light.csv" )
kable(Results_Speed_to_light , caption = " Temps mis pour voler à la lumière ", padding = 1 )| Reference_Treatment | Reference_Timing | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|---|
| (Intercept) | Dark | Day | -12.8495902 | 1.8877002 | 15.563859 | -6.8070079 | 0.0000049 |
| Treatment_bisFull | Dark | Day | 2.5772122 | 1.4289675 | 96.997560 | 1.8035486 | 0.0744065 |
| Treatment_bisSmart | Dark | Day | 1.6059039 | 1.6358418 | 36.483759 | 0.9816988 | 0.3327138 |
| Treatment_bisMixt_smart | Dark | Day | 2.1838642 | 1.5716379 | 9.435222 | 1.3895467 | 0.1965802 |
| SexMale | Dark | Day | 0.2386725 | 1.1496956 | 95.186718 | 0.2075963 | 0.8359877 |
| RegionLuxembourg | Dark | Day | 2.7064566 | 1.9236511 | 6.620815 | 1.4069374 | 0.2046123 |
| Treatment_FTLMix | Dark | Day | 4.1753794 | 1.5993913 | 105.954771 | 2.6106053 | 0.0103473 |
| Treatment_FTLNight | Dark | Day | 6.3967362 | 1.4994256 | 108.759682 | 4.2661245 | 0.0000426 |
| Light_orientationSouth | Dark | Day | -0.0697592 | 1.1224196 | 98.321727 | -0.0621507 | 0.9505690 |
| (Intercept)1 | Smart | Day | 7.1186914 | 0.7096695 | 46.131442 | 10.0309959 | 0.0000000 |
| Treatment_bisDark | Smart | Day | -0.2634896 | 0.6012533 | 48.407207 | -0.4382339 | 0.6631662 |
| Treatment_bisFull1 | Smart | Day | -0.9115651 | 0.5673725 | 48.631909 | -1.6066431 | 0.1146070 |
| Treatment_bisMixt_smart1 | Smart | Day | -0.8376421 | 0.6340025 | 50.000637 | -1.3211968 | 0.1924501 |
| SexMale1 | Smart | Day | 0.1534485 | 0.4369309 | 50.803862 | 0.3511963 | 0.7268934 |
| RegionLuxembourg1 | Smart | Day | -0.5369595 | 0.4806149 | 20.549394 | -1.1172344 | 0.2767869 |
| Treatment_FTLMix1 | Smart | Day | -1.1781324 | 0.6445252 | 49.565032 | -1.8279074 | 0.0735856 |
| Treatment_FTLNight1 | Smart | Day | -1.0428565 | 0.6062984 | 50.696778 | -1.7200383 | 0.0915253 |
| Light_orientationSouth1 | Smart | Day | -0.1184522 | 0.4307041 | 48.449929 | -0.2750200 | 0.7844703 |
| (Intercept)2 | Full | Day | -11.2436863 | 2.0845232 | 17.010205 | -5.3938889 | 0.0000484 |
| Treatment_bisDark1 | Full | Day | -1.6059039 | 1.6358418 | 36.483756 | -0.9816988 | 0.3327138 |
| Treatment_bisFull2 | Full | Day | 0.9713083 | 1.6762885 | 44.480067 | 0.5794398 | 0.5652158 |
| Treatment_bisMixt_smart2 | Full | Day | 0.5779603 | 1.8283831 | 2.113202 | 0.3161046 | 0.7804343 |
| SexMale2 | Full | Day | 0.2386725 | 1.1496956 | 95.186717 | 0.2075963 | 0.8359877 |
| RegionLuxembourg2 | Full | Day | 2.7064566 | 1.9236511 | 6.620815 | 1.4069374 | 0.2046123 |
| Treatment_FTLMix2 | Full | Day | 4.1753794 | 1.5993913 | 105.954771 | 2.6106053 | 0.0103473 |
| Treatment_FTLNight2 | Full | Day | 6.3967362 | 1.4994256 | 108.759682 | 4.2661245 | 0.0000426 |
| Light_orientationSouth2 | Full | Day | -0.0697592 | 1.1224196 | 98.321727 | -0.0621507 | 0.9505690 |
| (Intercept)3 | Mixt_smart | Day | -10.6657259 | 2.0659038 | 7.612956 | -5.1627409 | 0.0010056 |
| Treatment_bisDark2 | Mixt_smart | Day | -2.1838642 | 1.5716379 | 9.435222 | -1.3895467 | 0.1965802 |
| Treatment_bisFull3 | Mixt_smart | Day | 0.3933480 | 1.5821624 | 8.817670 | 0.2486142 | 0.8093527 |
| Treatment_bisSmart1 | Mixt_smart | Day | -0.5779603 | 1.8283831 | 2.113203 | -0.3161046 | 0.7804343 |
| SexMale3 | Mixt_smart | Day | 0.2386725 | 1.1496956 | 95.186718 | 0.2075963 | 0.8359877 |
| RegionLuxembourg3 | Mixt_smart | Day | 2.7064566 | 1.9236511 | 6.620815 | 1.4069374 | 0.2046123 |
| Treatment_FTLMix3 | Mixt_smart | Day | 4.1753794 | 1.5993913 | 105.954771 | 2.6106053 | 0.0103473 |
| Treatment_FTLNight3 | Mixt_smart | Day | 6.3967362 | 1.4994256 | 108.759682 | 4.2661245 | 0.0000426 |
| Light_orientationSouth3 | Mixt_smart | Day | -0.0697592 | 1.1224196 | 98.321727 | -0.0621507 | 0.9505690 |
| (Intercept)4 | Dark | Mixt | -8.6742108 | 2.0570495 | 17.231259 | -4.2168215 | 0.0005649 |
| Treatment_bisFull4 | Dark | Mixt | 2.5772122 | 1.4289675 | 96.997561 | 1.8035486 | 0.0744065 |
| Treatment_bisSmart2 | Dark | Mixt | 1.6059040 | 1.6358418 | 36.483768 | 0.9816988 | 0.3327138 |
| Treatment_bisMixt_smart3 | Dark | Mixt | 2.1838642 | 1.5716379 | 9.435226 | 1.3895467 | 0.1965802 |
| SexMale4 | Dark | Mixt | 0.2386725 | 1.1496956 | 95.186718 | 0.2075963 | 0.8359877 |
| RegionLuxembourg4 | Dark | Mixt | 2.7064566 | 1.9236511 | 6.620815 | 1.4069374 | 0.2046123 |
| Treatment_FTLDay | Dark | Mixt | -4.1753794 | 1.5993913 | 105.954771 | -2.6106054 | 0.0103473 |
| Treatment_FTLNight4 | Dark | Mixt | 2.2213568 | 1.3993185 | 104.902850 | 1.5874562 | 0.1154191 |
| Light_orientationSouth4 | Dark | Mixt | -0.0697592 | 1.1224196 | 98.321727 | -0.0621507 | 0.9505690 |
| (Intercept)5 | Dark | Night | -6.4528540 | 2.0006245 | 17.119976 | -3.2254198 | 0.0049329 |
| Treatment_bisFull5 | Dark | Night | 2.5772122 | 1.4289675 | 96.997560 | 1.8035486 | 0.0744065 |
| Treatment_bisSmart3 | Dark | Night | 1.6059039 | 1.6358418 | 36.483757 | 0.9816988 | 0.3327138 |
| Treatment_bisMixt_smart4 | Dark | Night | 2.1838642 | 1.5716379 | 9.435222 | 1.3895467 | 0.1965802 |
| SexMale5 | Dark | Night | 0.2386725 | 1.1496956 | 95.186718 | 0.2075963 | 0.8359877 |
| RegionLuxembourg5 | Dark | Night | 2.7064566 | 1.9236511 | 6.620815 | 1.4069374 | 0.2046123 |
| Treatment_FTLDay1 | Dark | Night | -6.3967362 | 1.4994256 | 108.759682 | -4.2661245 | 0.0000426 |
| Treatment_FTLMix4 | Dark | Night | -2.2213568 | 1.3993185 | 104.902850 | -1.5874562 | 0.1154191 |
| Light_orientationSouth5 | Dark | Night | -0.0697592 | 1.1224196 | 98.321727 | -0.0621507 | 0.9505690 |
Info_Speed_to_light <- "
Les individus expérimentés la nuits ou avec la manière mixte (30 min dans l'obscurité avant de faire l'expérience de jour) sont significativement plus rapide que ceux expérimentés le jour. Néanmoins, les individus expérimentés de la manière mixte ne sont pas significativement différent de ceux expérimentés la nuit. Nous pouvons également noter le fait que les individus du traitement Full sont quasiment significativement (p-val = 0.0744) plus rapides que ceux du traitement Dark.
"
Info_Speed_to_light## [1] "\nLes individus expérimentés la nuits ou avec la manière mixte (30 min dans l'obscurité avant de faire l'expérience de jour) sont significativement plus rapide que ceux expérimentés le jour. Néanmoins, les individus expérimentés de la manière mixte ne sont pas significativement différent de ceux expérimentés la nuit. Nous pouvons également noter le fait que les individus du traitement Full sont quasiment significativement (p-val = 0.0744) plus rapides que ceux du traitement Dark.\n"5.6.5 Visulaisation
ggplot(Data, aes(x=Treatment_FTL, y=log(Speed_to_light+0.000001), color = Treatment_FTL))+
geom_boxplot(data = Data %>% filter(Treatment_FTL != "NA"), outlier.shape = NA) +
geom_jitter(width = 0.2, height = 0.1, alpha = 0.75, aes(shape = Treatment_bis)) +
labs(title = "Vitesse pour voler à la lumière", x = "Tratiement", y = "log(vitesse pour voler à la lumière m/min)", color = "Timing", shape = "Traitement" ) +
theme_bw()## Warning: Removed 330 rows containing missing values (`geom_point()`).
5.7 FTL_by_First_move
5.7.1 Test
LM_FTL_by_First_move <- lmer(Flight_to_light ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis, data = filter(Data))## boundary (singular) fit: see help('isSingular')summary(LM_FTL_by_First_move)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Flight_to_light ~ First_move + Treatment_bis + Sex + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex +
## Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex +
## Light_orientation:Region + Light_orientation:Treatment_bis
## Data: filter(Data)
##
## REML criterion at convergence: 481.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.65484 -0.30711 -0.08629 0.33272 1.64804
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000e+00 0.000e+00
## Site (Intercept) 5.006e+04 2.237e+02
## Room (Intercept) 2.439e-05 4.939e-03
## Residual 1.706e+05 4.131e+02
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 458.7688 484.5210 22.1407
## First_move 0.6864 0.2787 25.2970
## Treatment_bisFull 50.8063 435.9813 21.5918
## Treatment_bisSmart 687.3076 743.5735 24.2343
## Treatment_bisMixt_smart -430.1680 833.9181 28.9967
## SexMale -221.2317 495.2646 28.9920
## RegionLuxembourg -123.4481 500.3388 22.7912
## Treatment_FTLMix 281.0479 546.0056 27.9143
## Treatment_FTLNight 569.9451 588.0985 28.8599
## Light_orientationSouth -279.3012 481.3959 24.6615
## Treatment_bisFull:SexMale -237.8285 458.8940 26.9305
## Treatment_bisSmart:SexMale 34.0253 501.5470 26.3300
## Treatment_bisMixt_smart:SexMale 569.9227 505.7951 28.1094
## Treatment_bisFull:RegionLuxembourg 669.2526 455.9144 22.1457
## Treatment_bisSmart:RegionLuxembourg 312.8539 571.7196 26.3189
## Treatment_bisMixt_smart:RegionLuxembourg -146.5530 531.5947 22.9519
## SexMale:Treatment_FTLMix 103.9081 525.5852 28.6237
## SexMale:Treatment_FTLNight 180.1437 491.0847 28.8606
## RegionLuxembourg:Treatment_FTLMix -574.4767 525.0307 27.7868
## RegionLuxembourg:Treatment_FTLNight -708.6101 498.5621 28.7557
## Treatment_bisFull:Treatment_FTLMix -322.7121 532.8287 25.5723
## Treatment_bisSmart:Treatment_FTLMix -698.5530 1022.4626 25.5066
## Treatment_bisMixt_smart:Treatment_FTLMix 265.1012 857.9328 28.9841
## Treatment_bisFull:Treatment_FTLNight -665.9761 437.3629 25.1925
## Treatment_bisSmart:Treatment_FTLNight -1116.2048 1001.2395 26.5237
## Treatment_bisMixt_smart:Treatment_FTLNight -41.0685 751.1272 28.4605
## SexMale:Light_orientationSouth -133.1684 346.5722 23.3404
## RegionLuxembourg:Light_orientationSouth 479.0263 440.9496 25.9508
## Treatment_bisFull:Light_orientationSouth 234.9765 428.6541 25.4788
## Treatment_bisSmart:Light_orientationSouth -72.2646 516.1990 26.7709
## Treatment_bisMixt_smart:Light_orientationSouth 215.8570 456.6777 26.8200
## t value Pr(>|t|)
## (Intercept) 0.947 0.3539
## First_move 2.462 0.0209 *
## Treatment_bisFull 0.117 0.9083
## Treatment_bisSmart 0.924 0.3644
## Treatment_bisMixt_smart -0.516 0.6099
## SexMale -0.447 0.6584
## RegionLuxembourg -0.247 0.8073
## Treatment_FTLMix 0.515 0.6108
## Treatment_FTLNight 0.969 0.3405
## Light_orientationSouth -0.580 0.5671
## Treatment_bisFull:SexMale -0.518 0.6085
## Treatment_bisSmart:SexMale 0.068 0.9464
## Treatment_bisMixt_smart:SexMale 1.127 0.2694
## Treatment_bisFull:RegionLuxembourg 1.468 0.1562
## Treatment_bisSmart:RegionLuxembourg 0.547 0.5888
## Treatment_bisMixt_smart:RegionLuxembourg -0.276 0.7853
## SexMale:Treatment_FTLMix 0.198 0.8447
## SexMale:Treatment_FTLNight 0.367 0.7164
## RegionLuxembourg:Treatment_FTLMix -1.094 0.2833
## RegionLuxembourg:Treatment_FTLNight -1.421 0.1660
## Treatment_bisFull:Treatment_FTLMix -0.606 0.5501
## Treatment_bisSmart:Treatment_FTLMix -0.683 0.5006
## Treatment_bisMixt_smart:Treatment_FTLMix 0.309 0.7595
## Treatment_bisFull:Treatment_FTLNight -1.523 0.1403
## Treatment_bisSmart:Treatment_FTLNight -1.115 0.2749
## Treatment_bisMixt_smart:Treatment_FTLNight -0.055 0.9568
## SexMale:Light_orientationSouth -0.384 0.7043
## RegionLuxembourg:Light_orientationSouth 1.086 0.2873
## Treatment_bisFull:Light_orientationSouth 0.548 0.5883
## Treatment_bisSmart:Light_orientationSouth -0.140 0.8897
## Treatment_bisMixt_smart:Light_orientationSouth 0.473 0.6403
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 31 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')qqnorm(resid(LM_FTL_by_First_move))
qqline(resid(LM_FTL_by_First_move))
Il faut modifier les variables
LM_FTL_by_First_move <- lmer(log(Flight_to_light+0.1) ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis, data = Data)## boundary (singular) fit: see help('isSingular')summary(LM_FTL_by_First_move)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Sex +
## Region + Treatment_FTL + Light_orientation + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region +
## Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis +
## Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis
## Data: Data
##
## REML criterion at convergence: 138.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.40767 -0.48397 -0.03492 0.54980 1.43879
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.2421 0.4921
## Site (Intercept) 0.0000 0.0000
## Room (Intercept) 0.0000 0.0000
## Residual 1.2793 1.1311
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 4.5206640 1.2752031 22.5814756
## First_move 0.0027742 0.0007637 25.9399670
## Treatment_bisFull 0.4905899 1.1985789 18.8173588
## Treatment_bisSmart 1.9616369 2.0467853 25.7519860
## Treatment_bisMixt_smart 1.7572440 2.2560738 28.8793898
## SexMale -0.4264251 1.3254690 28.8149143
## RegionLuxembourg 0.9364813 1.3158748 24.8838688
## Treatment_FTLMix -1.2701101 1.4414885 28.3839150
## Treatment_FTLNight 1.4607212 1.5872250 28.6864351
## Light_orientationSouth -0.3926240 1.3173256 24.7022116
## Treatment_bisFull:SexMale -1.0502182 1.2568793 28.6715341
## Treatment_bisSmart:SexMale 0.2014877 1.3573430 25.7011493
## Treatment_bisMixt_smart:SexMale 0.3672156 1.3766700 28.6817044
## Treatment_bisFull:RegionLuxembourg 0.3762882 1.2557452 20.8173587
## Treatment_bisSmart:RegionLuxembourg -0.2436433 1.5658389 25.9185577
## Treatment_bisMixt_smart:RegionLuxembourg -0.7540643 1.4469452 20.4052876
## SexMale:Treatment_FTLMix -0.0954151 1.4373403 28.9551454
## SexMale:Treatment_FTLNight 0.8437118 1.3414535 28.8059973
## RegionLuxembourg:Treatment_FTLMix -0.2636456 1.4250429 24.8713664
## RegionLuxembourg:Treatment_FTLNight -2.7770093 1.3581844 27.0932145
## Treatment_bisFull:Treatment_FTLMix 0.5770367 1.4360162 23.1770933
## Treatment_bisSmart:Treatment_FTLMix -0.2076286 2.8024666 27.0272499
## Treatment_bisMixt_smart:Treatment_FTLMix -2.4980074 2.3250355 28.8190234
## Treatment_bisFull:Treatment_FTLNight -1.8471187 1.2033707 26.1134533
## Treatment_bisSmart:Treatment_FTLNight -1.5201624 2.7453523 28.2815281
## Treatment_bisMixt_smart:Treatment_FTLNight -1.7034675 2.0056447 28.8982385
## SexMale:Light_orientationSouth -0.6923843 0.9697672 26.2831890
## RegionLuxembourg:Light_orientationSouth 1.5107996 1.2082026 25.9742090
## Treatment_bisFull:Light_orientationSouth 1.4261489 1.1876493 27.9277644
## Treatment_bisSmart:Light_orientationSouth -0.0356494 1.4122159 28.7377128
## Treatment_bisMixt_smart:Light_orientationSouth 0.0201753 1.2367939 25.3048323
## t value Pr(>|t|)
## (Intercept) 3.545 0.00176 **
## First_move 3.633 0.00121 **
## Treatment_bisFull 0.409 0.68693
## Treatment_bisSmart 0.958 0.34677
## Treatment_bisMixt_smart 0.779 0.44238
## SexMale -0.322 0.74999
## RegionLuxembourg 0.712 0.48328
## Treatment_FTLMix -0.881 0.38566
## Treatment_FTLNight 0.920 0.36509
## Light_orientationSouth -0.298 0.76816
## Treatment_bisFull:SexMale -0.836 0.41030
## Treatment_bisSmart:SexMale 0.148 0.88315
## Treatment_bisMixt_smart:SexMale 0.267 0.79158
## Treatment_bisFull:RegionLuxembourg 0.300 0.76741
## Treatment_bisSmart:RegionLuxembourg -0.156 0.87755
## Treatment_bisMixt_smart:RegionLuxembourg -0.521 0.60788
## SexMale:Treatment_FTLMix -0.066 0.94753
## SexMale:Treatment_FTLNight 0.629 0.53434
## RegionLuxembourg:Treatment_FTLMix -0.185 0.85472
## RegionLuxembourg:Treatment_FTLNight -2.045 0.05072 .
## Treatment_bisFull:Treatment_FTLMix 0.402 0.69149
## Treatment_bisSmart:Treatment_FTLMix -0.074 0.94149
## Treatment_bisMixt_smart:Treatment_FTLMix -1.074 0.29156
## Treatment_bisFull:Treatment_FTLNight -1.535 0.13682
## Treatment_bisSmart:Treatment_FTLNight -0.554 0.58412
## Treatment_bisMixt_smart:Treatment_FTLNight -0.849 0.40268
## SexMale:Light_orientationSouth -0.714 0.48154
## RegionLuxembourg:Light_orientationSouth 1.250 0.22228
## Treatment_bisFull:Light_orientationSouth 1.201 0.23991
## Treatment_bisSmart:Light_orientationSouth -0.025 0.98004
## Treatment_bisMixt_smart:Light_orientationSouth 0.016 0.98711
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 31 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')qqnorm(resid(LM_FTL_by_First_move))
qqline(resid(LM_FTL_by_First_move))
Peut mieux faire mais on s’en contentera
Homogénité des variances
plot(LM_FTL_by_First_move)
Distance de cook
plot(cooks.distance(LM_FTL_by_First_move))
5.7.2 Simplification du modèle
drop1(LM_FTL_by_First_move)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Treatment_FTL:Sex + Treatment_FTL:Region + Treatment_FTL:Treatment_bis + Light_orientation:Sex + Light_orientation:Region + Light_orientation:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## First_move 16.8825 16.8825 1 25.940 13.1966 0.001212
## Treatment_bis:Sex 2.8367 0.9456 3 24.688 0.7391 0.538797
## Treatment_bis:Region 1.3690 0.4563 3 22.821 0.3567 0.784750
## Sex:Treatment_FTL 1.3708 0.6854 2 28.815 0.5358 0.590939
## Region:Treatment_FTL 10.2933 5.1467 2 26.742 4.0230 0.029686
## Treatment_bis:Treatment_FTL 9.7723 1.6287 6 27.114 1.2731 0.302334
## Sex:Light_orientation 0.6521 0.6521 1 26.283 0.5098 0.481539
## Region:Light_orientation 2.0004 2.0004 1 25.974 1.5636 0.222283
## Treatment_bis:Light_orientation 2.9611 0.9870 3 27.964 0.7715 0.519697
##
## First_move **
## Treatment_bis:Sex
## Treatment_bis:Region
## Sex:Treatment_FTL
## Region:Treatment_FTL *
## Treatment_bis:Treatment_FTL
## Sex:Light_orientation
## Region:Light_orientation
## Treatment_bis:Light_orientation
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_FTL_by_First_move1 <- update(LM_FTL_by_First_move, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_FTL_by_First_move1)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Sex:Treatment_FTL + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Sex:Light_orientation + Region:Light_orientation + Treatment_bis:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## First_move 24.7990 24.7990 1 31.915 20.1358 8.799e-05
## Treatment_bis:Sex 3.4216 1.1405 3 27.932 0.9261 0.441091
## Sex:Treatment_FTL 2.0214 1.0107 2 31.418 0.8206 0.449359
## Region:Treatment_FTL 14.6080 7.3040 2 29.455 5.9306 0.006849
## Treatment_bis:Treatment_FTL 16.3227 2.7205 6 29.390 2.2089 0.070372
## Sex:Light_orientation 0.9104 0.9104 1 29.893 0.7392 0.396758
## Region:Light_orientation 2.9534 2.9534 1 27.731 2.3980 0.132827
## Treatment_bis:Light_orientation 3.2886 1.0962 3 31.094 0.8901 0.457116
##
## First_move ***
## Treatment_bis:Sex
## Sex:Treatment_FTL
## Region:Treatment_FTL **
## Treatment_bis:Treatment_FTL .
## Sex:Light_orientation
## Region:Light_orientation
## Treatment_bis:Light_orientation
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_FTL_by_First_move2 <- update(LM_FTL_by_First_move1, . ~ . - Treatment_bis:Light_orientation)## boundary (singular) fit: see help('isSingular')drop1(LM_FTL_by_First_move2)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Sex:Treatment_FTL + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Sex:Light_orientation + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## First_move 25.7744 25.7744 1 34.758 19.9656 7.995e-05 ***
## Treatment_bis:Sex 2.1451 0.7150 3 29.317 0.5539 0.649609
## Sex:Treatment_FTL 1.0387 0.5194 2 33.719 0.4023 0.671940
## Region:Treatment_FTL 14.0748 7.0374 2 30.030 5.4514 0.009555 **
## Treatment_bis:Treatment_FTL 14.5688 2.4281 6 32.128 1.8809 0.114626
## Sex:Light_orientation 0.1840 0.1840 1 33.209 0.1426 0.708158
## Region:Light_orientation 3.0205 3.0205 1 30.899 2.3398 0.136283
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_FTL_by_First_move3 <- update(LM_FTL_by_First_move2, . ~ . - Sex:Treatment_FTL)## boundary (singular) fit: see help('isSingular')drop1(LM_FTL_by_First_move3)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Sex:Light_orientation + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## First_move 25.0975 25.0975 1 36.948 21.3927 4.473e-05 ***
## Treatment_bis:Sex 2.0485 0.6828 3 31.222 0.5820 0.631216
## Region:Treatment_FTL 15.2699 7.6350 2 35.744 6.5079 0.003889 **
## Treatment_bis:Treatment_FTL 14.2613 2.3769 6 32.020 2.0260 0.090927 .
## Sex:Light_orientation 0.1573 0.1573 1 33.982 0.1341 0.716507
## Region:Light_orientation 3.0181 3.0181 1 30.781 2.5726 0.118942
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_FTL_by_First_move4 <- update(LM_FTL_by_First_move3, . ~ . - Sex:Light_orientation)## boundary (singular) fit: see help('isSingular')drop1(LM_FTL_by_First_move4)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## First_move 26.0939 26.0939 1 37.576 21.8001 3.791e-05 ***
## Treatment_bis:Sex 2.4231 0.8077 3 34.101 0.6748 0.573457
## Region:Treatment_FTL 15.7533 7.8766 2 36.269 6.5805 0.003645 **
## Treatment_bis:Treatment_FTL 14.4040 2.4007 6 35.308 2.0056 0.090975 .
## Region:Light_orientation 2.9022 2.9022 1 34.334 2.4246 0.128613
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_FTL_by_First_move5 <- update(LM_FTL_by_First_move4, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_FTL_by_First_move5)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## First_move 25.1341 25.1341 1 40.983 23.3721 1.909e-05 ***
## Sex 1.8001 1.8001 1 35.236 1.6739 0.204152
## Region:Treatment_FTL 16.9474 8.4737 2 40.305 7.8797 0.001293 **
## Treatment_bis:Treatment_FTL 16.0232 2.6705 6 37.166 2.4833 0.040368 *
## Region:Light_orientation 5.1916 5.1916 1 38.612 4.8276 0.034075 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_FTL_by_First_move6 <- update(LM_FTL_by_First_move5, . ~ . - Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_FTL_by_First_move6)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL + Treatment_bis:Treatment_FTL + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## First_move 26.3200 26.3200 1 40.479 22.1036 2.984e-05 ***
## Region:Treatment_FTL 17.2297 8.6148 2 39.449 7.2348 0.002105 **
## Treatment_bis:Treatment_FTL 15.5070 2.5845 6 40.273 2.1705 0.066059 .
## Region:Light_orientation 5.9456 5.9456 1 40.826 4.9932 0.030984 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_FTL_by_First_move7 <- update(LM_FTL_by_First_move6, . ~ . - Treatment_bis:Treatment_FTL)## boundary (singular) fit: see help('isSingular')drop1(LM_FTL_by_First_move7)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL + Region:Light_orientation
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## First_move 32.020 32.020 1 45.061 23.3073 1.624e-05 ***
## Treatment_bis 11.267 3.756 3 45.070 2.7336 0.054648 .
## Region:Treatment_FTL 18.590 9.295 2 44.910 6.7656 0.002702 **
## Region:Light_orientation 2.588 2.588 1 47.554 1.8835 0.176377
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_FTL_by_First_move8 <- update(LM_FTL_by_First_move7, . ~ . - Region:Light_orientation)## boundary (singular) fit: see help('isSingular')drop1(LM_FTL_by_First_move8)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## First_move 49.966 49.966 1 45.379 34.5505 4.609e-07 ***
## Treatment_bis 10.605 3.535 3 46.986 2.4444 0.075647 .
## Light_orientation 4.792 4.792 1 48.343 3.3136 0.074902 .
## Region:Treatment_FTL 22.548 11.274 2 45.271 7.7957 0.001232 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Au vu de la complexité du modèle de base, nous utilisons le BIC
BIC(LM_FTL_by_First_move)## [1] 282.0972BIC(LM_FTL_by_First_move8)## [1] 256.6461BIC(LM_FTL_by_First_move7)## [1] 257.729BIC(LM_FTL_by_First_move6)## [1] 258.782BIC(LM_FTL_by_First_move5)## [1] 261.7209BIC(LM_FTL_by_First_move4)## [1] 266.9854BIC(LM_FTL_by_First_move3)## [1] 269.6751BIC(LM_FTL_by_First_move2)## [1] 273.4821BIC(LM_FTL_by_First_move1)## [1] 277.5541Le meilleur modèle est le plus simplifié
LM_FTL_by_First_move <- LM_FTL_by_First_move85.7.3 Treatment VS Teatment_bis
AIC(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data))## boundary (singular) fit: see help('isSingular')## [1] 225.2309AIC(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data))## boundary (singular) fit: see help('isSingular')## [1] 228.0248summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 4.463238865 0.7238142958 42.59248
## First_move 0.003210518 0.0005461953 45.37934
## Treatment_bisFull -0.154709102 0.4459508043 46.70485
## Treatment_bisSmart 0.623988518 0.4936234677 46.47717
## Treatment_bisMixt_smart -0.729863048 0.4939461349 45.11992
## RegionLuxembourg 1.108700393 0.8295757898 38.57466
## Treatment_FTLMix -1.818700940 0.7098137022 38.83903
## Treatment_FTLNight 1.051929611 0.6814252455 41.21263
## Light_orientationSouth 0.637614152 0.3502738958 48.34264
## RegionLuxembourg:Treatment_FTLMix 0.545119326 1.0414989251 43.65128
## RegionLuxembourg:Treatment_FTLNight -2.554254866 0.9748974069 46.23410
## t value Pr(>|t|)
## (Intercept) 6.1662762 2.171262e-07
## First_move 5.8779665 4.609397e-07
## Treatment_bisFull -0.3469197 7.302100e-01
## Treatment_bisSmart 1.2640982 2.124979e-01
## Treatment_bisMixt_smart -1.4776167 1.464573e-01
## RegionLuxembourg 1.3364667 1.892269e-01
## Treatment_FTLMix -2.5622229 1.439439e-02
## Treatment_FTLNight 1.5437198 1.303010e-01
## Light_orientationSouth 1.8203302 7.490230e-02
## RegionLuxembourg:Treatment_FTLMix 0.5233988 6.033439e-01
## RegionLuxembourg:Treatment_FTLNight -2.6200243 1.185581e-02summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 4.692353438 0.8072534789 13.73228
## First_move 0.003063428 0.0005508164 45.43420
## TreatmentFull -0.109496098 0.4543715882 47.04508
## TreatmentSmart 0.042919240 0.4352120203 44.95577
## RegionLuxembourg 1.091384048 0.8434533552 40.67988
## Treatment_FTLMix -1.848885945 0.7189392884 39.96336
## Treatment_FTLNight 0.784744887 0.6762032751 41.15971
## Light_orientationSouth 0.466844418 0.3431429862 48.29462
## RegionLuxembourg:Treatment_FTLMix 0.294829518 1.0722105690 45.64827
## RegionLuxembourg:Treatment_FTLNight -2.482617429 0.9947859722 48.25633
## t value Pr(>|t|)
## (Intercept) 5.81273858 4.861816e-05
## First_move 5.56161363 1.353537e-06
## TreatmentFull -0.24098359 8.106150e-01
## TreatmentSmart 0.09861685 9.218809e-01
## RegionLuxembourg 1.29394713 2.029820e-01
## Treatment_FTLMix -2.57168578 1.394597e-02
## Treatment_FTLNight 1.16051625 2.525258e-01
## Light_orientationSouth 1.36049529 1.799895e-01
## RegionLuxembourg:Treatment_FTLMix 0.27497352 7.845774e-01
## RegionLuxembourg:Treatment_FTLNight -2.49562971 1.604410e-02On garde Treatment_bis
5.7.4 Résultats
Analyse des p-val
summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room) + Region:Treatment_FTL
## Data: Data
##
## REML criterion at convergence: 195.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.09824 -0.49951 -0.03767 0.42591 2.39093
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.033e-02 1.426e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 2.225e-09 4.717e-05
## Residual 1.446e+00 1.203e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 4.4632389 0.7238143 42.5924788 6.166
## First_move 0.0032105 0.0005462 45.3793363 5.878
## Treatment_bisFull -0.1547091 0.4459508 46.7048466 -0.347
## Treatment_bisSmart 0.6239885 0.4936235 46.4771663 1.264
## Treatment_bisMixt_smart -0.7298630 0.4939461 45.1199217 -1.478
## RegionLuxembourg 1.1087004 0.8295758 38.5746579 1.336
## Treatment_FTLMix -1.8187009 0.7098137 38.8390325 -2.562
## Treatment_FTLNight 1.0519296 0.6814252 41.2126319 1.544
## Light_orientationSouth 0.6376142 0.3502739 48.3426426 1.820
## RegionLuxembourg:Treatment_FTLMix 0.5451193 1.0414989 43.6512788 0.523
## RegionLuxembourg:Treatment_FTLNight -2.5542549 0.9748974 46.2340992 -2.620
## Pr(>|t|)
## (Intercept) 2.17e-07 ***
## First_move 4.61e-07 ***
## Treatment_bisFull 0.7302
## Treatment_bisSmart 0.2125
## Treatment_bisMixt_smart 0.1465
## RegionLuxembourg 0.1892
## Treatment_FTLMix 0.0144 *
## Treatment_FTLNight 0.1303
## Light_orientationSouth 0.0749 .
## RegionLuxembourg:Treatment_FTLMix 0.6033
## RegionLuxembourg:Treatment_FTLNight 0.0119 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_F Trtm_S Trt_M_ RgnLxm T_FTLM T_FTLN Lght_S
## First_move -0.482
## Trtmnt_bsFl -0.456 0.210
## Trtmnt_bsSm -0.475 0.109 0.537
## Trtmnt_bsM_ -0.276 -0.003 0.544 0.479
## ReginLxmbrg -0.618 0.152 0.093 0.236 0.114
## Trtmnt_FTLM -0.481 -0.221 0.050 0.142 0.076 0.441
## Trtmnt_FTLN -0.717 0.326 0.080 0.143 -0.091 0.521 0.471
## Lght_rnttnS -0.433 0.301 -0.003 0.148 -0.180 0.221 0.053 0.228
## RgnL:T_FTLM 0.406 0.183 -0.106 -0.268 -0.219 -0.774 -0.724 -0.319 -0.087
## RgnL:T_FTLN 0.551 -0.167 -0.058 -0.234 -0.013 -0.861 -0.376 -0.700 -0.251
## RL:T_FTLM
## First_move
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## ReginLxmbrg
## Trtmnt_FTLM
## Trtmnt_FTLN
## Lght_rnttnS
## RgnL:T_FTLM
## RgnL:T_FTLN 0.654
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room) + Region:Treatment_FTL
## Data: Data_ref_smart
##
## REML criterion at convergence: 195.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.09824 -0.49951 -0.03767 0.42591 2.39093
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.033e-02 1.426e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 2.225e-09 4.717e-05
## Residual 1.446e+00 1.203e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 5.0872274 0.6543759 40.9190037 7.774
## First_move 0.0032105 0.0005462 45.3793363 5.878
## Treatment_bisDark -0.6239885 0.4936235 46.4771662 -1.264
## Treatment_bisFull -0.7786976 0.4537666 46.9076418 -1.716
## Treatment_bisMixt_smart -1.3538516 0.5040639 48.6512049 -2.686
## RegionLuxembourg 1.1087004 0.8295758 38.5746580 1.336
## Treatment_FTLMix -1.8187009 0.7098137 38.8390327 -2.562
## Treatment_FTLNight 1.0519296 0.6814252 41.2126320 1.544
## Light_orientationSouth 0.6376142 0.3502739 48.3426426 1.820
## RegionLuxembourg:Treatment_FTLMix 0.5451193 1.0414989 43.6512790 0.523
## RegionLuxembourg:Treatment_FTLNight -2.5542549 0.9748974 46.2340993 -2.620
## Pr(>|t|)
## (Intercept) 1.38e-09 ***
## First_move 4.61e-07 ***
## Treatment_bisDark 0.21250
## Treatment_bisFull 0.09275 .
## Treatment_bisMixt_smart 0.00987 **
## RegionLuxembourg 0.18923
## Treatment_FTLMix 0.01439 *
## Treatment_FTLNight 0.13030
## Light_orientationSouth 0.07490 .
## RegionLuxembourg:Treatment_FTLMix 0.60334
## RegionLuxembourg:Treatment_FTLNight 0.01186 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_D Trtm_F Trt_M_ RgnLxm T_FTLM T_FTLN Lght_S
## First_move -0.451
## Trtmnt_bsDr -0.229 -0.109
## Trtmnt_bsFl -0.346 0.088 0.560
## Trtmnt_bsM_ -0.169 -0.110 0.510 0.562
## ReginLxmbrg -0.506 0.152 -0.236 -0.166 -0.120
## Trtmnt_FTLM -0.424 -0.221 -0.142 -0.106 -0.065 0.441
## Trtmnt_FTLN -0.685 0.326 -0.143 -0.077 -0.229 0.521 0.471
## Lght_rnttnS -0.367 0.301 -0.148 -0.164 -0.322 0.221 0.053 0.228
## RgnL:T_FTLM 0.247 0.183 0.268 0.188 0.048 -0.774 -0.724 -0.319 -0.087
## RgnL:T_FTLN 0.433 -0.167 0.234 0.198 0.217 -0.861 -0.376 -0.700 -0.251
## RL:T_FTLM
## First_move
## Trtmnt_bsDr
## Trtmnt_bsFl
## Trtmnt_bsM_
## ReginLxmbrg
## Trtmnt_FTLM
## Trtmnt_FTLN
## Lght_rnttnS
## RgnL:T_FTLM
## RgnL:T_FTLN 0.654
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room) + Region:Treatment_FTL
## Data: Data_ref_full
##
## REML criterion at convergence: 195.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.09824 -0.49951 -0.03767 0.42591 2.39093
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.033e-02 1.426e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 2.225e-09 4.717e-05
## Residual 1.446e+00 1.203e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 4.3085298 0.6545656 41.1846073 6.582
## First_move 0.0032105 0.0005462 45.3793363 5.878
## Treatment_bisDark 0.1547091 0.4459508 46.7048466 0.347
## Treatment_bisSmart 0.7786976 0.4537666 46.9076420 1.716
## Treatment_bisMixt_smart -0.5751539 0.4506316 48.8322907 -1.276
## RegionLuxembourg 1.1087004 0.8295758 38.5746579 1.336
## Treatment_FTLMix -1.8187009 0.7098137 38.8390326 -2.562
## Treatment_FTLNight 1.0519296 0.6814252 41.2126320 1.544
## Light_orientationSouth 0.6376142 0.3502739 48.3426426 1.820
## RegionLuxembourg:Treatment_FTLMix 0.5451193 1.0414989 43.6512787 0.523
## RegionLuxembourg:Treatment_FTLNight -2.5542549 0.9748974 46.2340992 -2.620
## Pr(>|t|)
## (Intercept) 6.30e-08 ***
## First_move 4.61e-07 ***
## Treatment_bisDark 0.7302
## Treatment_bisSmart 0.0927 .
## Treatment_bisMixt_smart 0.2079
## RegionLuxembourg 0.1892
## Treatment_FTLMix 0.0144 *
## Treatment_FTLNight 0.1303
## Light_orientationSouth 0.0749 .
## RegionLuxembourg:Treatment_FTLMix 0.6033
## RegionLuxembourg:Treatment_FTLNight 0.0119 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_D Trtm_S Trt_M_ RgnLxm T_FTLM T_FTLN Lght_S
## First_move -0.390
## Trtmnt_bsDr -0.177 -0.210
## Trtmnt_bsSm -0.347 -0.088 0.398
## Trtmnt_bsM_ -0.103 -0.211 0.393 0.379
## ReginLxmbrg -0.620 0.152 -0.093 0.166 0.033
## Trtmnt_FTLM -0.498 -0.221 -0.050 0.106 0.034 0.441
## Trtmnt_FTLN -0.738 0.326 -0.080 0.077 -0.179 0.521 0.471
## Lght_rnttnS -0.481 0.301 0.003 0.164 -0.195 0.221 0.053 0.228
## RgnL:T_FTLM 0.377 0.183 0.106 -0.188 -0.136 -0.774 -0.724 -0.319 -0.087
## RgnL:T_FTLN 0.570 -0.167 0.058 -0.198 0.043 -0.861 -0.376 -0.700 -0.251
## RL:T_FTLM
## First_move
## Trtmnt_bsDr
## Trtmnt_bsSm
## Trtmnt_bsM_
## ReginLxmbrg
## Trtmnt_FTLM
## Trtmnt_FTLN
## Lght_rnttnS
## RgnL:T_FTLM
## RgnL:T_FTLN 0.654
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data_ref_mixt_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room) + Region:Treatment_FTL
## Data: Data_ref_mixt_smart
##
## REML criterion at convergence: 195.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.09824 -0.49951 -0.03767 0.42591 2.39093
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.033e-02 1.426e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 2.225e-09 4.718e-05
## Residual 1.446e+00 1.203e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.7333758 0.7555112 43.4146328 4.942
## First_move 0.0032105 0.0005462 45.3793363 5.878
## Treatment_bisDark 0.7298630 0.4939461 45.1199224 1.478
## Treatment_bisFull 0.5751539 0.4506316 48.8322905 1.276
## Treatment_bisSmart 1.3538516 0.5040639 48.6512095 2.686
## RegionLuxembourg 1.1087004 0.8295758 38.5746582 1.336
## Treatment_FTLMix -1.8187009 0.7098137 38.8390327 -2.562
## Treatment_FTLNight 1.0519296 0.6814252 41.2126323 1.544
## Light_orientationSouth 0.6376142 0.3502739 48.3426426 1.820
## RegionLuxembourg:Treatment_FTLMix 0.5451193 1.0414989 43.6512789 0.523
## RegionLuxembourg:Treatment_FTLNight -2.5542549 0.9748974 46.2340994 -2.620
## Pr(>|t|)
## (Intercept) 1.20e-05 ***
## First_move 4.61e-07 ***
## Treatment_bisDark 0.14646
## Treatment_bisFull 0.20788
## Treatment_bisSmart 0.00987 **
## RegionLuxembourg 0.18923
## Treatment_FTLMix 0.01439 *
## Treatment_FTLNight 0.13030
## Light_orientationSouth 0.07490 .
## RegionLuxembourg:Treatment_FTLMix 0.60334
## RegionLuxembourg:Treatment_FTLNight 0.01186 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_D Trtm_F Trtm_S RgnLxm T_FTLM T_FTLN Lght_S
## First_move -0.464
## Trtmnt_bsDr -0.390 0.003
## Trtmnt_bsFl -0.507 0.211 0.557
## Trtmnt_bsSm -0.521 0.110 0.511 0.553
## ReginLxmbrg -0.518 0.152 -0.114 -0.033 0.120
## Trtmnt_FTLM -0.411 -0.221 -0.076 -0.034 0.065 0.441
## Trtmnt_FTLN -0.746 0.326 0.091 0.179 0.229 0.521 0.471
## Lght_rnttnS -0.533 0.301 0.180 0.195 0.322 0.221 0.053 0.228
## RgnL:T_FTLM 0.246 0.183 0.219 0.136 -0.048 -0.774 -0.724 -0.319 -0.087
## RgnL:T_FTLN 0.520 -0.167 0.013 -0.043 -0.217 -0.861 -0.376 -0.700 -0.251
## RL:T_FTLM
## First_move
## Trtmnt_bsDr
## Trtmnt_bsFl
## Trtmnt_bsSm
## ReginLxmbrg
## Trtmnt_FTLM
## Trtmnt_FTLN
## Lght_rnttnS
## RgnL:T_FTLM
## RgnL:T_FTLN 0.654
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data_refFTL_Mix))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room) + Region:Treatment_FTL
## Data: Data_refFTL_Mix
##
## REML criterion at convergence: 195.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.09824 -0.49951 -0.03767 0.42591 2.39093
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.033e-02 1.426e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 2.225e-09 4.717e-05
## Residual 1.446e+00 1.203e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 2.6445379 0.7306158 46.1457854 3.620
## First_move 0.0032105 0.0005462 45.3793362 5.878
## Treatment_bisFull -0.1547091 0.4459508 46.7048466 -0.347
## Treatment_bisSmart 0.6239885 0.4936235 46.4771662 1.264
## Treatment_bisMixt_smart -0.7298630 0.4939461 45.1199213 -1.478
## RegionLuxembourg 1.6538197 0.6592514 31.1147087 2.509
## Treatment_FTLDay 1.8187009 0.7098137 38.8390326 2.562
## Treatment_FTLNight 2.8706306 0.7157426 48.8963349 4.011
## Light_orientationSouth 0.6376142 0.3502739 48.3426426 1.820
## RegionLuxembourg:Treatment_FTLDay -0.5451193 1.0414989 43.6512789 -0.523
## RegionLuxembourg:Treatment_FTLNight -3.0993742 0.8413615 45.4581734 -3.684
## Pr(>|t|)
## (Intercept) 0.000730 ***
## First_move 4.61e-07 ***
## Treatment_bisFull 0.730210
## Treatment_bisSmart 0.212498
## Treatment_bisMixt_smart 0.146457
## RegionLuxembourg 0.017540 *
## Treatment_FTLDay 0.014394 *
## Treatment_FTLNight 0.000207 ***
## Light_orientationSouth 0.074902 .
## RegionLuxembourg:Treatment_FTLDay 0.603344
## RegionLuxembourg:Treatment_FTLNight 0.000609 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_F Trtm_S Trt_M_ RgnLxm T_FTLD T_FTLN Lght_S
## First_move -0.693
## Trtmnt_bsFl -0.403 0.210
## Trtmnt_bsSm -0.332 0.109 0.537
## Trtmnt_bsM_ -0.199 -0.003 0.544 0.479
## ReginLxmbrg -0.707 0.480 -0.050 -0.127 -0.203
## Trtmnt_FTLD -0.495 0.221 -0.050 -0.142 -0.076 0.589
## Trtmnt_FTLN -0.731 0.530 0.027 -0.005 -0.162 0.729 0.543
## Lght_rnttnS -0.378 0.301 -0.003 0.148 -0.180 0.141 -0.053 0.164
## RgnL:T_FTLD 0.301 -0.183 0.106 0.268 0.219 -0.605 -0.724 -0.414 0.087
## RgnL:T_FTLN 0.581 -0.420 0.064 0.061 0.256 -0.808 -0.460 -0.853 -0.183
## RL:T_FTLD
## First_move
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## ReginLxmbrg
## Trtmnt_FTLD
## Trtmnt_FTLN
## Lght_rnttnS
## RgnL:T_FTLD
## RgnL:T_FTLN 0.481
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data_refFTL_Night))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region +
## Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) +
## (1 | Room) + Region:Treatment_FTL
## Data: Data_refFTL_Night
##
## REML criterion at convergence: 195.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.09824 -0.49951 -0.03767 0.42591 2.39093
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.033e-02 1.426e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 2.225e-09 4.717e-05
## Residual 1.446e+00 1.203e+00
## Number of obs: 60, groups: Mother, 21; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 5.5151685 0.5302735 48.9892980 10.401
## First_move 0.0032105 0.0005462 45.3793363 5.878
## Treatment_bisFull -0.1547091 0.4459508 46.7048466 -0.347
## Treatment_bisSmart 0.6239885 0.4936235 46.4771665 1.264
## Treatment_bisMixt_smart -0.7298630 0.4939461 45.1199234 -1.478
## RegionLuxembourg -1.4455545 0.4958897 34.5349139 -2.915
## Treatment_FTLDay -1.0519296 0.6814252 41.2126321 -1.544
## Treatment_FTLMix -2.8706306 0.7157426 48.8963349 -4.011
## Light_orientationSouth 0.6376142 0.3502739 48.3426426 1.820
## RegionLuxembourg:Treatment_FTLDay 2.5542549 0.9748974 46.2340993 2.620
## RegionLuxembourg:Treatment_FTLMix 3.0993742 0.8413615 45.4581735 3.684
## Pr(>|t|)
## (Intercept) 5.39e-14 ***
## First_move 4.61e-07 ***
## Treatment_bisFull 0.730210
## Treatment_bisSmart 0.212498
## Treatment_bisMixt_smart 0.146457
## RegionLuxembourg 0.006204 **
## Treatment_FTLDay 0.130301
## Treatment_FTLMix 0.000207 ***
## Light_orientationSouth 0.074902 .
## RegionLuxembourg:Treatment_FTLDay 0.011856 *
## RegionLuxembourg:Treatment_FTLMix 0.000609 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_F Trtm_S Trt_M_ RgnLxm T_FTLD T_FTLM Lght_S
## First_move -0.240
## Trtmnt_bsFl -0.519 0.210
## Trtmnt_bsSm -0.464 0.109 0.537
## Trtmnt_bsM_ -0.493 -0.003 0.544 0.479
## ReginLxmbrg -0.581 -0.075 0.041 -0.066 0.165
## Trtmnt_FTLD -0.307 -0.326 -0.080 -0.143 0.091 0.505
## Trtmnt_FTLM -0.342 -0.530 -0.027 0.005 0.162 0.478 0.485
## Lght_rnttnS -0.299 0.301 -0.003 0.148 -0.180 -0.124 -0.228 -0.164
## RgnL:T_FTLD 0.148 0.167 0.058 0.234 0.013 -0.526 -0.700 -0.293 0.251
## RgnL:T_FTLM 0.350 0.420 -0.064 -0.061 -0.256 -0.622 -0.416 -0.853 0.183
## RL:T_FTLD
## First_move
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## ReginLxmbrg
## Trtmnt_FTLD
## Trtmnt_FTLM
## Lght_rnttnS
## RgnL:T_FTLD
## RgnL:T_FTLM 0.350
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference_Treatment = "Smart", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference_Treatment = "Full", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test4 <- data.frame(Reference_Treatment = "Mixt_smart", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data_ref_mixt_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test5 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Mixt", as.data.frame(( summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data_refFTL_Mix))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test6 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Night", as.data.frame(( summary(lmer(log(Flight_to_light + 0.1) ~ First_move + Treatment_bis + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) + Region:Treatment_FTL, data = Data_refFTL_Night))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_FTL_by_first_move <- rbind(test1,test2,test3,test4,test5,test6)
colnames(Results_FTL_by_first_move ) <- c("Reference_Treatment", "Reference_Timing" ,"Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_FTL_by_first_move , file = "output/Results_FTL_by_first_move.csv" )
kable(Results_FTL_by_first_move , caption = " Temps mis pour voler à la lumière en fonction du temps mis pour bouger ", padding = 1 )| Reference_Treatment | Reference_Timing | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|---|
| (Intercept) | Dark | Day | 4.4632389 | 0.7238143 | 42.59248 | 6.1662762 | 0.0000002 |
| First_move | Dark | Day | 0.0032105 | 0.0005462 | 45.37934 | 5.8779665 | 0.0000005 |
| Treatment_bisFull | Dark | Day | -0.1547091 | 0.4459508 | 46.70485 | -0.3469197 | 0.7302100 |
| Treatment_bisSmart | Dark | Day | 0.6239885 | 0.4936235 | 46.47717 | 1.2640982 | 0.2124979 |
| Treatment_bisMixt_smart | Dark | Day | -0.7298630 | 0.4939461 | 45.11992 | -1.4776167 | 0.1464573 |
| RegionLuxembourg | Dark | Day | 1.1087004 | 0.8295758 | 38.57466 | 1.3364667 | 0.1892269 |
| Treatment_FTLMix | Dark | Day | -1.8187009 | 0.7098137 | 38.83903 | -2.5622229 | 0.0143944 |
| Treatment_FTLNight | Dark | Day | 1.0519296 | 0.6814252 | 41.21263 | 1.5437198 | 0.1303010 |
| Light_orientationSouth | Dark | Day | 0.6376142 | 0.3502739 | 48.34264 | 1.8203302 | 0.0749023 |
| RegionLuxembourg:Treatment_FTLMix | Dark | Day | 0.5451193 | 1.0414989 | 43.65128 | 0.5233988 | 0.6033439 |
| RegionLuxembourg:Treatment_FTLNight | Dark | Day | -2.5542549 | 0.9748974 | 46.23410 | -2.6200243 | 0.0118558 |
| (Intercept)1 | Smart | Day | 5.0872274 | 0.6543759 | 40.91900 | 7.7741670 | 0.0000000 |
| First_move1 | Smart | Day | 0.0032105 | 0.0005462 | 45.37934 | 5.8779665 | 0.0000005 |
| Treatment_bisDark | Smart | Day | -0.6239885 | 0.4936235 | 46.47717 | -1.2640982 | 0.2124979 |
| Treatment_bisFull1 | Smart | Day | -0.7786976 | 0.4537666 | 46.90764 | -1.7160752 | 0.0927467 |
| Treatment_bisMixt_smart1 | Smart | Day | -1.3538516 | 0.5040639 | 48.65120 | -2.6858729 | 0.0098672 |
| RegionLuxembourg1 | Smart | Day | 1.1087004 | 0.8295758 | 38.57466 | 1.3364667 | 0.1892269 |
| Treatment_FTLMix1 | Smart | Day | -1.8187009 | 0.7098137 | 38.83903 | -2.5622229 | 0.0143944 |
| Treatment_FTLNight1 | Smart | Day | 1.0519296 | 0.6814252 | 41.21263 | 1.5437198 | 0.1303010 |
| Light_orientationSouth1 | Smart | Day | 0.6376142 | 0.3502739 | 48.34264 | 1.8203302 | 0.0749023 |
| RegionLuxembourg:Treatment_FTLMix1 | Smart | Day | 0.5451193 | 1.0414989 | 43.65128 | 0.5233988 | 0.6033439 |
| RegionLuxembourg:Treatment_FTLNight1 | Smart | Day | -2.5542549 | 0.9748974 | 46.23410 | -2.6200243 | 0.0118558 |
| (Intercept)2 | Full | Day | 4.3085298 | 0.6545656 | 41.18461 | 6.5822733 | 0.0000001 |
| First_move2 | Full | Day | 0.0032105 | 0.0005462 | 45.37934 | 5.8779665 | 0.0000005 |
| Treatment_bisDark1 | Full | Day | 0.1547091 | 0.4459508 | 46.70485 | 0.3469197 | 0.7302100 |
| Treatment_bisSmart1 | Full | Day | 0.7786976 | 0.4537666 | 46.90764 | 1.7160752 | 0.0927467 |
| Treatment_bisMixt_smart2 | Full | Day | -0.5751539 | 0.4506316 | 48.83229 | -1.2763285 | 0.2078764 |
| RegionLuxembourg2 | Full | Day | 1.1087004 | 0.8295758 | 38.57466 | 1.3364667 | 0.1892269 |
| Treatment_FTLMix2 | Full | Day | -1.8187009 | 0.7098137 | 38.83903 | -2.5622229 | 0.0143944 |
| Treatment_FTLNight2 | Full | Day | 1.0519296 | 0.6814252 | 41.21263 | 1.5437198 | 0.1303010 |
| Light_orientationSouth2 | Full | Day | 0.6376142 | 0.3502739 | 48.34264 | 1.8203302 | 0.0749023 |
| RegionLuxembourg:Treatment_FTLMix2 | Full | Day | 0.5451193 | 1.0414989 | 43.65128 | 0.5233988 | 0.6033439 |
| RegionLuxembourg:Treatment_FTLNight2 | Full | Day | -2.5542549 | 0.9748974 | 46.23410 | -2.6200243 | 0.0118558 |
| (Intercept)3 | Mixt_smart | Day | 3.7333758 | 0.7555112 | 43.41463 | 4.9415226 | 0.0000120 |
| First_move3 | Mixt_smart | Day | 0.0032105 | 0.0005462 | 45.37934 | 5.8779665 | 0.0000005 |
| Treatment_bisDark2 | Mixt_smart | Day | 0.7298630 | 0.4939461 | 45.11992 | 1.4776167 | 0.1464573 |
| Treatment_bisFull2 | Mixt_smart | Day | 0.5751539 | 0.4506316 | 48.83229 | 1.2763285 | 0.2078764 |
| Treatment_bisSmart2 | Mixt_smart | Day | 1.3538516 | 0.5040639 | 48.65121 | 2.6858729 | 0.0098672 |
| RegionLuxembourg3 | Mixt_smart | Day | 1.1087004 | 0.8295758 | 38.57466 | 1.3364667 | 0.1892269 |
| Treatment_FTLMix3 | Mixt_smart | Day | -1.8187009 | 0.7098137 | 38.83903 | -2.5622229 | 0.0143944 |
| Treatment_FTLNight3 | Mixt_smart | Day | 1.0519296 | 0.6814252 | 41.21263 | 1.5437198 | 0.1303010 |
| Light_orientationSouth3 | Mixt_smart | Day | 0.6376142 | 0.3502739 | 48.34264 | 1.8203302 | 0.0749023 |
| RegionLuxembourg:Treatment_FTLMix3 | Mixt_smart | Day | 0.5451193 | 1.0414989 | 43.65128 | 0.5233988 | 0.6033439 |
| RegionLuxembourg:Treatment_FTLNight3 | Mixt_smart | Day | -2.5542549 | 0.9748974 | 46.23410 | -2.6200243 | 0.0118558 |
| (Intercept)4 | Dark | Mixt | 2.6445379 | 0.7306158 | 46.14579 | 3.6196014 | 0.0007302 |
| First_move4 | Dark | Mixt | 0.0032105 | 0.0005462 | 45.37934 | 5.8779665 | 0.0000005 |
| Treatment_bisFull3 | Dark | Mixt | -0.1547091 | 0.4459508 | 46.70485 | -0.3469197 | 0.7302100 |
| Treatment_bisSmart3 | Dark | Mixt | 0.6239885 | 0.4936235 | 46.47717 | 1.2640982 | 0.2124979 |
| Treatment_bisMixt_smart3 | Dark | Mixt | -0.7298630 | 0.4939461 | 45.11992 | -1.4776167 | 0.1464573 |
| RegionLuxembourg4 | Dark | Mixt | 1.6538197 | 0.6592514 | 31.11471 | 2.5086327 | 0.0175405 |
| Treatment_FTLDay | Dark | Mixt | 1.8187009 | 0.7098137 | 38.83903 | 2.5622229 | 0.0143944 |
| Treatment_FTLNight4 | Dark | Mixt | 2.8706306 | 0.7157426 | 48.89633 | 4.0107022 | 0.0002068 |
| Light_orientationSouth4 | Dark | Mixt | 0.6376142 | 0.3502739 | 48.34264 | 1.8203302 | 0.0749023 |
| RegionLuxembourg:Treatment_FTLDay | Dark | Mixt | -0.5451193 | 1.0414989 | 43.65128 | -0.5233988 | 0.6033439 |
| RegionLuxembourg:Treatment_FTLNight4 | Dark | Mixt | -3.0993742 | 0.8413615 | 45.45817 | -3.6837602 | 0.0006092 |
| (Intercept)5 | Dark | Night | 5.5151685 | 0.5302735 | 48.98930 | 10.4006102 | 0.0000000 |
| First_move5 | Dark | Night | 0.0032105 | 0.0005462 | 45.37934 | 5.8779665 | 0.0000005 |
| Treatment_bisFull4 | Dark | Night | -0.1547091 | 0.4459508 | 46.70485 | -0.3469197 | 0.7302100 |
| Treatment_bisSmart4 | Dark | Night | 0.6239885 | 0.4936235 | 46.47717 | 1.2640982 | 0.2124979 |
| Treatment_bisMixt_smart4 | Dark | Night | -0.7298630 | 0.4939461 | 45.11992 | -1.4776167 | 0.1464573 |
| RegionLuxembourg5 | Dark | Night | -1.4455545 | 0.4958897 | 34.53491 | -2.9150728 | 0.0062041 |
| Treatment_FTLDay1 | Dark | Night | -1.0519296 | 0.6814252 | 41.21263 | -1.5437198 | 0.1303010 |
| Treatment_FTLMix4 | Dark | Night | -2.8706306 | 0.7157426 | 48.89633 | -4.0107022 | 0.0002068 |
| Light_orientationSouth5 | Dark | Night | 0.6376142 | 0.3502739 | 48.34264 | 1.8203302 | 0.0749023 |
| RegionLuxembourg:Treatment_FTLDay1 | Dark | Night | 2.5542549 | 0.9748974 | 46.23410 | 2.6200243 | 0.0118558 |
| RegionLuxembourg:Treatment_FTLMix4 | Dark | Night | 3.0993742 | 0.8413615 | 45.45817 | 3.6837602 | 0.0006092 |
Info_Flight_to_light_by_First_move <- "
En moyenne, au plus un individu a bougé rapidement, au plus il volera à la lampe rapidement.
Les individus expérimentés de jours avec 30 min à l'obscurité mettent significativement moins de temps pour atteindre la lampe par rapport aux individus testés à d'autres timing.
Les individus expérimentés de jours avec 30 min à l'obscurité descendant d'une mère provenant du luxembourg mettent significativement plus de temps pour atteindre la lampe par rapport aux mêmes individus descendants d'une mère provenant du Brabant.
Les individus mettent quasiement significativement (p-val = 0.0749) plus de temps pour aller à la lampe quand elle est au Sud.
Les individus descendant d'une mère provenant de la région luxembourgeoise et expérimentés la nuit mettent significativement moins de temps pour voler à la lumière.
Les individus du traitement Mixt-smart mettent significativement moins de temps pour voler à la lampe que les individus du traitement Smart.
"5.7.5 Visualisation
ggplot(data = Data, aes(x = log(First_move), y = log(Flight_to_light+0.1))) +
geom_smooth(method = "lm", aes(color = Treatment_FTL), se = T, alpha = 0.2) +
geom_point(aes(color = Treatment_FTL, shape = Treatment_bis), alpha = 0.75) +
labs(title = "Temps pour voler à la lumière en fonction du temps pour faire le premier mouvement", x = "log(Temps pour le premier mouvement (s))", y = "log(Temps pour voler à la lumière (s))", color = "Timing", shape = "Traitement") +
theme_bw() +
theme(title=element_text(size=10))## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 400 rows containing non-finite values (`stat_smooth()`).## Warning: Removed 390 rows containing missing values (`geom_point()`).
5.8 STL_by_First_move
5.8.1 Test
LM_Speed_to_light_by_First_move <- lmer(log(Speed_to_light+0.000001) ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) , data = Data)## boundary (singular) fit: see help('isSingular')summary(LM_Speed_to_light_by_First_move)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ First_move + Treatment_bis + Sex +
## Region + Treatment_FTL + Light_orientation + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data
##
## REML criterion at convergence: 692.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.01775 -0.65717 -0.07406 0.63276 2.20497
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.699e+00 1.642765
## Site (Intercept) 3.247e+00 1.802035
## Room (Intercept) 1.417e-08 0.000119
## Residual 3.416e+01 5.844406
## Number of obs: 110, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -13.417097 2.121696 24.497447 -6.324 1.41e-06 ***
## First_move 0.001244 0.001761 92.275774 0.707 0.48154
## Treatment_bisFull 2.734727 1.519617 93.663025 1.800 0.07514 .
## Treatment_bisSmart 1.013157 1.714339 91.897979 0.591 0.55598
## Treatment_bisMixt_smart 2.550798 1.644914 92.078674 1.551 0.12440
## SexMale -0.103134 1.186712 90.551400 -0.087 0.93094
## RegionLuxembourg 3.268222 1.840014 7.449481 1.776 0.11638
## Treatment_FTLMix 4.799654 1.679418 86.731824 2.858 0.00534 **
## Treatment_FTLNight 7.109570 1.639176 87.379616 4.337 3.85e-05 ***
## Light_orientationSouth -0.095795 1.176134 90.392439 -0.081 0.93527
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## First_move -0.471
## Trtmnt_bsFl -0.415 0.123
## Trtmnt_bsSm -0.321 0.055 0.440
## Trtmnt_bsM_ -0.302 -0.001 0.466 0.381
## SexMale -0.286 0.052 0.003 0.114 0.066
## ReginLxmbrg -0.425 0.163 0.031 -0.093 0.010 0.033
## Trtmnt_FTLM -0.335 0.123 0.080 0.015 -0.006 -0.108 -0.220
## Trtmnt_FTLN -0.411 0.310 0.051 -0.029 -0.020 -0.029 -0.111 0.597
## Lght_rnttnS -0.280 0.068 -0.087 0.021 -0.122 0.024 0.080 -0.005 -0.076
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')qqnorm(resid(LM_Speed_to_light_by_First_move))
qqline(resid(LM_Speed_to_light_by_First_move))
Homogénité des variances
plot(LM_Speed_to_light_by_First_move)
Distance de cook
plot(cooks.distance(LM_Speed_to_light_by_First_move))
5.8.2 Simplification du modèle
On est partit d’un modèle avec aucune interaction aussi non le modèle devient trop complexe pour très peu d’échantillons.
5.8.3 Treatment VS Treatment_bis
AIC(lmer(log(Speed_to_light+0.000001) ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) , data = Data))## boundary (singular) fit: see help('isSingular')## [1] 720.311AIC(lmer(log(Speed_to_light+0.000001) ~ First_move + Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) , data = Data))## [1] 722.0312summary(lmer(log(Speed_to_light+0.000001) ~ First_move + Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) , data = Data))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) -13.417096726 2.121696335 24.497447 -6.32375920
## First_move 0.001244351 0.001760816 92.275774 0.70669030
## Treatment_bisFull 2.734727118 1.519616597 93.663025 1.79961651
## Treatment_bisSmart 1.013156765 1.714338533 91.897979 0.59098990
## Treatment_bisMixt_smart 2.550798172 1.644914251 92.078674 1.55071802
## SexMale -0.103134245 1.186712445 90.551400 -0.08690753
## RegionLuxembourg 3.268222256 1.840014001 7.449481 1.77619423
## Treatment_FTLMix 4.799653803 1.679418069 86.731824 2.85792674
## Treatment_FTLNight 7.109570363 1.639176355 87.379616 4.33728216
## Light_orientationSouth -0.095794730 1.176133673 90.392439 -0.08144885
## Pr(>|t|)
## (Intercept) 1.407205e-06
## First_move 4.815397e-01
## Treatment_bisFull 7.514111e-02
## Treatment_bisSmart 5.559780e-01
## Treatment_bisMixt_smart 1.243997e-01
## SexMale 9.309369e-01
## RegionLuxembourg 1.163774e-01
## Treatment_FTLMix 5.338094e-03
## Treatment_FTLNight 3.854067e-05
## Light_orientationSouth 9.352651e-01summary(lmer(log(Speed_to_light+0.000001) ~ First_move + Treatment + Sex + Region + Treatment_FTL + Light_orientation + (1|Mother) + (1|Site) + (1|Room) , data = Data))$coeff## Estimate Std. Error df t value
## (Intercept) -13.47489204 2.133917682 25.129126 -6.31462598
## First_move 0.00131445 0.001748786 90.568592 0.75163586
## TreatmentFull 2.71170413 1.511502559 92.967695 1.79404535
## TreatmentSmart 1.79995243 1.387836559 91.122242 1.29694842
## SexMale -0.04639529 1.178675286 89.954337 -0.03936223
## RegionLuxembourg 3.21183656 1.830479874 7.403374 1.75464183
## Treatment_FTLMix 4.74954675 1.676179370 84.364983 2.83355519
## Treatment_FTLNight 7.00209744 1.632484787 83.439941 4.28922677
## Light_orientationSouth 0.06541316 1.159801323 88.959284 0.05640032
## Pr(>|t|)
## (Intercept) 1.282046e-06
## First_move 4.542189e-01
## TreatmentFull 7.605671e-02
## TreatmentSmart 1.979233e-01
## SexMale 9.686888e-01
## RegionLuxembourg 1.204269e-01
## Treatment_FTLMix 5.757649e-03
## Treatment_FTLNight 4.794276e-05
## Light_orientationSouth 9.551494e-01Il serait légèrement préférable de continuer avec Treatment_bis
5.8.4 Résultats
Analyse des p-val
summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ First_move + Treatment_bis + Sex +
## Region + Treatment_FTL + Light_orientation + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data
##
## REML criterion at convergence: 692.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.01775 -0.65717 -0.07406 0.63276 2.20497
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.699e+00 1.642765
## Site (Intercept) 3.247e+00 1.802035
## Room (Intercept) 1.417e-08 0.000119
## Residual 3.416e+01 5.844406
## Number of obs: 110, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -13.417097 2.121696 24.497447 -6.324 1.41e-06 ***
## First_move 0.001244 0.001761 92.275774 0.707 0.48154
## Treatment_bisFull 2.734727 1.519617 93.663025 1.800 0.07514 .
## Treatment_bisSmart 1.013157 1.714339 91.897979 0.591 0.55598
## Treatment_bisMixt_smart 2.550798 1.644914 92.078674 1.551 0.12440
## SexMale -0.103134 1.186712 90.551400 -0.087 0.93094
## RegionLuxembourg 3.268222 1.840014 7.449481 1.776 0.11638
## Treatment_FTLMix 4.799654 1.679418 86.731824 2.858 0.00534 **
## Treatment_FTLNight 7.109570 1.639176 87.379616 4.337 3.85e-05 ***
## Light_orientationSouth -0.095795 1.176134 90.392439 -0.081 0.93527
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## First_move -0.471
## Trtmnt_bsFl -0.415 0.123
## Trtmnt_bsSm -0.321 0.055 0.440
## Trtmnt_bsM_ -0.302 -0.001 0.466 0.381
## SexMale -0.286 0.052 0.003 0.114 0.066
## ReginLxmbrg -0.425 0.163 0.031 -0.093 0.010 0.033
## Trtmnt_FTLM -0.335 0.123 0.080 0.015 -0.006 -0.108 -0.220
## Trtmnt_FTLN -0.411 0.310 0.051 -0.029 -0.020 -0.029 -0.111 0.597
## Lght_rnttnS -0.280 0.068 -0.087 0.021 -0.122 0.024 0.080 -0.005 -0.076
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ First_move + Treatment_bis + Sex +
## Region + Treatment_FTL + Light_orientation + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data_ref_full
##
## REML criterion at convergence: 692.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.01775 -0.65717 -0.07406 0.63276 2.20497
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.699e+00 1.642765
## Site (Intercept) 3.247e+00 1.802035
## Room (Intercept) 1.417e-08 0.000119
## Residual 3.416e+01 5.844406
## Number of obs: 110, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -10.682370 2.033615 26.782549 -5.253 1.58e-05 ***
## First_move 0.001244 0.001761 92.275774 0.707 0.48154
## Treatment_bisDark -2.734727 1.519617 93.663024 -1.800 0.07514 .
## Treatment_bisSmart -1.721570 1.719342 92.071638 -1.001 0.31931
## Treatment_bisMixt_smart -0.183929 1.638545 87.263545 -0.112 0.91088
## SexMale -0.103134 1.186712 90.551400 -0.087 0.93094
## RegionLuxembourg 3.268222 1.840014 7.449481 1.776 0.11638
## Treatment_FTLMix 4.799654 1.679418 86.731824 2.858 0.00534 **
## Treatment_FTLNight 7.109570 1.639176 87.379616 4.337 3.85e-05 ***
## Light_orientationSouth -0.095795 1.176134 90.392439 -0.081 0.93527
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## First_move -0.400
## Trtmnt_bsDr -0.314 -0.123
## Trtmnt_bsSm -0.285 -0.053 0.445
## Trtmnt_bsM_ -0.258 -0.114 0.460 0.380
## SexMale -0.296 0.052 -0.003 0.111 0.064
## ReginLxmbrg -0.420 0.163 -0.031 -0.121 -0.019 0.033
## Trtmnt_FTLM -0.290 0.123 -0.080 -0.056 -0.081 -0.108 -0.220
## Trtmnt_FTLN -0.391 0.310 -0.051 -0.074 -0.067 -0.029 -0.111 0.597
## Lght_rnttnS -0.357 0.068 0.087 0.098 -0.043 0.024 0.080 -0.005 -0.076
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ First_move + Treatment_bis + Sex +
## Region + Treatment_FTL + Light_orientation + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data_ref_smart
##
## REML criterion at convergence: 692.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.01775 -0.65717 -0.07406 0.63276 2.20497
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.699e+00 1.642765
## Site (Intercept) 3.247e+00 1.802035
## Room (Intercept) 1.417e-08 0.000119
## Residual 3.416e+01 5.844406
## Number of obs: 110, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -12.403940 2.258758 32.509707 -5.491 4.53e-06 ***
## First_move 0.001244 0.001761 92.275774 0.707 0.48154
## Treatment_bisDark -1.013157 1.714339 91.897979 -0.591 0.55598
## Treatment_bisFull 1.721570 1.719342 92.071639 1.001 0.31931
## Treatment_bisMixt_smart 1.537641 1.870205 94.894187 0.822 0.41304
## SexMale -0.103134 1.186712 90.551400 -0.087 0.93094
## RegionLuxembourg 3.268222 1.840014 7.449481 1.776 0.11638
## Treatment_FTLMix 4.799654 1.679418 86.731824 2.858 0.00534 **
## Treatment_FTLNight 7.109570 1.639176 87.379616 4.337 3.85e-05 ***
## Light_orientationSouth -0.095795 1.176134 90.392439 -0.081 0.93527
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_FTLM T_FTLN
## First_move -0.400
## Trtmnt_bsDr -0.457 -0.055
## Trtmnt_bsFl -0.505 0.053 0.608
## Trtmnt_bsM_ -0.414 -0.051 0.582 0.586
## SexMale -0.182 0.052 -0.114 -0.111 -0.046
## ReginLxmbrg -0.470 0.163 0.093 0.121 0.094 0.033
## Trtmnt_FTLM -0.303 0.123 -0.015 0.056 -0.019 -0.108 -0.220
## Trtmnt_FTLN -0.408 0.310 0.029 0.074 0.009 -0.029 -0.111 0.597
## Lght_rnttnS -0.247 0.068 -0.021 -0.098 -0.127 0.024 0.080 -0.005 -0.076
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_mixt_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ First_move + Treatment_bis + Sex +
## Region + Treatment_FTL + Light_orientation + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data_ref_mixt_smart
##
## REML criterion at convergence: 692.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.01775 -0.65717 -0.07406 0.63276 2.20497
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.699e+00 1.642765
## Site (Intercept) 3.247e+00 1.802035
## Room (Intercept) 1.417e-08 0.000119
## Residual 3.416e+01 5.844406
## Number of obs: 110, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -10.866299 2.258045 36.101393 -4.812 2.65e-05 ***
## First_move 0.001244 0.001761 92.275774 0.707 0.48154
## Treatment_bisDark -2.550798 1.644914 92.078677 -1.551 0.12440
## Treatment_bisFull 0.183929 1.638545 87.263551 0.112 0.91088
## Treatment_bisSmart -1.537641 1.870205 94.894206 -0.822 0.41304
## SexMale -0.103134 1.186712 90.551400 -0.087 0.93094
## RegionLuxembourg 3.268222 1.840014 7.449481 1.776 0.11638
## Treatment_FTLMix 4.799654 1.679418 86.731824 2.858 0.00534 **
## Treatment_FTLNight 7.109570 1.639176 87.379616 4.337 3.85e-05 ***
## Light_orientationSouth -0.095795 1.176134 90.392439 -0.081 0.93527
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_FTLM T_FTLN
## First_move -0.443
## Trtmnt_bsDr -0.445 0.001
## Trtmnt_bsFl -0.493 0.114 0.572
## Trtmnt_bsSm -0.414 0.051 0.531 0.526
## SexMale -0.221 0.052 -0.066 -0.064 0.046
## ReginLxmbrg -0.392 0.163 -0.010 0.019 -0.094 0.033
## Trtmnt_FTLM -0.319 0.123 0.006 0.081 0.019 -0.108 -0.220
## Trtmnt_FTLN -0.401 0.310 0.020 0.067 -0.009 -0.029 -0.111 0.597
## Lght_rnttnS -0.352 0.068 0.122 0.043 0.127 0.024 0.080 -0.005 -0.076
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_refFTL_Night))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ First_move + Treatment_bis + Sex +
## Region + Treatment_FTL + Light_orientation + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data_refFTL_Night
##
## REML criterion at convergence: 692.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.01775 -0.65717 -0.07406 0.63276 2.20497
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.699e+00 1.642765
## Site (Intercept) 3.247e+00 1.802035
## Room (Intercept) 1.417e-08 0.000119
## Residual 3.416e+01 5.844406
## Number of obs: 110, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -6.307526 2.080642 21.030478 -3.032 0.00634 **
## First_move 0.001244 0.001761 92.275774 0.707 0.48154
## Treatment_bisFull 2.734727 1.519617 93.663025 1.800 0.07514 .
## Treatment_bisSmart 1.013157 1.714339 91.897978 0.591 0.55598
## Treatment_bisMixt_smart 2.550798 1.644914 92.078671 1.551 0.12440
## SexMale -0.103134 1.186712 90.551400 -0.087 0.93094
## RegionLuxembourg 3.268222 1.840014 7.449481 1.776 0.11638
## Treatment_FTLDay -7.109570 1.639176 87.379615 -4.337 3.85e-05 ***
## Treatment_FTLMix -2.309917 1.489258 93.918429 -1.551 0.12425
## Light_orientationSouth -0.095795 1.176134 90.392439 -0.081 0.93527
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLD T_FTLM
## First_move -0.236
## Trtmnt_bsFl -0.383 0.123
## Trtmnt_bsSm -0.351 0.055 0.440
## Trtmnt_bsM_ -0.324 -0.001 0.466 0.381
## SexMale -0.315 0.052 0.003 0.114 0.066
## ReginLxmbrg -0.521 0.163 0.031 -0.093 0.010 0.033
## Trtmnt_FTLD -0.369 -0.310 -0.051 0.029 0.020 0.029 0.111
## Trtmnt_FTLM -0.260 -0.202 0.035 0.049 0.015 -0.090 -0.125 0.427
## Lght_rnttnS -0.346 0.068 -0.087 0.021 -0.122 0.024 0.080 0.076 0.078
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_refFTL_Mix))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Speed_to_light + 1e-06) ~ First_move + Treatment_bis + Sex +
## Region + Treatment_FTL + Light_orientation + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data_refFTL_Mix
##
## REML criterion at convergence: 692.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.01775 -0.65717 -0.07406 0.63276 2.20497
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.699e+00 1.642765
## Site (Intercept) 3.247e+00 1.802035
## Room (Intercept) 1.417e-08 0.000119
## Residual 3.416e+01 5.844406
## Number of obs: 110, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -8.617443 2.221448 24.591749 -3.879 0.000691 ***
## First_move 0.001244 0.001761 92.275774 0.707 0.481540
## Treatment_bisFull 2.734727 1.519617 93.663024 1.800 0.075141 .
## Treatment_bisSmart 1.013157 1.714339 91.897978 0.591 0.555978
## Treatment_bisMixt_smart 2.550798 1.644914 92.078671 1.551 0.124400
## SexMale -0.103134 1.186712 90.551400 -0.087 0.930937
## RegionLuxembourg 3.268222 1.840014 7.449481 1.776 0.116377
## Treatment_FTLDay -4.799654 1.679418 86.731824 -2.858 0.005338 **
## Treatment_FTLNight 2.309917 1.489258 93.918429 1.551 0.124253
## Light_orientationSouth -0.095795 1.176134 90.392439 -0.081 0.935265
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Frst_m Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_FTLD T_FTLN
## First_move -0.357
## Trtmnt_bsFl -0.336 0.123
## Trtmnt_bsSm -0.296 0.055 0.440
## Trtmnt_bsM_ -0.293 -0.001 0.466 0.381
## SexMale -0.355 0.052 0.003 0.114 0.066
## ReginLxmbrg -0.572 0.163 0.031 -0.093 0.010 0.033
## Trtmnt_FTLD -0.436 -0.123 -0.080 -0.015 0.006 0.108 0.220
## Trtmnt_FTLN -0.427 0.202 -0.035 -0.049 -0.015 0.090 0.125 0.470
## Lght_rnttnS -0.271 0.068 -0.087 0.021 -0.122 0.024 0.080 0.005 -0.078
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room), data = Data))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference_Treatment = "Smart", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference_Treatment = "Full", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test4 <- data.frame(Reference_Treatment = "Mixt_smart", Reference_Timing = "Day", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_ref_mixt_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test5 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Mixt", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_refFTL_Mix))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test6 <- data.frame(Reference_Treatment = "Dark", Reference_Timing = "Night", as.data.frame(( summary(lmer(log(Speed_to_light+0.000001) ~ First_move +Treatment_bis + Sex + Region + Treatment_FTL + Light_orientation + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_refFTL_Night))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_SPL_by_first_move <- rbind(test1,test2,test3,test4,test5,test6)
colnames(Results_SPL_by_first_move ) <- c("Reference_Treatment", "Reference_Timing" ,"Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_SPL_by_first_move , file = "output/Results_SPL_by_first_move.csv" )
kable(Results_SPL_by_first_move , caption = "Vitesse pour voler à la lumière en fonction du temps mis pour bouger", padding = 1 )| Reference_Treatment | Reference_Timing | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|---|
| (Intercept) | Dark | Day | -13.4170967 | 2.1216963 | 24.497447 | -6.3237592 | 0.0000014 |
| First_move | Dark | Day | 0.0012444 | 0.0017608 | 92.275774 | 0.7066903 | 0.4815397 |
| Treatment_bisFull | Dark | Day | 2.7347271 | 1.5196166 | 93.663025 | 1.7996165 | 0.0751411 |
| Treatment_bisSmart | Dark | Day | 1.0131568 | 1.7143385 | 91.897979 | 0.5909899 | 0.5559780 |
| Treatment_bisMixt_smart | Dark | Day | 2.5507982 | 1.6449143 | 92.078674 | 1.5507180 | 0.1243997 |
| SexMale | Dark | Day | -0.1031342 | 1.1867124 | 90.551400 | -0.0869075 | 0.9309369 |
| RegionLuxembourg | Dark | Day | 3.2682223 | 1.8400140 | 7.449481 | 1.7761942 | 0.1163774 |
| Treatment_FTLMix | Dark | Day | 4.7996538 | 1.6794181 | 86.731824 | 2.8579267 | 0.0053381 |
| Treatment_FTLNight | Dark | Day | 7.1095704 | 1.6391764 | 87.379616 | 4.3372822 | 0.0000385 |
| Light_orientationSouth | Dark | Day | -0.0957947 | 1.1761337 | 90.392439 | -0.0814488 | 0.9352651 |
| (Intercept)1 | Smart | Day | -12.4039400 | 2.2587576 | 32.509707 | -5.4914879 | 0.0000045 |
| First_move1 | Smart | Day | 0.0012444 | 0.0017608 | 92.275774 | 0.7066903 | 0.4815397 |
| Treatment_bisDark | Smart | Day | -1.0131568 | 1.7143385 | 91.897979 | -0.5909899 | 0.5559780 |
| Treatment_bisFull1 | Smart | Day | 1.7215704 | 1.7193416 | 92.071639 | 1.0012963 | 0.3193079 |
| Treatment_bisMixt_smart1 | Smart | Day | 1.5376414 | 1.8702050 | 94.894187 | 0.8221780 | 0.4130367 |
| SexMale1 | Smart | Day | -0.1031342 | 1.1867124 | 90.551400 | -0.0869075 | 0.9309369 |
| RegionLuxembourg1 | Smart | Day | 3.2682223 | 1.8400140 | 7.449481 | 1.7761942 | 0.1163774 |
| Treatment_FTLMix1 | Smart | Day | 4.7996538 | 1.6794181 | 86.731824 | 2.8579267 | 0.0053381 |
| Treatment_FTLNight1 | Smart | Day | 7.1095704 | 1.6391764 | 87.379616 | 4.3372822 | 0.0000385 |
| Light_orientationSouth1 | Smart | Day | -0.0957947 | 1.1761337 | 90.392439 | -0.0814488 | 0.9352651 |
| (Intercept)2 | Full | Day | -10.6823696 | 2.0336153 | 26.782549 | -5.2528959 | 0.0000158 |
| First_move2 | Full | Day | 0.0012444 | 0.0017608 | 92.275774 | 0.7066903 | 0.4815397 |
| Treatment_bisDark1 | Full | Day | -2.7347271 | 1.5196166 | 93.663025 | -1.7996165 | 0.0751411 |
| Treatment_bisSmart1 | Full | Day | -1.7215704 | 1.7193416 | 92.071638 | -1.0012963 | 0.3193079 |
| Treatment_bisMixt_smart2 | Full | Day | -0.1839289 | 1.6385450 | 87.263545 | -0.1122514 | 0.9108819 |
| SexMale2 | Full | Day | -0.1031342 | 1.1867124 | 90.551400 | -0.0869075 | 0.9309369 |
| RegionLuxembourg2 | Full | Day | 3.2682223 | 1.8400140 | 7.449481 | 1.7761942 | 0.1163774 |
| Treatment_FTLMix2 | Full | Day | 4.7996538 | 1.6794181 | 86.731824 | 2.8579267 | 0.0053381 |
| Treatment_FTLNight2 | Full | Day | 7.1095704 | 1.6391764 | 87.379616 | 4.3372822 | 0.0000385 |
| Light_orientationSouth2 | Full | Day | -0.0957947 | 1.1761337 | 90.392439 | -0.0814488 | 0.9352651 |
| (Intercept)3 | Mixt_smart | Day | -10.8662986 | 2.2580447 | 36.101393 | -4.8122601 | 0.0000265 |
| First_move3 | Mixt_smart | Day | 0.0012444 | 0.0017608 | 92.275774 | 0.7066903 | 0.4815397 |
| Treatment_bisDark2 | Mixt_smart | Day | -2.5507982 | 1.6449143 | 92.078677 | -1.5507180 | 0.1243997 |
| Treatment_bisFull2 | Mixt_smart | Day | 0.1839289 | 1.6385450 | 87.263551 | 0.1122514 | 0.9108819 |
| Treatment_bisSmart2 | Mixt_smart | Day | -1.5376414 | 1.8702050 | 94.894206 | -0.8221780 | 0.4130367 |
| SexMale3 | Mixt_smart | Day | -0.1031342 | 1.1867124 | 90.551400 | -0.0869075 | 0.9309369 |
| RegionLuxembourg3 | Mixt_smart | Day | 3.2682223 | 1.8400140 | 7.449481 | 1.7761942 | 0.1163774 |
| Treatment_FTLMix3 | Mixt_smart | Day | 4.7996538 | 1.6794181 | 86.731824 | 2.8579267 | 0.0053381 |
| Treatment_FTLNight3 | Mixt_smart | Day | 7.1095704 | 1.6391764 | 87.379616 | 4.3372822 | 0.0000385 |
| Light_orientationSouth3 | Mixt_smart | Day | -0.0957947 | 1.1761337 | 90.392439 | -0.0814488 | 0.9352651 |
| (Intercept)4 | Dark | Mixt | -8.6174429 | 2.2214479 | 24.591749 | -3.8792010 | 0.0006907 |
| First_move4 | Dark | Mixt | 0.0012444 | 0.0017608 | 92.275774 | 0.7066903 | 0.4815397 |
| Treatment_bisFull3 | Dark | Mixt | 2.7347271 | 1.5196166 | 93.663025 | 1.7996165 | 0.0751411 |
| Treatment_bisSmart3 | Dark | Mixt | 1.0131568 | 1.7143385 | 91.897978 | 0.5909899 | 0.5559780 |
| Treatment_bisMixt_smart3 | Dark | Mixt | 2.5507982 | 1.6449143 | 92.078671 | 1.5507180 | 0.1243997 |
| SexMale4 | Dark | Mixt | -0.1031342 | 1.1867124 | 90.551400 | -0.0869075 | 0.9309369 |
| RegionLuxembourg4 | Dark | Mixt | 3.2682223 | 1.8400140 | 7.449480 | 1.7761942 | 0.1163774 |
| Treatment_FTLDay | Dark | Mixt | -4.7996538 | 1.6794181 | 86.731824 | -2.8579267 | 0.0053381 |
| Treatment_FTLNight4 | Dark | Mixt | 2.3099166 | 1.4892579 | 93.918429 | 1.5510521 | 0.1242526 |
| Light_orientationSouth4 | Dark | Mixt | -0.0957947 | 1.1761337 | 90.392439 | -0.0814488 | 0.9352651 |
| (Intercept)5 | Dark | Night | -6.3075264 | 2.0806416 | 21.030478 | -3.0315294 | 0.0063400 |
| First_move5 | Dark | Night | 0.0012444 | 0.0017608 | 92.275774 | 0.7066903 | 0.4815397 |
| Treatment_bisFull4 | Dark | Night | 2.7347271 | 1.5196166 | 93.663025 | 1.7996165 | 0.0751411 |
| Treatment_bisSmart4 | Dark | Night | 1.0131568 | 1.7143385 | 91.897978 | 0.5909899 | 0.5559780 |
| Treatment_bisMixt_smart4 | Dark | Night | 2.5507982 | 1.6449143 | 92.078671 | 1.5507180 | 0.1243997 |
| SexMale5 | Dark | Night | -0.1031342 | 1.1867124 | 90.551400 | -0.0869075 | 0.9309369 |
| RegionLuxembourg5 | Dark | Night | 3.2682223 | 1.8400140 | 7.449480 | 1.7761942 | 0.1163774 |
| Treatment_FTLDay1 | Dark | Night | -7.1095704 | 1.6391764 | 87.379615 | -4.3372822 | 0.0000385 |
| Treatment_FTLMix4 | Dark | Night | -2.3099166 | 1.4892579 | 93.918429 | -1.5510521 | 0.1242526 |
| Light_orientationSouth5 | Dark | Night | -0.0957947 | 1.1761337 | 90.392439 | -0.0814488 | 0.9352651 |
Info_Speed_to_light_by_First_move <- "
Aucun effet significatif de First move.
Les individus venants du traitement Full sont quasiement significativement (p-val = 0.07514) plus rapide que ceux du traitement Dark.
Les individus expérimentés durant la nuit ou en timing mixte sont significativement plus rapide que ceux de jour.
Les individus étants expérimentés dans les conditions mixtes sont plus lent que les individus expérimentés durant la nuit mais pas de manière significative (p-val = 0.124253).
"5.8.5 Visualisation
ggplot(data = Data, aes(x = log(First_move), y = log(Speed_to_light+0.000001))) +
geom_smooth(method = "lm", aes(color = Treatment_FTL), se = T, alpha = 0.2) +
geom_point(aes(color = Treatment_FTL, shape = Treatment_bis), alpha = 0.75) +
labs(title = "Vitesse de déplacement à la lumière en fonction du temps pour le premier mouvement", x = "log(Temps mis pour faire le premier mouvement (s) ", y = "log(Vitesse pour aller à la lumière (min/s))", color = "Timing", shape = "Traitement") +
theme_bw() +
theme(title=element_text(size=10))## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 349 rows containing non-finite values (`stat_smooth()`).## Warning: Removed 339 rows containing missing values (`geom_point()`).
6 Split by Species
6.1 Total_molt OP
Vu que c’est une variable de comptage, nous comptons faire un glm de type poisson
6.1.1 Test
GLM_Total_molt_OP <- glmer(Total_molt ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Region , family = poisson, data = Data_OP)## boundary (singular) fit: see help('isSingular')summary(GLM_Total_molt_OP)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region +
## Sex:Region
## Data: Data_OP
##
## AIC BIC logLik deviance df.resid
## 393.1 431.3 -183.6 367.1 126
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.3352 -0.4717 0.1827 0.2777 1.6632
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0 0
## Site (Intercept) 0 0
## Room (Intercept) 0 0
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.52979 0.15002 3.532 0.000413 ***
## Treatment_bisFull -0.25607 0.26808 -0.955 0.339480
## Treatment_bisSmart 0.04200 0.35589 0.118 0.906060
## SexMale 0.02922 0.22234 0.131 0.895431
## RegionLuxembourg -0.03272 0.21397 -0.153 0.878478
## Treatment_bisFull:SexMale 0.06870 0.29733 0.231 0.817268
## Treatment_bisSmart:SexMale -0.10748 0.41449 -0.259 0.795398
## Treatment_bisFull:RegionLuxembourg 0.32306 0.29816 1.084 0.278570
## Treatment_bisSmart:RegionLuxembourg 0.03914 0.41722 0.094 0.925251
## SexMale:RegionLuxembourg -0.08501 0.27212 -0.312 0.754725
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm T_F:SM T_S:SM T_F:RL T_S:RL
## Trtmnt_bsFl -0.447
## Trtmnt_bsSm -0.361 0.223
## SexMale -0.580 0.130 0.141
## ReginLxmbrg -0.619 0.163 0.163 0.265
## Trtmnt_F:SM 0.261 -0.580 -0.136 -0.450 0.082
## Trtmnt_S:SM 0.185 -0.142 -0.473 -0.319 0.062 0.297
## Trtmnt_F:RL 0.284 -0.632 -0.146 0.086 -0.459 0.062 0.009
## Trtmnt_S:RL 0.225 -0.136 -0.626 0.023 -0.364 -0.001 -0.075 0.276
## SxMl:RgnLxm 0.316 0.180 0.057 -0.545 -0.511 -0.139 -0.107 -0.139 -0.029
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Pas d’effet significatifs
Vérification des hypothèses
resid_panel(GLM_Total_molt_OP, plots = c("resid"), smoother = TRUE)## `geom_smooth()` using formula = 'y ~ x'
Le modèle pourrait être siplifié par AIC (surtout pour les interactions)
6.1.2 Sipmplification du modèle
Simplification par AIC/BIC
drop1(GLM_Total_molt_OP)## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')## Single term deletions
##
## Model:
## Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region +
## Sex:Region
## npar AIC
## <none> 393.13
## Treatment_bis:Sex 2 389.30
## Treatment_bis:Region 2 390.36
## Sex:Region 1 391.23GLM_Total_molt2_OP <- update(GLM_Total_molt_OP, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(GLM_Total_molt2_OP)## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')## Single term deletions
##
## Model:
## Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Region + Sex:Region
## npar AIC
## <none> 389.30
## Treatment_bis:Region 2 386.51
## Sex:Region 1 387.40GLM_Total_molt3_OP <- update(GLM_Total_molt2_OP, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(GLM_Total_molt3_OP)## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')## Single term deletions
##
## Model:
## Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## npar AIC
## <none> 386.51
## Treatment_bis 2 382.63
## Sex:Region 1 384.55Modèle final, aucune interactions n’était significative
GLM_Total_molt_OP <- GLM_Total_molt3_OP
summary(GLM_Total_molt_OP)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## Data: Data_OP
##
## AIC BIC logLik deviance df.resid
## 386.5 412.9 -184.3 368.5 130
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.3136 -0.4910 0.2565 0.2931 1.9117
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0 0
## Site (Intercept) 0 0
## Room (Intercept) 0 0
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.486245 0.136864 3.553 0.000381 ***
## Treatment_bisFull -0.048515 0.146899 -0.330 0.741205
## Treatment_bisSmart -0.003917 0.205580 -0.019 0.984797
## SexMale 0.012236 0.192056 0.064 0.949201
## RegionLuxembourg 0.063288 0.180318 0.351 0.725604
## SexMale:RegionLuxembourg -0.049736 0.266602 -0.187 0.852009
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm
## Trtmnt_bsFl -0.319
## Trtmnt_bsSm -0.238 0.288
## SexMale -0.588 -0.115 -0.026
## ReginLxmbrg -0.633 -0.081 -0.055 0.482
## SxMl:RgnLxm 0.440 0.049 -0.025 -0.717 -0.674
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')6.1.3 Treatment VS Treatment_bis
AIC(GLM_Total_molt_OP)## [1] 386.5136AIC(update(GLM_Total_molt_OP, . ~ . - Treatment_bis + Treatment))## boundary (singular) fit: see help('isSingular')## [1] 386.3491summary(GLM_Total_molt_OP)$coeff## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.486245105 0.1368636 3.55277208 0.0003811946
## Treatment_bisFull -0.048514668 0.1468992 -0.33025830 0.7412047961
## Treatment_bisSmart -0.003917321 0.2055798 -0.01905499 0.9847972341
## SexMale 0.012235869 0.1920557 0.06371000 0.9492011455
## RegionLuxembourg 0.063287922 0.1803179 0.35097969 0.7256035888
## SexMale:RegionLuxembourg -0.049735933 0.2666017 -0.18655521 0.8520093850summary(update(GLM_Total_molt_OP, . ~ . - Treatment_bis + Treatment))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.45373071 0.1551115 2.92519115 0.003442447
## SexMale 0.01267160 0.1920041 0.06599650 0.947380613
## RegionLuxembourg 0.05773210 0.1805075 0.31983223 0.749095514
## TreatmentFull -0.01457958 0.1633023 -0.08927969 0.928859638
## TreatmentSmart 0.06659543 0.1640351 0.40598292 0.684755152
## SexMale:RegionLuxembourg -0.04465214 0.2668129 -0.16735376 0.867091705Aucune différence de significativité entre treatment et treatment_bis, on peut garder treatment_bis qui est meilleur scientifiquement parlant.
6.1.4 Résultats
summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, family = poisson, data = Data_OP))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## Data: Data_OP
##
## AIC BIC logLik deviance df.resid
## 386.5 412.9 -184.3 368.5 130
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.3136 -0.4910 0.2565 0.2931 1.9117
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0 0
## Site (Intercept) 0 0
## Room (Intercept) 0 0
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.486245 0.136864 3.553 0.000381 ***
## Treatment_bisFull -0.048515 0.146899 -0.330 0.741205
## Treatment_bisSmart -0.003917 0.205580 -0.019 0.984797
## SexMale 0.012236 0.192056 0.064 0.949201
## RegionLuxembourg 0.063288 0.180318 0.351 0.725604
## SexMale:RegionLuxembourg -0.049736 0.266602 -0.187 0.852009
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm
## Trtmnt_bsFl -0.319
## Trtmnt_bsSm -0.238 0.288
## SexMale -0.588 -0.115 -0.026
## ReginLxmbrg -0.633 -0.081 -0.055 0.482
## SxMl:RgnLxm 0.440 0.049 -0.025 -0.717 -0.674
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, family = poisson, data = Data_OP_ref_smart))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## Data: Data_OP_ref_smart
##
## AIC BIC logLik deviance df.resid
## 386.5 412.9 -184.3 368.5 130
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.3136 -0.4910 0.2565 0.2931 1.9117
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0 0
## Site (Intercept) 0 0
## Room (Intercept) 0 0
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.482328 0.218165 2.211 0.027 *
## Treatment_bisDark 0.003917 0.205580 0.019 0.985
## Treatment_bisFull -0.044597 0.215493 -0.207 0.836
## SexMale 0.012236 0.192056 0.064 0.949
## RegionLuxembourg 0.063288 0.180318 0.351 0.726
## SexMale:RegionLuxembourg -0.049736 0.266602 -0.187 0.852
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F SexMal RgnLxm
## Trtmnt_bsDr -0.793
## Trtmnt_bsFl -0.708 0.758
## SexMale -0.393 0.026 -0.054
## ReginLxmbrg -0.450 0.055 -0.002 0.482
## SxMl:RgnLxm 0.252 0.025 0.057 -0.717 -0.674
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, family = poisson, data = Data_OP_ref_full))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## Data: Data_OP_ref_full
##
## AIC BIC logLik deviance df.resid
## 386.5 412.9 -184.3 368.5 130
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.3136 -0.4910 0.2565 0.2931 1.9117
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0 0
## Site (Intercept) 0 0
## Room (Intercept) 0 0
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.43773 0.16584 2.640 0.0083 **
## Treatment_bisDark 0.04851 0.14690 0.330 0.7412
## Treatment_bisSmart 0.04460 0.21549 0.207 0.8360
## SexMale 0.01224 0.19206 0.064 0.9492
## RegionLuxembourg 0.06329 0.18032 0.351 0.7256
## SexMale:RegionLuxembourg -0.04974 0.26660 -0.187 0.8520
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S SexMal RgnLxm
## Trtmnt_bsDr -0.623
## Trtmnt_bsSm -0.369 0.407
## SexMale -0.587 0.115 0.054
## ReginLxmbrg -0.594 0.081 0.002 0.482
## SxMl:RgnLxm 0.407 -0.049 -0.057 -0.717 -0.674
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame((summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, family = poisson, data = Data_OP))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame((summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, family = poisson, data = Data_OP_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame((summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, family = poisson, data = Data_OP_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Total_molt_OP <- rbind(test1,test2,test3)
colnames(Results_Total_molt_OP) <- c("Reference","Estimate", "Std. Error", "z value", "Pr(>|z|)")
write.csv2(Results_Total_molt_OP, file = "output/Results_Total_molt_OP.csv")
kable(Results_Total_molt_OP, caption = "Nombre total de mues OP", padding = 1 )| Reference | Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|---|
| (Intercept) | Dark | 0.4862451 | 0.1368636 | 3.5527721 | 0.0003812 |
| Treatment_bisFull | Dark | -0.0485147 | 0.1468992 | -0.3302583 | 0.7412048 |
| Treatment_bisSmart | Dark | -0.0039173 | 0.2055798 | -0.0190550 | 0.9847972 |
| SexMale | Dark | 0.0122359 | 0.1920557 | 0.0637100 | 0.9492011 |
| RegionLuxembourg | Dark | 0.0632879 | 0.1803179 | 0.3509797 | 0.7256036 |
| SexMale:RegionLuxembourg | Dark | -0.0497359 | 0.2666017 | -0.1865552 | 0.8520094 |
| (Intercept)1 | Smart | 0.4823278 | 0.2181653 | 2.2108365 | 0.0270472 |
| Treatment_bisDark | Smart | 0.0039173 | 0.2055798 | 0.0190550 | 0.9847972 |
| Treatment_bisFull1 | Smart | -0.0445973 | 0.2154928 | -0.2069551 | 0.8360449 |
| SexMale1 | Smart | 0.0122359 | 0.1920558 | 0.0637100 | 0.9492012 |
| RegionLuxembourg1 | Smart | 0.0632879 | 0.1803180 | 0.3509796 | 0.7256037 |
| SexMale:RegionLuxembourg1 | Smart | -0.0497359 | 0.2666018 | -0.1865551 | 0.8520095 |
| (Intercept)2 | Full | 0.4377304 | 0.1658354 | 2.6395471 | 0.0083017 |
| Treatment_bisDark1 | Full | 0.0485147 | 0.1468991 | 0.3302584 | 0.7412047 |
| Treatment_bisSmart1 | Full | 0.0445973 | 0.2154928 | 0.2069551 | 0.8360449 |
| SexMale2 | Full | 0.0122359 | 0.1920556 | 0.0637100 | 0.9492011 |
| RegionLuxembourg2 | Full | 0.0632879 | 0.1803178 | 0.3509799 | 0.7256034 |
| SexMale:RegionLuxembourg2 | Full | -0.0497359 | 0.2666015 | -0.1865554 | 0.8520093 |
Info_Total_molt_OP <- "
Aucun effet significatif
"
Info_Total_molt_OP## [1] "\nAucun effet significatif\n"6.2 Total_molt AE
Vu que c’est une variable de comptage, nous comptons faire un glm de type poisson
6.2.1 Test
GLM_Total_molt_AE <- glmer(Total_molt ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Region , family = poisson, data = Data_AE)## boundary (singular) fit: see help('isSingular')summary(GLM_Total_molt_AE)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region +
## Sex:Region
## Data: Data_AE
##
## AIC BIC logLik deviance df.resid
## 598.6 648.3 -283.3 566.6 149
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.85168 -0.29760 -0.02683 0.35037 1.27936
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000000 0.00000
## Site (Intercept) 0.001461 0.03822
## Room (Intercept) 0.000000 0.00000
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.263775 0.118915 10.628 <2e-16
## Treatment_bisFull -0.147804 0.169427 -0.872 0.383
## Treatment_bisSmart 0.058173 0.187460 0.310 0.756
## Treatment_bisMixt_smart -0.068014 0.197910 -0.344 0.731
## SexMale -0.004123 0.165806 -0.025 0.980
## RegionLuxembourg 0.061470 0.165136 0.372 0.710
## Treatment_bisFull:SexMale 0.056400 0.210073 0.268 0.788
## Treatment_bisSmart:SexMale -0.128764 0.249517 -0.516 0.606
## Treatment_bisMixt_smart:SexMale -0.082381 0.246444 -0.334 0.738
## Treatment_bisFull:RegionLuxembourg 0.090312 0.208530 0.433 0.665
## Treatment_bisSmart:RegionLuxembourg -0.061967 0.239124 -0.259 0.796
## Treatment_bisMixt_smart:RegionLuxembourg 0.167184 0.244110 0.685 0.493
## SexMale:RegionLuxembourg 0.084125 0.168281 0.500 0.617
##
## (Intercept) ***
## Treatment_bisFull
## Treatment_bisSmart
## Treatment_bisMixt_smart
## SexMale
## RegionLuxembourg
## Treatment_bisFull:SexMale
## Treatment_bisSmart:SexMale
## Treatment_bisMixt_smart:SexMale
## Treatment_bisFull:RegionLuxembourg
## Treatment_bisSmart:RegionLuxembourg
## Treatment_bisMixt_smart:RegionLuxembourg
## SexMale:RegionLuxembourg
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 13 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Pas d’effet significatifs
Vérification des hypothèses
resid_panel(GLM_Total_molt_AE, plots = c("resid"), smoother = TRUE)## `geom_smooth()` using formula = 'y ~ x'
Le modèle pourrait être siplifié par AIC (surtout pour les interactions)
6.2.2 Sipmplification du modèle
Simplification par AIC/BIC
drop1(GLM_Total_molt_AE)## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')## Single term deletions
##
## Model:
## Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region +
## Sex:Region
## npar AIC
## <none> 598.63
## Treatment_bis:Sex 3 593.31
## Treatment_bis:Region 3 593.52
## Sex:Region 1 596.88GLM_Total_molt2_AE <- update(GLM_Total_molt_AE, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(GLM_Total_molt2_AE)## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')## Single term deletions
##
## Model:
## Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Region + Sex:Region
## npar AIC
## <none> 593.31
## Treatment_bis:Region 3 588.22
## Sex:Region 1 591.52GLM_Total_molt3_AE <- update(GLM_Total_molt2_AE, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(GLM_Total_molt3_AE)## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')## Single term deletions
##
## Model:
## Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## npar AIC
## <none> 588.22
## Treatment_bis 3 582.83
## Sex:Region 1 586.49Modèle final, aucune interactions n’était significative
GLM_Total_molt_AE <- GLM_Total_molt3_AE
summary(GLM_Total_molt_AE)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## Data: Data_AE
##
## AIC BIC logLik deviance df.resid
## 588.2 619.3 -284.1 568.2 155
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8177 -0.3005 -0.0176 0.3129 1.3558
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.00000 0.00000
## Site (Intercept) 0.00168 0.04099
## Room (Intercept) 0.00000 0.00000
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.25340 0.09608 13.046 <2e-16 ***
## Treatment_bisFull -0.07918 0.10390 -0.762 0.446
## Treatment_bisSmart -0.02561 0.11910 -0.215 0.830
## Treatment_bisMixt_smart -0.02337 0.12161 -0.192 0.848
## SexMale -0.02681 0.11680 -0.230 0.818
## RegionLuxembourg 0.10462 0.11250 0.930 0.352
## SexMale:RegionLuxembourg 0.08672 0.16709 0.519 0.604
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm
## Trtmnt_bsFl -0.499
## Trtmnt_bsSm -0.442 0.423
## Trtmnt_bsM_ -0.433 0.416 0.361
## SexMale -0.485 -0.043 0.025 -0.018
## ReginLxmbrg -0.526 -0.028 -0.058 -0.016 0.422
## SxMl:RgnLxm 0.332 0.037 0.014 0.009 -0.698 -0.638
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')6.2.3 Treatment VS Treatment_bis
AIC(GLM_Total_molt_AE)## [1] 588.2157AIC(update(GLM_Total_molt_AE, . ~ . - Treatment_bis + Treatment))## boundary (singular) fit: see help('isSingular')## [1] 586.2159summary(GLM_Total_molt_AE)$coeff## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.25339959 0.0960771 13.0457678 6.717682e-39
## Treatment_bisFull -0.07917892 0.1038985 -0.7620796 4.460125e-01
## Treatment_bisSmart -0.02560763 0.1190957 -0.2150173 8.297538e-01
## Treatment_bisMixt_smart -0.02336661 0.1216071 -0.1921483 8.476260e-01
## SexMale -0.02681319 0.1168015 -0.2295620 8.184322e-01
## RegionLuxembourg 0.10461994 0.1125019 0.9299393 3.524025e-01
## SexMale:RegionLuxembourg 0.08672455 0.1670898 0.5190297 6.037400e-01summary(update(GLM_Total_molt_AE, . ~ . - Treatment_bis + Treatment))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.25339688 0.09607333 13.0462527 6.675070e-39
## SexMale -0.02673650 0.11671376 -0.2290775 8.188087e-01
## RegionLuxembourg 0.10454904 0.11242188 0.9299705 3.523863e-01
## TreatmentFull -0.07916520 0.10389824 -0.7619494 4.460902e-01
## TreatmentSmart -0.02453236 0.09926301 -0.2471450 8.047960e-01
## SexMale:RegionLuxembourg 0.08674486 0.16708641 0.5191617 6.036480e-01Aucune différence de significativité entre treatment et treatment_bis
6.2.4 Résultats
summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, data = Data_AE, family = poisson))## boundary (singular) fit: see help('isSingular')## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## Data: Data_AE
##
## AIC BIC logLik deviance df.resid
## 588.2 619.3 -284.1 568.2 155
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8177 -0.3005 -0.0176 0.3129 1.3558
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.00000 0.00000
## Site (Intercept) 0.00168 0.04099
## Room (Intercept) 0.00000 0.00000
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.25340 0.09608 13.046 <2e-16 ***
## Treatment_bisFull -0.07918 0.10390 -0.762 0.446
## Treatment_bisSmart -0.02561 0.11910 -0.215 0.830
## Treatment_bisMixt_smart -0.02337 0.12161 -0.192 0.848
## SexMale -0.02681 0.11680 -0.230 0.818
## RegionLuxembourg 0.10462 0.11250 0.930 0.352
## SexMale:RegionLuxembourg 0.08672 0.16709 0.519 0.604
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm
## Trtmnt_bsFl -0.499
## Trtmnt_bsSm -0.442 0.423
## Trtmnt_bsM_ -0.433 0.416 0.361
## SexMale -0.485 -0.043 0.025 -0.018
## ReginLxmbrg -0.526 -0.028 -0.058 -0.016 0.422
## SxMl:RgnLxm 0.332 0.037 0.014 0.009 -0.698 -0.638
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, data = Data_AE_ref_smart, family = poisson))## boundary (singular) fit: see help('isSingular')## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## Data: Data_AE_ref_smart
##
## AIC BIC logLik deviance df.resid
## 588.2 619.3 -284.1 568.2 155
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.81768 -0.30049 -0.01761 0.31285 1.35587
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000000 0.000
## Site (Intercept) 0.001681 0.041
## Room (Intercept) 0.000000 0.000
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.227792 0.115314 10.647 <2e-16 ***
## Treatment_bisDark 0.025602 0.119096 0.215 0.830
## Treatment_bisFull -0.053548 0.120457 -0.445 0.657
## Treatment_bisMixt_smart 0.002248 0.136061 0.017 0.987
## SexMale -0.026821 0.116802 -0.230 0.818
## RegionLuxembourg 0.104594 0.112503 0.930 0.353
## SexMale:RegionLuxembourg 0.086754 0.167090 0.519 0.604
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm
## Trtmnt_bsDr -0.664
## Trtmnt_bsFl -0.639 0.624
## Trtmnt_bsM_ -0.571 0.553 0.548
## SexMale -0.378 -0.025 -0.063 -0.039
## ReginLxmbrg -0.498 0.058 0.032 0.036 0.422
## SxMl:RgnLxm 0.290 -0.014 0.019 -0.004 -0.698 -0.638
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, data = Data_AE_ref_full, family = poisson))## boundary (singular) fit: see help('isSingular')## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## Data: Data_AE_ref_full
##
## AIC BIC logLik deviance df.resid
## 588.2 619.3 -284.1 568.2 155
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.81767 -0.30048 -0.01762 0.31286 1.35587
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000000 0.000
## Site (Intercept) 0.001681 0.041
## Room (Intercept) 0.000000 0.000
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.17425 0.10029 11.708 <2e-16 ***
## Treatment_bisDark 0.07914 0.10390 0.762 0.446
## Treatment_bisSmart 0.05354 0.12046 0.444 0.657
## Treatment_bisMixt_smart 0.05580 0.12277 0.455 0.649
## SexMale -0.02682 0.11680 -0.230 0.818
## RegionLuxembourg 0.10460 0.11250 0.930 0.352
## SexMale:RegionLuxembourg 0.08675 0.16709 0.519 0.604
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm
## Trtmnt_bsDr -0.558
## Trtmnt_bsSm -0.466 0.444
## Trtmnt_bsM_ -0.456 0.434 0.374
## SexMale -0.510 0.043 0.063 0.018
## ReginLxmbrg -0.533 0.028 -0.032 0.009 0.422
## SxMl:RgnLxm 0.356 -0.037 -0.019 -0.023 -0.698 -0.638
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, data = Data_AE_ref_full, family = poisson))## boundary (singular) fit: see help('isSingular')## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Sex:Region
## Data: Data_AE_ref_full
##
## AIC BIC logLik deviance df.resid
## 588.2 619.3 -284.1 568.2 155
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.81767 -0.30048 -0.01762 0.31286 1.35587
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000000 0.000
## Site (Intercept) 0.001681 0.041
## Room (Intercept) 0.000000 0.000
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.17425 0.10029 11.708 <2e-16 ***
## Treatment_bisDark 0.07914 0.10390 0.762 0.446
## Treatment_bisSmart 0.05354 0.12046 0.444 0.657
## Treatment_bisMixt_smart 0.05580 0.12277 0.455 0.649
## SexMale -0.02682 0.11680 -0.230 0.818
## RegionLuxembourg 0.10460 0.11250 0.930 0.352
## SexMale:RegionLuxembourg 0.08675 0.16709 0.519 0.604
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm
## Trtmnt_bsDr -0.558
## Trtmnt_bsSm -0.466 0.444
## Trtmnt_bsM_ -0.456 0.434 0.374
## SexMale -0.510 0.043 0.063 0.018
## ReginLxmbrg -0.533 0.028 -0.032 0.009 0.422
## SxMl:RgnLxm 0.356 -0.037 -0.019 -0.023 -0.698 -0.638
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, data = Data_AE, family = poisson))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, data = Data_AE_ref_smart, family = poisson))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, data = Data_AE_ref_full, family = poisson))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test4 <- data.frame(Reference = "Mixt_smart", as.data.frame(( summary(glmer(Total_molt ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Sex:Region, data = Data_AE_ref_mixt_smart, family = poisson))$coeff)[,])) ## boundary (singular) fit: see help('isSingular')Results_Total_molt_AE <- rbind(test1,test2,test3,test4)
colnames(Results_Total_molt_AE ) <- c("Reference","Estimate", "Std. Error", "z value", "Pr(>|z|)")
write.csv2( Results_Total_molt_AE, file = "output/Results_Total_molt_AE.csv" )
kable(Results_Total_molt_AE , caption = " Nombre total de mues AE ", padding = 1 )| Reference | Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|---|
| (Intercept) | Dark | 1.2533996 | 0.0960771 | 13.0457678 | 0.0000000 |
| Treatment_bisFull | Dark | -0.0791789 | 0.1038985 | -0.7620796 | 0.4460125 |
| Treatment_bisSmart | Dark | -0.0256076 | 0.1190957 | -0.2150173 | 0.8297538 |
| Treatment_bisMixt_smart | Dark | -0.0233666 | 0.1216071 | -0.1921483 | 0.8476260 |
| SexMale | Dark | -0.0268132 | 0.1168015 | -0.2295620 | 0.8184322 |
| RegionLuxembourg | Dark | 0.1046199 | 0.1125019 | 0.9299393 | 0.3524025 |
| SexMale:RegionLuxembourg | Dark | 0.0867246 | 0.1670898 | 0.5190297 | 0.6037400 |
| (Intercept)1 | Smart | 1.2277921 | 0.1153139 | 10.6473891 | 0.0000000 |
| Treatment_bisDark | Smart | 0.0256021 | 0.1190965 | 0.2149691 | 0.8297914 |
| Treatment_bisFull1 | Smart | -0.0535476 | 0.1204570 | -0.4445371 | 0.6566543 |
| Treatment_bisMixt_smart1 | Smart | 0.0022477 | 0.1360605 | 0.0165200 | 0.9868195 |
| SexMale1 | Smart | -0.0268207 | 0.1168015 | -0.2296260 | 0.8183824 |
| RegionLuxembourg1 | Smart | 0.1045939 | 0.1125026 | 0.9297022 | 0.3525253 |
| SexMale:RegionLuxembourg1 | Smart | 0.0867544 | 0.1670901 | 0.5192071 | 0.6036163 |
| (Intercept)2 | Full | 1.1742453 | 0.1002937 | 11.7080620 | 0.0000000 |
| Treatment_bisDark1 | Full | 0.0791422 | 0.1038985 | 0.7617263 | 0.4462234 |
| Treatment_bisSmart1 | Full | 0.0535413 | 0.1204569 | 0.4444847 | 0.6566922 |
| Treatment_bisMixt_smart2 | Full | 0.0558013 | 0.1227738 | 0.4545049 | 0.6494655 |
| SexMale2 | Full | -0.0268181 | 0.1168015 | -0.2296038 | 0.8183997 |
| RegionLuxembourg2 | Full | 0.1046034 | 0.1125026 | 0.9297858 | 0.3524820 |
| SexMale:RegionLuxembourg2 | Full | 0.0867451 | 0.1670900 | 0.5191518 | 0.6036549 |
| (Intercept)3 | Mixt_smart | 1.2300293 | 0.1179253 | 10.4305769 | 0.0000000 |
| Treatment_bisDark2 | Mixt_smart | 0.0233765 | 0.1216072 | 0.1922296 | 0.8475624 |
| Treatment_bisFull2 | Mixt_smart | -0.0557830 | 0.1227740 | -0.4543548 | 0.6495735 |
| Treatment_bisSmart2 | Mixt_smart | -0.0022566 | 0.1360609 | -0.0165850 | 0.9867677 |
| SexMale3 | Mixt_smart | -0.0268038 | 0.1168010 | -0.2294826 | 0.8184939 |
| RegionLuxembourg3 | Mixt_smart | 0.1046209 | 0.1125020 | 0.9299465 | 0.3523988 |
| SexMale:RegionLuxembourg3 | Mixt_smart | 0.0867120 | 0.1670895 | 0.5189554 | 0.6037919 |
Info_Total_molt_AE <- "
Aucun effet significatif
"
Info_Total_molt_AE## [1] "\nAucun effet significatif\n"6.3 Diapause OP
6.3.1 Test
GLM_Diapause_OP <- glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_OP, family = binomial)## boundary (singular) fit: see help('isSingular')summary(GLM_Diapause_OP)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_OP
##
## AIC BIC logLik deviance df.resid
## 113.7 149.0 -44.9 89.7 127
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.70211 -0.41489 -0.33654 -0.00003 2.68571
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.610e-01 6.008e-01
## Site (Intercept) 1.274e-10 1.129e-05
## Room (Intercept) 4.152e-10 2.038e-05
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.93804 0.60041 -3.228 0.00125 **
## Treatment_bisFull 0.53178 0.97859 0.543 0.58685
## Treatment_bisSmart 0.33979 1.30885 0.260 0.79517
## SexMale 0.37934 0.65921 0.575 0.56498
## RegionLuxembourg -0.04201 0.77203 -0.054 0.95661
## Treatment_bisFull:SexMale -1.72193 1.50534 -1.144 0.25267
## Treatment_bisSmart:SexMale -19.25642 9641.21023 -0.002 0.99841
## Treatment_bisFull:RegionLuxembourg -18.25665 4692.29814 -0.004 0.99690
## Treatment_bisSmart:RegionLuxembourg 0.01103 1.80291 0.006 0.99512
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm T_F:SM T_S:SM T_F:RL
## Trtmnt_bsFl -0.505
## Trtmnt_bsSm -0.342 0.210
## SexMale -0.497 0.304 0.240
## ReginLxmbrg -0.568 0.264 0.164 -0.036
## Trtmnt_F:SM 0.235 -0.593 -0.094 -0.431 -0.001
## Trtmnt_S:SM 0.000 0.000 0.000 0.000 0.000 0.000
## Trtmnt_F:RL 0.000 0.000 0.000 0.000 0.000 0.000 0.000
## Trtmnt_S:RL 0.157 -0.097 -0.682 0.009 -0.322 -0.011 0.000 0.000
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')6.3.2 Simplification du modèle
drop1(GLM_Diapause_OP)## Single term deletions
##
## Model:
## Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## npar AIC
## <none> 113.74
## Treatment_bis:Sex 2 113.24
## Treatment_bis:Region 2 113.78GLM_Diapause1_OP <- update(GLM_Diapause_OP, . ~ . - Treatment_bis:Sex)
AIC(GLM_Diapause1_OP)## [1] 113.2411AIC(glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP, family = binomial))## [1] 113.0036GLM_Diapause_OP <- glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP, family = binomial)## boundary (singular) fit: see help('isSingular')6.3.3 Treatment VS Treatment_bis
AIC(glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP, family = binomial))## boundary (singular) fit: see help('isSingular')## [1] 113.0036AIC(glmer(Diapause ~ Treatment + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP, family = binomial))## boundary (singular) fit: see help('isSingular')## [1] 110.2848summary(glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP, family = binomial))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.5383308 0.5835173 -2.6363069 0.00838139
## Treatment_bisFull -1.0197762 0.6953539 -1.4665572 0.14249656
## Treatment_bisSmart -0.4659057 0.8578540 -0.5431060 0.58705683
## SexMale -0.1806979 0.5579441 -0.3238638 0.74604115
## RegionLuxembourg -0.4975839 0.7190727 -0.6919800 0.48894987summary(glmer(Diapause ~ Treatment + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP, family = binomial))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.1922173 0.6288869 -1.8957578 0.05799208
## TreatmentFull -1.3861118 0.7189575 -1.9279468 0.05386175
## TreatmentSmart -1.1175479 0.6726800 -1.6613366 0.09664587
## SexMale -0.2208998 0.5644002 -0.3913886 0.69551000
## RegionLuxembourg -0.4581785 0.7457911 -0.6143523 0.53898252Il vaut mieux garder treatment
6.3.4 Résultats
Analyse des p-val
summary(glmer(Diapause ~ Treatment + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP, family = binomial))## boundary (singular) fit: see help('isSingular')## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room)
## Data: Data_OP
##
## AIC BIC logLik deviance df.resid
## 110.3 133.8 -47.1 94.3 131
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.9322 -0.4109 -0.2479 -0.2104 3.5143
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.097e-01 7.140e-01
## Site (Intercept) 4.129e-10 2.032e-05
## Room (Intercept) 0.000e+00 0.000e+00
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.1922 0.6289 -1.896 0.0580 .
## TreatmentFull -1.3861 0.7190 -1.928 0.0539 .
## TreatmentSmart -1.1175 0.6727 -1.661 0.0966 .
## SexMale -0.2209 0.5644 -0.391 0.6955
## RegionLuxembourg -0.4582 0.7458 -0.614 0.5390
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnF TrtmnS SexMal
## TreatmntFll -0.277
## TretmntSmrt -0.280 0.300
## SexMale -0.335 -0.078 0.048
## ReginLxmbrg -0.551 -0.024 -0.064 -0.028
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(glmer(Diapause ~ Treatment + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP_ref_smart, family = binomial))## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room)
## Data: Data_OP_ref_smart
##
## AIC BIC logLik deviance df.resid
## 110.3 133.8 -47.1 94.3 131
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.9326 -0.4109 -0.2479 -0.2104 3.5150
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.110e-01 0.714816
## Site (Intercept) 9.000e-06 0.003000
## Room (Intercept) 2.692e-06 0.001641
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.3103 0.7819 -2.955 0.00313 **
## TreatmentDark 1.1173 0.6727 1.661 0.09671 .
## TreatmentFull -0.2689 0.8243 -0.326 0.74431
## SexMale -0.2212 0.5644 -0.392 0.69512
## RegionLuxembourg -0.4571 0.7462 -0.613 0.54016
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnF SexMal
## TreatmntDrk -0.635
## TreatmntFll -0.487 0.555
## SexMale -0.228 -0.048 -0.107
## ReginLxmbrg -0.499 0.064 0.031 -0.028
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.00689381 (tol = 0.002, component 1)summary(glmer(Diapause ~ Treatment + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP_ref_full, family = binomial))## boundary (singular) fit: see help('isSingular')## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room)
## Data: Data_OP_ref_full
##
## AIC BIC logLik deviance df.resid
## 110.3 133.8 -47.1 94.3 131
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.9322 -0.4109 -0.2479 -0.2104 3.5145
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.097e-01 7.139e-01
## Site (Intercept) 3.545e-09 5.954e-05
## Room (Intercept) 2.899e-10 1.703e-05
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.5784 0.8137 -3.169 0.00153 **
## TreatmentDark 1.3862 0.7190 1.928 0.05385 .
## TreatmentSmart 0.2686 0.8243 0.326 0.74452
## SexMale -0.2209 0.5644 -0.391 0.69555
## RegionLuxembourg -0.4582 0.7458 -0.614 0.53899
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnS SexMal
## TreatmntDrk -0.670
## TretmntSmrt -0.545 0.628
## SexMale -0.328 0.078 0.107
## ReginLxmbrg -0.447 0.024 -0.031 -0.028
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(glmer(Diapause ~ Treatment + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP, family = binomial))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(glmer(Diapause ~ Treatment + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP_ref_smart, family = binomial))$coeff)[,]))## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00689381 (tol = 0.002, component 1)test3 <- data.frame(Reference = "Full", as.data.frame(( summary(glmer(Diapause ~ Treatment + Sex + Region + (1|Mother) + (1|Site) + (1|Room), data = Data_OP_ref_full, family = binomial))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Diapause_OP <- rbind(test1,test2,test3)
colnames(Results_Diapause_OP ) <- c("Reference","Estimate", "Std. Error", "z value", "Pr(>|z|)")
write.csv2( Results_Diapause_OP , file = "output/Results_Diapause_OP.csv" )
kable(Results_Diapause_OP , caption = " Diapause OP ", padding = 1 )| Reference | Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|---|
| (Intercept) | Dark | -1.1922173 | 0.6288869 | -1.8957578 | 0.0579921 |
| TreatmentFull | Dark | -1.3861118 | 0.7189575 | -1.9279468 | 0.0538617 |
| TreatmentSmart | Dark | -1.1175479 | 0.6726800 | -1.6613366 | 0.0966459 |
| SexMale | Dark | -0.2208998 | 0.5644002 | -0.3913886 | 0.6955100 |
| RegionLuxembourg | Dark | -0.4581785 | 0.7457911 | -0.6143523 | 0.5389825 |
| (Intercept)1 | Smart | -2.3103071 | 0.7818686 | -2.9548532 | 0.0031282 |
| TreatmentDark | Smart | 1.1173213 | 0.6726738 | 1.6610150 | 0.0967104 |
| TreatmentFull1 | Smart | -0.2688523 | 0.8243078 | -0.3261552 | 0.7443069 |
| SexMale1 | Smart | -0.2212116 | 0.5644356 | -0.3919165 | 0.6951199 |
| RegionLuxembourg1 | Smart | -0.4571072 | 0.7462111 | -0.6125709 | 0.5401601 |
| (Intercept)2 | Full | -2.5783911 | 0.8137345 | -3.1685902 | 0.0015318 |
| TreatmentDark1 | Full | 1.3861830 | 0.7189671 | 1.9280202 | 0.0538526 |
| TreatmentSmart1 | Full | 0.2686228 | 0.8243133 | 0.3258747 | 0.7445192 |
| SexMale2 | Full | -0.2208663 | 0.5643993 | -0.3913299 | 0.6955534 |
| RegionLuxembourg2 | Full | -0.4581691 | 0.7457825 | -0.6143468 | 0.5389862 |
Info_Diapause_OP <-"
Aucun des paramètres sélectionnés n'est significatif mais les individus du traitements Full ont quasiement significativements (p-val = 0.0539) une plus faible probabilité d'être en diapause que les individus du traitement Dark.
"6.4 Diapause AE
6.4.1 Test
GLM_Diapause_AE <- glmer(Diapause ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE, family = binomial)## boundary (singular) fit: see help('isSingular')summary(GLM_Diapause_AE)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_AE
##
## AIC BIC logLik deviance df.resid
## 84.5 131.1 -27.2 54.5 150
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.2621 -0.2014 0.0000 0.0000 6.0246
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000 0.000
## Site (Intercept) 2.419 1.555
## Room (Intercept) 0.000 0.000
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.070 1.308 -2.348 0.0189
## Treatment_bisFull 1.868 1.309 1.427 0.1536
## Treatment_bisSmart -19.403 21265.855 -0.001 0.9993
## Treatment_bisMixt_smart -43.129 52867.052 -0.001 0.9993
## SexMale -19.759 24403.393 -0.001 0.9994
## RegionLuxembourg -19.593 16593.170 -0.001 0.9991
## Treatment_bisFull:SexMale 17.505 24403.393 0.001 0.9994
## Treatment_bisSmart:SexMale 40.943 32369.154 0.001 0.9990
## Treatment_bisMixt_smart:SexMale 42.791 47428.388 0.001 0.9993
## Treatment_bisFull:RegionLuxembourg 18.383 16593.170 0.001 0.9991
## Treatment_bisSmart:RegionLuxembourg -5.582 271826.080 0.000 1.0000
## Treatment_bisMixt_smart:RegionLuxembourg 40.271 37634.287 0.001 0.9991
##
## (Intercept) *
## Treatment_bisFull
## Treatment_bisSmart
## Treatment_bisMixt_smart
## SexMale
## RegionLuxembourg
## Treatment_bisFull:SexMale
## Treatment_bisSmart:SexMale
## Treatment_bisMixt_smart:SexMale
## Treatment_bisFull:RegionLuxembourg
## Treatment_bisSmart:RegionLuxembourg
## Treatment_bisMixt_smart:RegionLuxembourg
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM T_M_:S
## Trtmnt_bsFl -0.748
## Trtmnt_bsSm 0.000 0.000
## Trtmnt_bsM_ 0.000 0.000 0.000
## SexMale 0.000 0.000 0.000 0.000
## ReginLxmbrg 0.000 0.000 0.000 0.000 0.000
## Trtmnt_F:SM 0.000 0.000 0.000 0.000 -1.000 0.000
## Trtmnt_S:SM 0.000 0.000 -0.657 0.000 -0.754 0.000 0.754
## Trtmn_M_:SM 0.000 0.000 0.000 -0.660 -0.515 0.000 0.515 0.388
## Trtmnt_F:RL 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000
## Trtmnt_S:RL 0.000 0.000 0.000 0.000 0.000 -0.061 0.000 0.000 0.000
## Trtmn_M_:RL 0.000 0.000 0.000 -0.573 0.000 -0.441 0.000 0.000 0.000
## T_F:RL T_S:RL
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_F:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## Trtmnt_F:RL
## Trtmnt_S:RL 0.061
## Trtmn_M_:RL 0.441 0.027
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')6.4.2 Simplification du modèle
drop1(GLM_Diapause_AE)## boundary (singular) fit: see help('isSingular')## Single term deletions
##
## Model:
## Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## npar AIC
## <none> 84.490
## Treatment_bis:Sex 3 88.846
## Treatment_bis:Region 3 82.414GLM_Diapause1_AE <- update(GLM_Diapause_AE, . ~ . - Treatment_bis:Region)
drop1(GLM_Diapause1_AE)## Single term deletions
##
## Model:
## Diapause ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex
## npar AIC
## <none> 82.414
## Region 1 81.154
## Treatment_bis:Sex 3 86.730GLM_Diapause_AE <- glmer(Diapause ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1|Mother) + (1|Site) + (1|Room), data = Data_AE, family = binomial)## boundary (singular) fit: see help('isSingular')6.4.3 Treatment VS Treatment_bis
AIC(glmer(Diapause ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1|Mother) + (1|Site) + (1|Room), data = Data_AE, family = binomial))## boundary (singular) fit: see help('isSingular')## [1] 82.41361AIC(glmer(Diapause ~ Treatment + Sex + Region + Treatment:Sex + (1|Mother) + (1|Site) + (1|Room), data = Data_AE, family = binomial))## boundary (singular) fit: see help('isSingular')## [1] 78.68738summary(glmer(Diapause ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1|Mother) + (1|Site) + (1|Room), data = Data_AE, family = binomial))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.479122 1.280532 -2.71693428 0.006588969
## Treatment_bisFull 2.210197 1.192416 1.85354611 0.063804123
## Treatment_bisSmart -19.223144 592.969459 -0.03241844 0.974138359
## Treatment_bisMixt_smart -20.187756 366.887936 -0.05502431 0.956119097
## SexMale -19.453899 260.237462 -0.07475441 0.940410113
## RegionLuxembourg -1.155446 1.527478 -0.75644019 0.449385317
## Treatment_bisFull:SexMale 17.281962 260.238690 0.06640812 0.947052905
## Treatment_bisSmart:SexMale 40.278179 556.803635 0.07233821 0.942332757
## Treatment_bisMixt_smart:SexMale 40.354707 394.738420 0.10223152 0.918572913summary(glmer(Diapause ~ Treatment + Sex + Region + Treatment:Sex + (1|Mother) + (1|Site) + (1|Room), data = Data_AE, family = binomial))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.477686 1.258433 -2.76350571 0.005718409
## TreatmentFull 2.200500 1.181990 1.86169087 0.062646676
## TreatmentSmart -18.903029 1643.105392 -0.01150445 0.990820977
## SexMale -18.259327 621.035110 -0.02940144 0.976544423
## RegionLuxembourg -1.039567 1.446369 -0.71874273 0.472299450
## TreatmentFull:SexMale 16.118509 621.034465 0.02595429 0.979293797
## TreatmentSmart:SexMale 38.265406 1456.455366 0.02627297 0.979039615Il vaut mieux garder treatment
6.4.4 Résultats
Analyse des p-val
summary(glmer(Diapause ~ Treatment + Sex + Region + Treatment_bis:Sex + (1|Mother) + (1|Site) + (1|Room), data = Data_AE, family = binomial))## fixed-effect model matrix is rank deficient so dropping 2 columns / coefficients## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment + Sex + Region + Treatment_bis:Sex + (1 |
## Mother) + (1 | Site) + (1 | Room)
## Data: Data_AE
##
## AIC BIC logLik deviance df.resid
## 82.4 119.7 -29.2 58.4 153
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.2913 -0.1992 -0.0833 0.0000 5.5202
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.007e-05 0.005484
## Site (Intercept) 2.279e+00 1.509567
## Room (Intercept) 1.259e-06 0.001122
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.4791 1.3273 -2.621 0.00876 **
## TreatmentFull 19.4110 15811.6683 0.001 0.99902
## TreatmentSmart 20.0856 15811.6683 0.001 0.99899
## SexMale -19.3726 15811.6683 -0.001 0.99902
## RegionLuxembourg -1.1554 1.3136 -0.880 0.37909
## SexFemale:Treatment_bisFull -17.2008 15811.6683 -0.001 0.99913
## SexFemale:Treatment_bisSmart -37.9449 17563.3624 -0.002 0.99828
## SexMale:Treatment_bisSmart 0.8881 1.7244 0.515 0.60656
## SexFemale:Treatment_bisMixt_smart -38.7115 19020.5388 -0.002 0.99838
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnF TrtmnS SexMal RgnLxm SF:T_F SF:T_S SM:T_S
## TreatmntFll 0.000
## TretmntSmrt 0.000 1.000
## SexMale 0.000 -1.000 -1.000
## ReginLxmbrg -0.340 0.000 0.000 0.000
## SxFml:Trt_F 0.000 -1.000 -1.000 1.000 0.000
## SxFml:Trt_S 0.000 -0.900 -0.900 0.900 0.000 0.900
## SxMl:Trtm_S 0.021 0.000 0.000 0.000 -0.045 0.000 0.000
## SxFml:Tr_M_ 0.000 -0.831 -0.831 0.831 0.000 0.831 0.748 0.000
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 2 columns / coefficients
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## unable to evaluate scaled gradient
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluessummary(glmer(Diapause ~ Treatment + Sex + Region + Treatment_bis:Sex + (1|Mother) + (1|Site) + (1|Room), data = Data_AE_ref_full, family = binomial))## fixed-effect model matrix is rank deficient so dropping 2 columns / coefficients## boundary (singular) fit: see help('isSingular')## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: Diapause ~ Treatment + Sex + Region + Treatment_bis:Sex + (1 |
## Mother) + (1 | Site) + (1 | Room)
## Data: Data_AE_ref_full
##
## AIC BIC logLik deviance df.resid
## 82.4 119.7 -29.2 58.4 153
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.2914 -0.1992 -0.0833 0.0000 5.5205
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000 0.00
## Site (Intercept) 2.279 1.51
## Room (Intercept) 0.000 0.00
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.269e+00 8.878e-01 -1.429 0.1529
## TreatmentDark -2.464e+01 2.165e+05 0.000 0.9999
## TreatmentSmart 6.748e-01 1.661e+00 0.406 0.6845
## SexMale -2.172e+00 1.292e+00 -1.681 0.0927 .
## RegionLuxembourg -1.155e+00 1.314e+00 -0.880 0.3791
## SexFemale:Treatment_bisDark 2.243e+01 2.165e+05 0.000 0.9999
## SexFemale:Treatment_bisSmart -1.690e+02 1.501e+07 0.000 1.0000
## SexMale:Treatment_bisSmart 8.881e-01 1.724e+00 0.515 0.6065
## SexFemale:Treatment_bisMixt_smart -1.803e+02 1.678e+07 0.000 1.0000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnS SexMal RgnLxm SF:T_D SF:T_S SM:T_S
## TreatmntDrk 0.000
## TretmntSmrt 0.013 0.000
## SexMale -0.286 0.000 -0.630
## ReginLxmbrg -0.571 0.000 -0.014 0.051
## SxFml:Trt_D 0.000 -1.000 0.000 0.000 0.000
## SxFml:Trt_S 0.000 0.000 0.000 0.000 0.000 0.000
## SxMl:Trtm_S 0.030 0.000 -0.510 -0.020 -0.045 0.000 0.000
## SxFml:Tr_M_ 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 2 columns / coefficients
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(glmer(Diapause ~ Treatment + Sex + Region + Treatment_bis:Sex + (1|Mother) + (1|Site) + (1|Room), data = Data_AE, family = binomial))$coeff)[,]))## fixed-effect model matrix is rank deficient so dropping 2 columns / coefficients## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvalues## Warning in vcov.merMod(object, use.hessian = use.hessian): variance-covariance matrix computed from finite-difference Hessian is
## not positive definite or contains NA values: falling back to var-cov estimated from RX## Warning in vcov.merMod(object, correlation = correlation, sigm = sig): variance-covariance matrix computed from finite-difference Hessian is
## not positive definite or contains NA values: falling back to var-cov estimated from RXtest2 <- data.frame(Reference = "Smart", as.data.frame(( summary(glmer(Diapause ~ Treatment + Sex + Region + Treatment_bis:Sex + (1|Mother) + (1|Site) + (1|Room), data = Data_AE_ref_full, family = binomial))$coeff)[,]))## fixed-effect model matrix is rank deficient so dropping 2 columns / coefficients## boundary (singular) fit: see help('isSingular')## Warning in vcov.merMod(object, use.hessian = use.hessian): variance-covariance matrix computed from finite-difference Hessian is
## not positive definite or contains NA values: falling back to var-cov estimated from RX
## Warning in vcov.merMod(object, use.hessian = use.hessian): variance-covariance matrix computed from finite-difference Hessian is
## not positive definite or contains NA values: falling back to var-cov estimated from RXResults_Diapause_AE <- rbind(test1,test2)
colnames(Results_Diapause_AE ) <- c("Reference","Estimate", "Std. Error", "z value", "Pr(>|z|)")
write.csv2( Results_Diapause_AE , file = "output/Results_Diapause_AE.csv" )
kable(Results_Diapause_AE , caption = " Diapause AE ", padding = 1 )| Reference | Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|---|
| (Intercept) | Dark | -3.4791485 | 1.327303e+00 | -2.6212170 | 0.0087616 |
| TreatmentFull | Dark | 19.4109581 | 1.581167e+04 | 0.0012276 | 0.9990205 |
| TreatmentSmart | Dark | 20.0856412 | 1.581167e+04 | 0.0012703 | 0.9989864 |
| SexMale | Dark | -19.3725899 | 1.581167e+04 | -0.0012252 | 0.9990224 |
| RegionLuxembourg | Dark | -1.1553667 | 1.313561e+00 | -0.8795685 | 0.3790931 |
| SexFemale:Treatment_bisFull | Dark | -17.2007606 | 1.581167e+04 | -0.0010879 | 0.9991320 |
| SexFemale:Treatment_bisSmart | Dark | -37.9449212 | 1.756336e+04 | -0.0021605 | 0.9982762 |
| SexMale:Treatment_bisSmart | Dark | 0.8880640 | 1.724417e+00 | 0.5149939 | 0.6065573 |
| SexFemale:Treatment_bisMixt_smart | Dark | -38.7115363 | 1.902054e+04 | -0.0020352 | 0.9983761 |
| (Intercept)1 | Smart | -1.2689256 | 8.878030e-01 | -1.4292873 | 0.1529217 |
| TreatmentDark | Smart | -24.6442357 | 2.164656e+05 | -0.0001138 | 0.9999092 |
| TreatmentSmart1 | Smart | 0.6747943 | 1.660676e+00 | 0.4063372 | 0.6844949 |
| SexMale1 | Smart | -2.1719363 | 1.291803e+00 | -1.6813213 | 0.0927005 |
| RegionLuxembourg1 | Smart | -1.1554460 | 1.313586e+00 | -0.8796120 | 0.3790695 |
| SexFemale:Treatment_bisDark | Smart | 22.4340391 | 2.164656e+05 | 0.0001036 | 0.9999173 |
| SexFemale:Treatment_bisSmart1 | Smart | -168.9557808 | 1.500600e+07 | -0.0000113 | 0.9999910 |
| SexMale:Treatment_bisSmart1 | Smart | 0.8880807 | 1.724407e+00 | 0.5150063 | 0.6065486 |
| SexFemale:Treatment_bisMixt_smart1 | Smart | -180.3280889 | 1.677722e+07 | -0.0000107 | 0.9999914 |
Info_Diapause_AE <-"
Aucun des facteurs repris ne s'avère significatif.
"6.5 TT_pupation OP
6.5.1 Test
LM_TT_pupation_OP <- lmer(TT_pupation ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_OP)## boundary (singular) fit: see help('isSingular')summary(LM_TT_pupation_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_OP
##
## REML criterion at convergence: 602
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.45945 -0.60793 -0.06979 0.62440 2.53240
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.826e+00 1.9560376
## Site (Intercept) 8.949e-09 0.0000946
## Room (Intercept) 0.000e+00 0.0000000
## Residual 4.163e+00 2.0402435
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 15.02193 0.89649 10.84024 16.756
## Treatment_bisFull -0.47255 0.66966 120.05094 -0.706
## Treatment_bisSmart -0.36411 0.98124 120.30282 -0.371
## SexMale -0.58369 0.49716 119.35550 -1.174
## RegionLuxembourg -0.18131 1.24845 10.21058 -0.145
## Treatment_bisFull:SexMale -0.21553 0.78291 120.17333 -0.275
## Treatment_bisSmart:SexMale -0.08466 1.13599 121.98001 -0.075
## Treatment_bisFull:RegionLuxembourg 0.81149 0.76755 119.60400 1.057
## Treatment_bisSmart:RegionLuxembourg 1.41543 1.13659 120.69955 1.245
## Pr(>|t|)
## (Intercept) 4.28e-09 ***
## Treatment_bisFull 0.482
## Treatment_bisSmart 0.711
## SexMale 0.243
## RegionLuxembourg 0.887
## Treatment_bisFull:SexMale 0.784
## Treatment_bisSmart:SexMale 0.941
## Treatment_bisFull:RegionLuxembourg 0.293
## Treatment_bisSmart:RegionLuxembourg 0.215
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm T_F:SM T_S:SM T_F:RL
## Trtmnt_bsFl -0.256
## Trtmnt_bsSm -0.155 0.224
## SexMale -0.197 0.269 0.198
## ReginLxmbrg -0.684 0.127 0.067 -0.029
## Trtmnt_F:SM 0.135 -0.568 -0.129 -0.634 0.028
## Trtmnt_S:SM 0.082 -0.123 -0.487 -0.456 0.040 0.298
## Trtmnt_F:RL 0.164 -0.591 -0.140 0.039 -0.259 0.009 -0.022
## Trtmnt_S:RL 0.098 -0.127 -0.595 0.031 -0.181 -0.040 -0.127 0.277
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Normalité des résidus
qqnorm(resid(LM_TT_pupation_OP))
qqline(resid(LM_TT_pupation_OP))
Homogénité des variances
plot(LM_TT_pupation_OP)
Distance de cook
plot(cooks.distance(LM_TT_pupation_OP))
6.5.2 Simplification du modèle
drop1(LM_TT_pupation_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.3157 0.1579 2 121.02 0.0379 0.9628
## Treatment_bis:Region 8.7427 4.3714 2 120.25 1.0502 0.3531LM_TT_pupation1_OP <- update(LM_TT_pupation_OP, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_TT_pupation1_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 14.5126 14.513 1 122.35 3.5428 0.06218 .
## Treatment_bis:Region 8.7461 4.373 2 122.25 1.0675 0.34704
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_TT_pupation2_OP <- update(LM_TT_pupation1_OP, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_TT_pupation2_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room)
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 3.9397 1.9699 2 124.438 0.4814 0.61905
## Sex 14.5677 14.5677 1 124.254 3.5603 0.06151 .
## Region 0.2717 0.2717 1 8.904 0.0664 0.80252
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1On a plus d’interactions, nous pouvons nous arrêter ici
LM_TT_pupation_OP <- LM_TT_pupation2_OP6.5.3 Treatment VS Treatment_bis
AIC(lmer(TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] 628.8124AIC(lmer(TT_pupation ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] 629.7694summary(lmer(TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 14.8358273 0.8847806 9.993524 16.7678031 1.203012e-08
## Treatment_bisFull -0.1725540 0.3831668 123.907326 -0.4503363 6.532549e-01
## Treatment_bisSmart 0.3866638 0.5527276 124.887166 0.6995558 4.855057e-01
## SexMale -0.6684056 0.3542391 124.254186 -1.8868770 6.151027e-02
## RegionLuxembourg 0.3129471 1.2145570 8.903706 0.2576636 8.025228e-01summary(lmer(TT_pupation ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 14.86569007 0.9092172 10.913056 16.3499870 5.080861e-09
## TreatmentFull -0.22772494 0.4220603 123.587713 -0.5395555 5.904744e-01
## TreatmentSmart 0.04939317 0.4350396 123.965021 0.1135372 9.097883e-01
## SexMale -0.64459955 0.3536232 124.018063 -1.8228429 7.073596e-02
## RegionLuxembourg 0.34650054 1.2211154 8.894624 0.2837574 7.830906e-01Aucune différence significative
6.5.4 Résultats
Analyse des P-val
summary(lmer(TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room)
## Data: Data_OP
##
## REML criterion at convergence: 610.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3490 -0.5984 -0.1176 0.5181 2.6717
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.961 1.990
## Site (Intercept) 0.000 0.000
## Room (Intercept) 0.000 0.000
## Residual 4.092 2.023
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 14.8358 0.8848 9.9935 16.768 1.2e-08 ***
## Treatment_bisFull -0.1726 0.3832 123.9073 -0.450 0.6533
## Treatment_bisSmart 0.3867 0.5527 124.8872 0.700 0.4855
## SexMale -0.6684 0.3542 124.2542 -1.887 0.0615 .
## RegionLuxembourg 0.3129 1.2146 8.9037 0.258 0.8025
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal
## Trtmnt_bsFl -0.151
## Trtmnt_bsSm -0.086 0.296
## SexMale -0.144 -0.134 -0.089
## ReginLxmbrg -0.686 -0.014 -0.043 0.004
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room)
## Data: Data_OP_ref_full
##
## REML criterion at convergence: 610.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3490 -0.5984 -0.1176 0.5181 2.6717
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.961 1.990
## Site (Intercept) 0.000 0.000
## Room (Intercept) 0.000 0.000
## Residual 4.092 2.023
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 14.6633 0.9095 11.2160 16.122 4.14e-09 ***
## Treatment_bisDark 0.1726 0.3832 123.9073 0.450 0.6533
## Treatment_bisSmart 0.5592 0.5719 124.7909 0.978 0.3300
## SexMale -0.6684 0.3542 124.2542 -1.887 0.0615 .
## RegionLuxembourg 0.3129 1.2146 8.9037 0.258 0.8025
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S SexMal
## Trtmnt_bsDr -0.274
## Trtmnt_bsSm -0.145 0.384
## SexMale -0.197 0.134 0.003
## ReginLxmbrg -0.673 0.014 -0.032 0.004
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room)
## Data: Data_OP_ref_smart
##
## REML criterion at convergence: 610.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3490 -0.5984 -0.1176 0.5181 2.6717
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.961 1.990
## Site (Intercept) 0.000 0.000
## Room (Intercept) 0.000 0.000
## Residual 4.092 2.023
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 15.2225 1.0019 16.2439 15.193 5.03e-11 ***
## Treatment_bisDark -0.3867 0.5527 124.8872 -0.700 0.4855
## Treatment_bisFull -0.5592 0.5719 124.7909 -0.978 0.3300
## SexMale -0.6684 0.3542 124.2542 -1.887 0.0615 .
## RegionLuxembourg 0.3129 1.2146 8.9037 0.258 0.8025
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F SexMal
## Trtmnt_bsDr -0.475
## Trtmnt_bsFl -0.439 0.768
## SexMale -0.177 0.089 -0.003
## ReginLxmbrg -0.629 0.043 0.032 0.004
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP))
$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP_ref_smart))
$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP_ref_full))
$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_TT_pupation_OP <- rbind(test1,test2,test3)
colnames(Results_TT_pupation_OP ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_TT_pupation_OP , file = "output/Results_TT_pupation_OP.csv" )
kable(Results_TT_pupation_OP , caption = " Temps pour entrer en chrysalide OP ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 14.8358273 | 0.8847806 | 9.993524 | 16.7678031 | 0.0000000 |
| Treatment_bisFull | Dark | -0.1725540 | 0.3831668 | 123.907326 | -0.4503363 | 0.6532549 |
| Treatment_bisSmart | Dark | 0.3866638 | 0.5527276 | 124.887166 | 0.6995558 | 0.4855057 |
| SexMale | Dark | -0.6684056 | 0.3542391 | 124.254186 | -1.8868770 | 0.0615103 |
| RegionLuxembourg | Dark | 0.3129471 | 1.2145570 | 8.903706 | 0.2576636 | 0.8025228 |
| (Intercept)1 | Smart | 15.2224911 | 1.0019155 | 16.243857 | 15.1933879 | 0.0000000 |
| Treatment_bisDark | Smart | -0.3866638 | 0.5527276 | 124.887166 | -0.6995558 | 0.4855057 |
| Treatment_bisFull1 | Smart | -0.5592178 | 0.5718510 | 124.790868 | -0.9779082 | 0.3300117 |
| SexMale1 | Smart | -0.6684056 | 0.3542391 | 124.254186 | -1.8868770 | 0.0615103 |
| RegionLuxembourg1 | Smart | 0.3129471 | 1.2145570 | 8.903706 | 0.2576636 | 0.8025228 |
| (Intercept)2 | Full | 14.6632733 | 0.9095338 | 11.215986 | 16.1217470 | 0.0000000 |
| Treatment_bisDark1 | Full | 0.1725540 | 0.3831668 | 123.907326 | 0.4503363 | 0.6532549 |
| Treatment_bisSmart1 | Full | 0.5592178 | 0.5718510 | 124.790868 | 0.9779082 | 0.3300117 |
| SexMale2 | Full | -0.6684056 | 0.3542391 | 124.254186 | -1.8868770 | 0.0615103 |
| RegionLuxembourg2 | Full | 0.3129471 | 1.2145570 | 8.903706 | 0.2576636 | 0.8025228 |
Infos_TT_pupation_OP <- "
Mâle presque significativement plus rapide mais c'est tout
"
Infos_TT_pupation_OP## [1] "\nMâle presque significativement plus rapide mais c'est tout\n"6.6 TT_pupation AE
6.6.1 Test
LM_TT_pupation_AE <- lmer(TT_pupation ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)## boundary (singular) fit: see help('isSingular')summary(LM_TT_pupation_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: 1233.5
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.6434 -0.6315 -0.1904 0.3115 3.8242
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 10.15 3.186
## Site (Intercept) 32.31 5.684
## Room (Intercept) 0.00 0.000
## Residual 132.06 11.492
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 44.2774 3.6308 20.1945 12.195
## Treatment_bisFull -3.8390 3.6159 141.0138 -1.062
## Treatment_bisSmart -4.1040 4.1892 140.4374 -0.980
## Treatment_bisMixt_smart -1.6233 4.2992 141.4031 -0.378
## SexMale 0.3753 3.3456 144.8243 0.112
## RegionLuxembourg 5.3725 4.8686 18.9736 1.104
## Treatment_bisFull:SexMale 2.5994 4.6580 142.8523 0.558
## Treatment_bisSmart:SexMale -1.2746 5.6524 147.1038 -0.226
## Treatment_bisMixt_smart:SexMale -5.9932 5.6222 145.6177 -1.066
## Treatment_bisFull:RegionLuxembourg 5.8975 4.6430 142.3144 1.270
## Treatment_bisSmart:RegionLuxembourg -6.6351 5.2952 137.6381 -1.253
## Treatment_bisMixt_smart:RegionLuxembourg 13.0384 5.5123 142.4527 2.365
## Pr(>|t|)
## (Intercept) 9.02e-11 ***
## Treatment_bisFull 0.2902
## Treatment_bisSmart 0.3289
## Treatment_bisMixt_smart 0.7063
## SexMale 0.9108
## RegionLuxembourg 0.2836
## Treatment_bisFull:SexMale 0.5777
## Treatment_bisSmart:SexMale 0.8219
## Treatment_bisMixt_smart:SexMale 0.2882
## Treatment_bisFull:RegionLuxembourg 0.2061
## Treatment_bisSmart:RegionLuxembourg 0.2123
## Treatment_bisMixt_smart:RegionLuxembourg 0.0194 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM T_M_:S
## Trtmnt_bsFl -0.475
## Trtmnt_bsSm -0.409 0.418
## Trtmnt_bsM_ -0.401 0.407 0.356
## SexMale -0.357 0.365 0.318 0.316
## ReginLxmbrg -0.634 0.243 0.205 0.199 -0.047
## Trtmnt_F:SM 0.252 -0.558 -0.229 -0.229 -0.715 0.031
## Trtmnt_S:SM 0.224 -0.222 -0.481 -0.201 -0.596 0.020 0.427
## Trtmn_M_:SM 0.201 -0.216 -0.193 -0.547 -0.606 0.042 0.435 0.375
## Trtmnt_F:RL 0.259 -0.532 -0.221 -0.211 0.031 -0.487 -0.007 -0.024 -0.032
## Trtmnt_S:RL 0.217 -0.224 -0.584 -0.184 0.035 -0.416 -0.026 -0.047 -0.029
## Trtmn_M_:RL 0.219 -0.214 -0.176 -0.515 0.035 -0.411 -0.029 -0.044 -0.056
## T_F:RL T_S:RL
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_F:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## Trtmnt_F:RL
## Trtmnt_S:RL 0.445
## Trtmn_M_:RL 0.445 0.375
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Normalité des résidus
qqnorm(resid(LM_TT_pupation_AE))
qqline(resid(LM_TT_pupation_AE))
on va changer les variables pour la normlité
LM_TT_pupation_AE <- lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)
summary(LM_TT_pupation_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: 26.7
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7522 -0.7113 -0.1251 0.4975 3.5229
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.035e-03 6.352e-02
## Site (Intercept) 1.596e-02 1.263e-01
## Room (Intercept) 1.683e-09 4.102e-05
## Residual 4.880e-02 2.209e-01
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 3.727700 0.074789 18.913487
## Treatment_bisFull -0.049799 0.069570 140.897669
## Treatment_bisSmart -0.063499 0.080609 140.306436
## Treatment_bisMixt_smart -0.003782 0.082723 141.208570
## SexMale 0.014702 0.064452 144.202865
## RegionLuxembourg 0.137796 0.100542 17.888419
## Treatment_bisFull:SexMale 0.047749 0.089669 142.395943
## Treatment_bisSmart:SexMale -0.025900 0.108948 146.299619
## Treatment_bisMixt_smart:SexMale -0.121506 0.108356 144.782853
## Treatment_bisFull:RegionLuxembourg 0.087540 0.089382 142.002105
## Treatment_bisSmart:RegionLuxembourg -0.154330 0.101842 137.807876
## Treatment_bisMixt_smart:RegionLuxembourg 0.241384 0.106128 142.084559
## t value Pr(>|t|)
## (Intercept) 49.843 <2e-16 ***
## Treatment_bisFull -0.716 0.4753
## Treatment_bisSmart -0.788 0.4322
## Treatment_bisMixt_smart -0.046 0.9636
## SexMale 0.228 0.8199
## RegionLuxembourg 1.371 0.1875
## Treatment_bisFull:SexMale 0.533 0.5952
## Treatment_bisSmart:SexMale -0.238 0.8124
## Treatment_bisMixt_smart:SexMale -1.121 0.2640
## Treatment_bisFull:RegionLuxembourg 0.979 0.3291
## Treatment_bisSmart:RegionLuxembourg -1.515 0.1320
## Treatment_bisMixt_smart:RegionLuxembourg 2.274 0.0244 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM T_M_:S
## Trtmnt_bsFl -0.444
## Trtmnt_bsSm -0.382 0.419
## Trtmnt_bsM_ -0.374 0.407 0.356
## SexMale -0.332 0.364 0.318 0.317
## ReginLxmbrg -0.647 0.227 0.192 0.185 -0.045
## Trtmnt_F:SM 0.234 -0.558 -0.229 -0.229 -0.715 0.029
## Trtmnt_S:SM 0.210 -0.223 -0.482 -0.202 -0.595 0.017 0.427
## Trtmn_M_:SM 0.186 -0.215 -0.193 -0.547 -0.606 0.041 0.435 0.376
## Trtmnt_F:RL 0.243 -0.532 -0.221 -0.211 0.030 -0.454 -0.007 -0.024 -0.033
## Trtmnt_S:RL 0.202 -0.224 -0.583 -0.184 0.035 -0.388 -0.026 -0.047 -0.030
## Trtmn_M_:RL 0.205 -0.214 -0.175 -0.514 0.035 -0.383 -0.029 -0.045 -0.057
## T_F:RL T_S:RL
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_F:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## Trtmnt_F:RL
## Trtmnt_S:RL 0.446
## Trtmn_M_:RL 0.446 0.375Normalité des résidus
qqnorm(resid(LM_TT_pupation_AE))
qqline(resid(LM_TT_pupation_AE))
On a vu mieux mais c’est passable
Homogénité des variances
plot(LM_TT_pupation_AE)
Distance de cook
plot(cooks.distance(LM_TT_pupation_AE))
6.6.2 Simplification du modèle
drop1(LM_TT_pupation_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.12547 0.041825 3 144.43 0.8571 0.464989
## Treatment_bis:Region 0.60784 0.202612 3 139.47 4.1521 0.007475 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_TT_pupation1_AE <- update(LM_TT_pupation_AE, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_TT_pupation1_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 0.00086 0.00086 1 147.53 0.0178 0.894088
## Treatment_bis:Region 0.59337 0.19779 3 142.36 4.0906 0.008054 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1On a plus d’interactions, nous pouvons nous arrêter ici
LM_TT_pupation_AE <- LM_TT_pupation1_AE6.6.3 Treatment VS Treatment_bis
AIC(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE))## boundary (singular) fit: see help('isSingular')## [1] 46.57387AIC(lmer(log(TT_pupation) ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region, data = Data_AE))## [1] 55.09817summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 3.730223205 0.07267785 15.92756
## Treatment_bisFull -0.025346748 0.05742573 141.05583
## Treatment_bisSmart -0.071769793 0.07028877 140.34241
## Treatment_bisMixt_smart -0.055765049 0.06896240 142.48142
## SexMale 0.004833461 0.03624287 147.53480
## RegionLuxembourg 0.141065196 0.10142588 17.48479
## Treatment_bisFull:RegionLuxembourg 0.083329462 0.08899521 144.91426
## Treatment_bisSmart:RegionLuxembourg -0.156870585 0.10129398 140.77135
## Treatment_bisMixt_smart:RegionLuxembourg 0.234981708 0.10553265 144.89788
## t value Pr(>|t|)
## (Intercept) 51.3254449 4.041975e-19
## Treatment_bisFull -0.4413831 6.596115e-01
## Treatment_bisSmart -1.0210706 3.089779e-01
## Treatment_bisMixt_smart -0.8086298 4.200763e-01
## SexMale 0.1333631 8.940880e-01
## RegionLuxembourg 1.3908205 1.817283e-01
## Treatment_bisFull:RegionLuxembourg 0.9363365 3.506578e-01
## Treatment_bisSmart:RegionLuxembourg -1.5486664 1.237072e-01
## Treatment_bisMixt_smart:RegionLuxembourg 2.2266257 2.751530e-02summary(lmer(log(TT_pupation) ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region, data = Data_AE))$coeff## Estimate Std. Error df t value
## (Intercept) 3.727275648 0.08231733 7.972213 45.2793573
## TreatmentFull -0.030251953 0.06068200 142.616997 -0.4985326
## TreatmentSmart -0.067656742 0.06032158 144.162915 -1.1216010
## SexMale 0.016566041 0.03808825 149.267773 0.4349383
## RegionLuxembourg 0.148222348 0.09964665 19.036282 1.4874795
## TreatmentFull:RegionLuxembourg 0.077130107 0.09391471 146.616611 0.8212783
## TreatmentSmart:RegionLuxembourg 0.009738645 0.09026273 145.003643 0.1078922
## Pr(>|t|)
## (Intercept) 6.669934e-11
## TreatmentFull 6.188767e-01
## TreatmentSmart 2.638968e-01
## SexMale 6.642354e-01
## RegionLuxembourg 1.532657e-01
## TreatmentFull:RegionLuxembourg 4.128212e-01
## TreatmentSmart:RegionLuxembourg 9.142303e-01Treatment_bis est mieux mais il y a aucune différence significatives
6.6.4 Résultats
Analyse des P-val
summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: 20.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7966 -0.7170 -0.1319 0.4654 3.4962
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.004651 0.0682
## Site (Intercept) 0.016315 0.1277
## Room (Intercept) 0.000000 0.0000
## Residual 0.048352 0.2199
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 3.730223 0.072678 15.927558
## Treatment_bisFull -0.025347 0.057426 141.055825
## Treatment_bisSmart -0.071770 0.070289 140.342406
## Treatment_bisMixt_smart -0.055765 0.068962 142.481416
## SexMale 0.004833 0.036243 147.534799
## RegionLuxembourg 0.141065 0.101426 17.484790
## Treatment_bisFull:RegionLuxembourg 0.083329 0.088995 144.914259
## Treatment_bisSmart:RegionLuxembourg -0.156871 0.101294 140.771354
## Treatment_bisMixt_smart:RegionLuxembourg 0.234982 0.105533 144.897884
## t value Pr(>|t|)
## (Intercept) 51.325 <2e-16 ***
## Treatment_bisFull -0.441 0.6596
## Treatment_bisSmart -1.021 0.3090
## Treatment_bisMixt_smart -0.809 0.4201
## SexMale 0.133 0.8941
## RegionLuxembourg 1.391 0.1817
## Treatment_bisFull:RegionLuxembourg 0.936 0.3507
## Treatment_bisSmart:RegionLuxembourg -1.549 0.1237
## Treatment_bisMixt_smart:RegionLuxembourg 2.227 0.0275 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:RL T_S:RL
## Trtmnt_bsFl -0.391
## Trtmnt_bsSm -0.323 0.411
## Trtmnt_bsM_ -0.335 0.425 0.345
## SexMale -0.198 -0.047 0.035 -0.021
## ReginLxmbrg -0.684 0.288 0.226 0.244 -0.024
## Trtmnt_F:RL 0.255 -0.645 -0.266 -0.274 0.018 -0.447
## Trtmnt_S:RL 0.219 -0.287 -0.693 -0.240 0.001 -0.382 0.445
## Trtmn_M_:RL 0.225 -0.277 -0.226 -0.653 -0.016 -0.376 0.446 0.374
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE_ref_full
##
## REML criterion at convergence: 20.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7966 -0.7170 -0.1319 0.4654 3.4962
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.004651 0.0682
## Site (Intercept) 0.016315 0.1277
## Room (Intercept) 0.000000 0.0000
## Residual 0.048352 0.2199
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 3.704876 0.072897 16.458332
## Treatment_bisDark 0.025347 0.057426 141.055825
## Treatment_bisSmart -0.046423 0.070124 138.684052
## Treatment_bisMixt_smart -0.030418 0.068443 139.646914
## SexMale 0.004833 0.036243 147.534799
## RegionLuxembourg 0.224395 0.100684 17.426481
## Treatment_bisDark:RegionLuxembourg -0.083329 0.088995 144.914259
## Treatment_bisSmart:RegionLuxembourg -0.240200 0.100750 140.268830
## Treatment_bisMixt_smart:RegionLuxembourg 0.151652 0.103368 141.401768
## t value Pr(>|t|)
## (Intercept) 50.823 <2e-16 ***
## Treatment_bisDark 0.441 0.6596
## Treatment_bisSmart -0.662 0.5091
## Treatment_bisMixt_smart -0.444 0.6574
## SexMale 0.133 0.8941
## RegionLuxembourg 2.229 0.0393 *
## Treatment_bisDark:RegionLuxembourg -0.936 0.3507
## Treatment_bisSmart:RegionLuxembourg -2.384 0.0185 *
## Treatment_bisMixt_smart:RegionLuxembourg 1.467 0.1446
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_D:RL T_S:RL
## Trtmnt_bsDr -0.398
## Trtmnt_bsSm -0.324 0.407
## Trtmnt_bsM_ -0.333 0.410 0.338
## SexMale -0.234 0.047 0.073 0.018
## ReginLxmbrg -0.682 0.280 0.222 0.238 -0.009
## Trtmnt_D:RL 0.254 -0.645 -0.261 -0.265 -0.018 -0.434
## Trtmnt_S:RL 0.217 -0.281 -0.693 -0.235 -0.015 -0.374 0.436
## Trtmn_M_:RL 0.225 -0.273 -0.225 -0.662 -0.032 -0.358 0.406 0.357
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE_ref_smart
##
## REML criterion at convergence: 20.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7966 -0.7170 -0.1319 0.4654 3.4962
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.004651 0.0682
## Site (Intercept) 0.016315 0.1277
## Room (Intercept) 0.000000 0.0000
## Residual 0.048352 0.2199
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 3.658453 0.083180 26.780046
## Treatment_bisDark 0.071770 0.070289 140.342406
## Treatment_bisFull 0.046423 0.070124 138.684052
## Treatment_bisMixt_smart 0.016005 0.079726 139.234651
## SexMale 0.004833 0.036243 147.534799
## RegionLuxembourg -0.015805 0.112663 26.449320
## Treatment_bisDark:RegionLuxembourg 0.156871 0.101294 140.771354
## Treatment_bisFull:RegionLuxembourg 0.240200 0.100750 140.268830
## Treatment_bisMixt_smart:RegionLuxembourg 0.391852 0.115762 141.419410
## t value Pr(>|t|)
## (Intercept) 43.982 < 2e-16 ***
## Treatment_bisDark 1.021 0.308978
## Treatment_bisFull 0.662 0.509059
## Treatment_bisMixt_smart 0.201 0.841190
## SexMale 0.133 0.894088
## RegionLuxembourg -0.140 0.889495
## Treatment_bisDark:RegionLuxembourg 1.549 0.123707
## Treatment_bisFull:RegionLuxembourg 2.384 0.018459 *
## Treatment_bisMixt_smart:RegionLuxembourg 3.385 0.000922 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.562
## Trtmnt_bsFl -0.559 0.665
## Trtmnt_bsM_ -0.497 0.584 0.589
## SexMale -0.143 -0.035 -0.073 -0.049
## ReginLxmbrg -0.720 0.420 0.422 0.373 -0.021
## Trtmnt_D:RL 0.394 -0.693 -0.460 -0.404 -0.001 -0.555
## Trtmnt_F:RL 0.394 -0.462 -0.693 -0.408 0.015 -0.560 0.612
## Trtmn_M_:RL 0.350 -0.400 -0.402 -0.686 -0.016 -0.488 0.534 0.552
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_mixt_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE_ref_mixt_smart
##
## REML criterion at convergence: 20.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7966 -0.7170 -0.1319 0.4654 3.4962
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.004651 0.0682
## Site (Intercept) 0.016315 0.1277
## Room (Intercept) 0.000000 0.0000
## Residual 0.048352 0.2199
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.674458 0.081727 25.792872 44.960
## Treatment_bisDark 0.055765 0.068962 142.481416 0.809
## Treatment_bisFull 0.030418 0.068443 139.646914 0.444
## Treatment_bisSmart -0.016005 0.079726 139.234651 -0.201
## SexMale 0.004833 0.036243 147.534799 0.133
## RegionLuxembourg 0.376047 0.115644 28.846394 3.252
## Treatment_bisDark:RegionLuxembourg -0.234982 0.105533 144.897884 -2.227
## Treatment_bisFull:RegionLuxembourg -0.151652 0.103368 141.401768 -1.467
## Treatment_bisSmart:RegionLuxembourg -0.391852 0.115762 141.419410 -3.385
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisDark 0.420076
## Treatment_bisFull 0.657419
## Treatment_bisSmart 0.841190
## SexMale 0.894088
## RegionLuxembourg 0.002918 **
## Treatment_bisDark:RegionLuxembourg 0.027515 *
## Treatment_bisFull:RegionLuxembourg 0.144566
## Treatment_bisSmart:RegionLuxembourg 0.000922 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.546
## Trtmnt_bsFl -0.541 0.651
## Trtmnt_bsSm -0.469 0.561 0.561
## SexMale -0.194 0.021 -0.018 0.049
## ReginLxmbrg -0.673 0.382 0.385 0.323 -0.036
## Trtmnt_D:RL 0.351 -0.653 -0.426 -0.365 0.016 -0.583
## Trtmnt_F:RL 0.354 -0.430 -0.662 -0.371 0.032 -0.582 0.637
## Trtmnt_S:RL 0.314 -0.385 -0.387 -0.686 0.016 -0.526 0.584 0.582
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test4 <- data.frame(Reference = "Mixt_smart", as.data.frame(( summary(lmer(log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_mixt_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_TT_puapation_AE <- rbind(test1,test2,test3, test4)
colnames(Results_TT_puapation_AE ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_TT_puapation_AE , file = "output/Results_TT_puapation_AE.csv" )
kable(Results_TT_puapation_AE , caption = " Temps pour entrer en chrysalide AE ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 3.7302232 | 0.0726779 | 15.92756 | 51.3254449 | 0.0000000 |
| Treatment_bisFull | Dark | -0.0253467 | 0.0574257 | 141.05583 | -0.4413831 | 0.6596115 |
| Treatment_bisSmart | Dark | -0.0717698 | 0.0702888 | 140.34241 | -1.0210706 | 0.3089779 |
| Treatment_bisMixt_smart | Dark | -0.0557650 | 0.0689624 | 142.48142 | -0.8086298 | 0.4200763 |
| SexMale | Dark | 0.0048335 | 0.0362429 | 147.53480 | 0.1333631 | 0.8940880 |
| RegionLuxembourg | Dark | 0.1410652 | 0.1014259 | 17.48479 | 1.3908205 | 0.1817283 |
| Treatment_bisFull:RegionLuxembourg | Dark | 0.0833295 | 0.0889952 | 144.91426 | 0.9363365 | 0.3506578 |
| Treatment_bisSmart:RegionLuxembourg | Dark | -0.1568706 | 0.1012940 | 140.77135 | -1.5486664 | 0.1237072 |
| Treatment_bisMixt_smart:RegionLuxembourg | Dark | 0.2349817 | 0.1055326 | 144.89788 | 2.2266257 | 0.0275153 |
| (Intercept)1 | Smart | 3.6584534 | 0.0831800 | 26.78005 | 43.9823472 | 0.0000000 |
| Treatment_bisDark | Smart | 0.0717698 | 0.0702888 | 140.34241 | 1.0210706 | 0.3089779 |
| Treatment_bisFull1 | Smart | 0.0464230 | 0.0701237 | 138.68405 | 0.6620167 | 0.5090591 |
| Treatment_bisMixt_smart1 | Smart | 0.0160047 | 0.0797264 | 139.23465 | 0.2007459 | 0.8411902 |
| SexMale1 | Smart | 0.0048335 | 0.0362429 | 147.53480 | 0.1333631 | 0.8940880 |
| RegionLuxembourg1 | Smart | -0.0158054 | 0.1126633 | 26.44932 | -0.1402887 | 0.8894948 |
| Treatment_bisDark:RegionLuxembourg | Smart | 0.1568706 | 0.1012940 | 140.77135 | 1.5486664 | 0.1237072 |
| Treatment_bisFull:RegionLuxembourg1 | Smart | 0.2402000 | 0.1007504 | 140.26883 | 2.3841095 | 0.0184588 |
| Treatment_bisMixt_smart:RegionLuxembourg1 | Smart | 0.3918523 | 0.1157621 | 141.41941 | 3.3849784 | 0.0009215 |
| (Intercept)2 | Full | 3.7048765 | 0.0728969 | 16.45833 | 50.8234938 | 0.0000000 |
| Treatment_bisDark1 | Full | 0.0253467 | 0.0574257 | 141.05583 | 0.4413831 | 0.6596115 |
| Treatment_bisSmart1 | Full | -0.0464230 | 0.0701237 | 138.68405 | -0.6620167 | 0.5090591 |
| Treatment_bisMixt_smart2 | Full | -0.0304183 | 0.0684432 | 139.64691 | -0.4444316 | 0.6574186 |
| SexMale2 | Full | 0.0048335 | 0.0362429 | 147.53480 | 0.1333631 | 0.8940880 |
| RegionLuxembourg2 | Full | 0.2243947 | 0.1006837 | 17.42648 | 2.2287087 | 0.0392648 |
| Treatment_bisDark:RegionLuxembourg1 | Full | -0.0833295 | 0.0889952 | 144.91426 | -0.9363365 | 0.3506578 |
| Treatment_bisSmart:RegionLuxembourg1 | Full | -0.2402000 | 0.1007504 | 140.26883 | -2.3841095 | 0.0184588 |
| Treatment_bisMixt_smart:RegionLuxembourg2 | Full | 0.1516522 | 0.1033678 | 141.40177 | 1.4671126 | 0.1445661 |
| (Intercept)3 | Mixt_smart | 3.6744582 | 0.0817268 | 25.79287 | 44.9602738 | 0.0000000 |
| Treatment_bisDark2 | Mixt_smart | 0.0557650 | 0.0689624 | 142.48142 | 0.8086298 | 0.4200763 |
| Treatment_bisFull2 | Mixt_smart | 0.0304183 | 0.0684432 | 139.64691 | 0.4444316 | 0.6574186 |
| Treatment_bisSmart2 | Mixt_smart | -0.0160047 | 0.0797264 | 139.23465 | -0.2007459 | 0.8411902 |
| SexMale3 | Mixt_smart | 0.0048335 | 0.0362429 | 147.53480 | 0.1333631 | 0.8940880 |
| RegionLuxembourg3 | Mixt_smart | 0.3760469 | 0.1156445 | 28.84639 | 3.2517495 | 0.0029183 |
| Treatment_bisDark:RegionLuxembourg2 | Mixt_smart | -0.2349817 | 0.1055326 | 144.89788 | -2.2266257 | 0.0275153 |
| Treatment_bisFull:RegionLuxembourg2 | Mixt_smart | -0.1516522 | 0.1033678 | 141.40177 | -1.4671126 | 0.1445661 |
| Treatment_bisSmart:RegionLuxembourg2 | Mixt_smart | -0.3918523 | 0.1157621 | 141.41941 | -3.3849784 | 0.0009215 |
Infos_TT_pupation_AE <- "
Le traitement Mixt-smart en région luxembourgoise est significativement plus lent que l'effet de la région luxembourgeoise et du traitement mixt-smart additionné sauf quand on le compare au traitement full où là, la région luxembourg est elle même significativement plus lent
Le traitement Smart en région luxembourgeoise est significativement plus rapide que l'effet de la région luxembourgeoise et du traitement smart additioné quand il est comparé au traitement full.
"
Infos_TT_pupation_AE## [1] "\n\nLe traitement Mixt-smart en région luxembourgoise est significativement plus lent que l'effet de la région luxembourgeoise et du traitement mixt-smart additionné sauf quand on le compare au traitement full où là, la région luxembourg est elle même significativement plus lent\nLe traitement Smart en région luxembourgeoise est significativement plus rapide que l'effet de la région luxembourgeoise et du traitement smart additioné quand il est comparé au traitement full.\n"6.7 Time_in_pupa OP
6.7.1 Test
LM_Time_in_pupa_OP <- lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_OP)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvalues## Warning: Model failed to converge with 1 negative eigenvalue: -1.5e+00summary(LM_TT_pupation_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room)
## Data: Data_OP
##
## REML criterion at convergence: 610.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3490 -0.5984 -0.1176 0.5181 2.6717
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.961 1.990
## Site (Intercept) 0.000 0.000
## Room (Intercept) 0.000 0.000
## Residual 4.092 2.023
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 14.8358 0.8848 9.9935 16.768 1.2e-08 ***
## Treatment_bisFull -0.1726 0.3832 123.9073 -0.450 0.6533
## Treatment_bisSmart 0.3867 0.5527 124.8872 0.700 0.4855
## SexMale -0.6684 0.3542 124.2542 -1.887 0.0615 .
## RegionLuxembourg 0.3129 1.2146 8.9037 0.258 0.8025
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal
## Trtmnt_bsFl -0.151
## Trtmnt_bsSm -0.086 0.296
## SexMale -0.144 -0.134 -0.089
## ReginLxmbrg -0.686 -0.014 -0.043 0.004
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification de la normalité
qqnorm(resid(LM_Time_in_pupa_OP))
qqline(resid(LM_Time_in_pupa_OP))
Je pense que cela est suffisemment bon
Homogénité des variances
plot(LM_Time_in_pupa_OP)
Distance de cook
plot(cooks.distance(LM_Time_in_pupa_OP))
6.7.2 Simplification du modèle
drop1(LM_Time_in_pupa_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.30299 0.151496 2 105.6 0.1693 0.8445
## Treatment_bis:Region 0.15798 0.078991 2 104.1 0.0883 0.9156LM_Time_in_pupa1_OP <- update(LM_Time_in_pupa_OP, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_Time_in_pupa1_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Region 0.77601 0.77601 1 7.652 0.8840 0.3758
## Treatment_bis:Sex 0.26920 0.13460 2 107.238 0.1533 0.8580LM_Time_in_pupa2_OP <- update(LM_Time_in_pupa1_OP, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_Time_in_pupa2_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room)
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 4.3408 2.1704 2 108.30 2.5110 0.0859 .
## Sex 5.3431 5.3431 1 110.65 6.1817 0.0144 *
## Region 0.7657 0.7657 1 7.79 0.8859 0.3748
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Nous n’avons plus d’interactions, nous nous arrêtons là.
Regardons si les simplifications étaient utiles
AIC(LM_Time_in_pupa2_OP)## [1] 363.8339AIC(LM_Time_in_pupa_OP)## [1] 370.4407Les simplifications étaient utiles
LM_Time_in_pupa_OP <- LM_Time_in_pupa2_OP6.7.3 Treatment VS Treatment_bis
AIC(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] 363.8339AIC(lmer(Time_in_pupa ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] 366.1591summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 13.1595521 0.2712871 10.642247 48.5078417 7.812250e-14
## Treatment_bisFull 0.1938076 0.1874238 107.589573 1.0340608 3.034265e-01
## Treatment_bisSmart -0.4176188 0.2714114 109.458784 -1.5386928 1.267652e-01
## SexMale 0.4377398 0.1760601 110.646314 2.4863097 1.440167e-02
## RegionLuxembourg -0.3346356 0.3555258 7.790118 -0.9412416 3.748476e-01summary(lmer(Time_in_pupa ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 13.080301905 0.3050927 11.324364 42.87320555 6.853904e-14
## TreatmentFull 0.293937176 0.2106132 105.368043 1.39562577 1.657613e-01
## TreatmentSmart 0.003233417 0.2178996 106.724953 0.01483903 9.881883e-01
## SexMale 0.427762682 0.1770008 110.669123 2.41672675 1.729567e-02
## RegionLuxembourg -0.360048801 0.3489861 7.580957 -1.03169961 3.339998e-01Selon les summary le choix de treatment ou treatment_bis est discutable mais on peut alors se pencher sur l’AIC qui nous encourage à prendre treatment_bis.
6.7.4 Résultats
Analysons les P-val
summary(LM_Time_in_pupa_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data_OP
##
## REML criterion at convergence: 345.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.78449 -0.67249 0.02252 0.43274 3.10875
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.736e-01 5.231e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 1.121e-09 3.349e-05
## Residual 8.643e-01 9.297e-01
## Number of obs: 122, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 13.1596 0.2713 10.6422 48.508 7.81e-14 ***
## Treatment_bisFull 0.1938 0.1874 107.5896 1.034 0.3034
## Treatment_bisSmart -0.4176 0.2714 109.4588 -1.539 0.1268
## SexMale 0.4377 0.1761 110.6463 2.486 0.0144 *
## RegionLuxembourg -0.3346 0.3555 7.7901 -0.941 0.3748
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal
## Trtmnt_bsFl -0.227
## Trtmnt_bsSm -0.135 0.328
## SexMale -0.239 -0.172 -0.136
## ReginLxmbrg -0.647 -0.048 -0.069 0.030
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data_OP_ref_full
##
## REML criterion at convergence: 345.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.78449 -0.67249 0.02252 0.43274 3.10875
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.736e-01 5.231e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 1.121e-09 3.349e-05
## Residual 8.643e-01 9.297e-01
## Number of obs: 122, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 13.3534 0.2926 14.5443 45.629 <2e-16 ***
## Treatment_bisDark -0.1938 0.1874 107.5896 -1.034 0.3034
## Treatment_bisSmart -0.6114 0.2746 108.2893 -2.227 0.0280 *
## SexMale 0.4377 0.1761 110.6463 2.486 0.0144 *
## RegionLuxembourg -0.3346 0.3555 7.7901 -0.941 0.3748
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S SexMal
## Trtmnt_bsDr -0.430
## Trtmnt_bsSm -0.209 0.358
## SexMale -0.332 0.172 -0.017
## ReginLxmbrg -0.631 0.048 -0.035 0.030
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room)
## Data: Data_OP_ref_smart
##
## REML criterion at convergence: 345.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.78449 -0.67249 0.02252 0.43274 3.10875
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.736e-01 5.231e-01
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 1.121e-09 3.349e-05
## Residual 8.643e-01 9.297e-01
## Number of obs: 122, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 12.7419 0.3570 29.1673 35.696 <2e-16 ***
## Treatment_bisDark 0.4176 0.2714 109.4587 1.539 0.1268
## Treatment_bisFull 0.6114 0.2746 108.2893 2.227 0.0280 *
## SexMale 0.4377 0.1761 110.6463 2.486 0.0144 *
## RegionLuxembourg -0.3346 0.3555 7.7901 -0.941 0.3748
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F SexMal
## Trtmnt_bsDr -0.658
## Trtmnt_bsFl -0.598 0.764
## SexMale -0.285 0.136 0.017
## ReginLxmbrg -0.544 0.069 0.035 0.030
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(LM_Time_in_pupa_OP)$coeff)[,]))
test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) , data = Data_OP_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Time_in_pupa_OP <- rbind(test1,test2,test3)
colnames(Results_Time_in_pupa_OP ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Time_in_pupa_OP , file = "output/Results_Time_in_pupa_OP.csv" )
kable(Results_Time_in_pupa_OP , caption = " Temps en chrysalide OP ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 13.1595521 | 0.2712871 | 10.642247 | 48.5078417 | 0.0000000 |
| Treatment_bisFull | Dark | 0.1938076 | 0.1874238 | 107.589573 | 1.0340608 | 0.3034265 |
| Treatment_bisSmart | Dark | -0.4176188 | 0.2714114 | 109.458784 | -1.5386928 | 0.1267652 |
| SexMale | Dark | 0.4377398 | 0.1760601 | 110.646314 | 2.4863097 | 0.0144017 |
| RegionLuxembourg | Dark | -0.3346356 | 0.3555258 | 7.790118 | -0.9412416 | 0.3748476 |
| (Intercept)1 | Smart | 12.7419333 | 0.3569619 | 29.167327 | 35.6955006 | 0.0000000 |
| Treatment_bisDark | Smart | 0.4176188 | 0.2714114 | 109.458746 | 1.5386928 | 0.1267652 |
| Treatment_bisFull1 | Smart | 0.6114264 | 0.2745973 | 108.289262 | 2.2266295 | 0.0280420 |
| SexMale1 | Smart | 0.4377398 | 0.1760601 | 110.646314 | 2.4863097 | 0.0144017 |
| RegionLuxembourg1 | Smart | -0.3346356 | 0.3555258 | 7.790118 | -0.9412416 | 0.3748476 |
| (Intercept)2 | Full | 13.3533597 | 0.2926481 | 14.544267 | 45.6294128 | 0.0000000 |
| Treatment_bisDark1 | Full | -0.1938076 | 0.1874238 | 107.589572 | -1.0340608 | 0.3034265 |
| Treatment_bisSmart1 | Full | -0.6114264 | 0.2745973 | 108.289262 | -2.2266295 | 0.0280420 |
| SexMale2 | Full | 0.4377398 | 0.1760601 | 110.646314 | 2.4863097 | 0.0144017 |
| RegionLuxembourg2 | Full | -0.3346356 | 0.3555258 | 7.790118 | -0.9412416 | 0.3748476 |
Info_time_in_pupa_OP <- "
Les mâmes passent significativement (0.0144) plus de temps (0.44 jours) en chrysaldie
Les individus du traitement Smart passent significativement (0.0280) moins de temps (0.61 jours) en chrysalide que les individus du traitement Full.
"
Info_time_in_pupa_OP## [1] "\nLes mâmes passent significativement (0.0144) plus de temps (0.44 jours) en chrysaldie\nLes individus du traitement Smart passent significativement (0.0280) moins de temps (0.61 jours) en chrysalide que les individus du traitement Full.\n"6.8 Time_in_pupa AE
6.8.1 Test
LM_Time_in_pupa_AE <- lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)## boundary (singular) fit: see help('isSingular')summary(LM_TT_pupation_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: 20.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7966 -0.7170 -0.1319 0.4654 3.4962
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.004651 0.0682
## Site (Intercept) 0.016315 0.1277
## Room (Intercept) 0.000000 0.0000
## Residual 0.048352 0.2199
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 3.730223 0.072678 15.927558
## Treatment_bisFull -0.025347 0.057426 141.055825
## Treatment_bisSmart -0.071770 0.070289 140.342406
## Treatment_bisMixt_smart -0.055765 0.068962 142.481416
## SexMale 0.004833 0.036243 147.534799
## RegionLuxembourg 0.141065 0.101426 17.484790
## Treatment_bisFull:RegionLuxembourg 0.083329 0.088995 144.914259
## Treatment_bisSmart:RegionLuxembourg -0.156871 0.101294 140.771354
## Treatment_bisMixt_smart:RegionLuxembourg 0.234982 0.105533 144.897884
## t value Pr(>|t|)
## (Intercept) 51.325 <2e-16 ***
## Treatment_bisFull -0.441 0.6596
## Treatment_bisSmart -1.021 0.3090
## Treatment_bisMixt_smart -0.809 0.4201
## SexMale 0.133 0.8941
## RegionLuxembourg 1.391 0.1817
## Treatment_bisFull:RegionLuxembourg 0.936 0.3507
## Treatment_bisSmart:RegionLuxembourg -1.549 0.1237
## Treatment_bisMixt_smart:RegionLuxembourg 2.227 0.0275 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:RL T_S:RL
## Trtmnt_bsFl -0.391
## Trtmnt_bsSm -0.323 0.411
## Trtmnt_bsM_ -0.335 0.425 0.345
## SexMale -0.198 -0.047 0.035 -0.021
## ReginLxmbrg -0.684 0.288 0.226 0.244 -0.024
## Trtmnt_F:RL 0.255 -0.645 -0.266 -0.274 0.018 -0.447
## Trtmnt_S:RL 0.219 -0.287 -0.693 -0.240 0.001 -0.382 0.445
## Trtmn_M_:RL 0.225 -0.277 -0.226 -0.653 -0.016 -0.376 0.446 0.374
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification de la normalité
qqnorm(resid(LM_Time_in_pupa_AE))
qqline(resid(LM_Time_in_pupa_AE))
Ca a vraiment l’air nickel
Homogénité des variances
plot(LM_Time_in_pupa_AE)
Distance de cook
plot(cooks.distance(LM_Time_in_pupa_AE))
6.8.2 Simplification du modèle
drop1(LM_Time_in_pupa_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.0656 0.0219 3 124.14 0.0299 0.993017
## Treatment_bis:Region 12.3671 4.1224 3 115.36 5.6310 0.001227 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Time_in_pupa1_AE <- update(LM_Time_in_pupa_AE, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_Time_in_pupa1_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 8.2058 8.2058 1 125.37 11.457 0.0009512 ***
## Treatment_bis:Region 12.4191 4.1397 3 118.37 5.780 0.0010082 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Le reste est significatif, nous devrions nous arrêter là
Regardons si les simplifications étaient utiles
AIC(LM_Time_in_pupa1_AE)## [1] 398.363AIC(LM_Time_in_pupa_AE)## [1] 404.4193Les simplifications étaient utiles
LM_Time_in_pupa_AE <- LM_Time_in_pupa1_AE6.8.3 Treatment VS Treatment_bis
AIC(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE))## boundary (singular) fit: see help('isSingular')## [1] 398.363AIC(lmer(Time_in_pupa ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region, data = Data_AE))## boundary (singular) fit: see help('isSingular')## [1] 408.0205summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 13.2970982 0.5286168 1.288974
## Treatment_bisFull 0.6459053 0.2428622 115.687832
## Treatment_bisSmart 0.5220222 0.3019492 112.881842
## Treatment_bisMixt_smart 0.3398202 0.2925367 122.350649
## SexMale 0.5061546 0.1495354 125.374447
## RegionLuxembourg 0.3184147 0.2917477 59.901894
## Treatment_bisFull:RegionLuxembourg -0.7260823 0.3781777 119.272967
## Treatment_bisSmart:RegionLuxembourg -0.6232444 0.4115138 113.785957
## Treatment_bisMixt_smart:RegionLuxembourg 0.9440774 0.4263108 122.436231
## t value Pr(>|t|)
## (Intercept) 25.154512 0.0108038334
## Treatment_bisFull 2.659554 0.0089340385
## Treatment_bisSmart 1.728841 0.0865715601
## Treatment_bisMixt_smart 1.161633 0.2476456996
## SexMale 3.384849 0.0009511929
## RegionLuxembourg 1.091404 0.2794655434
## Treatment_bisFull:RegionLuxembourg -1.919950 0.0572523089
## Treatment_bisSmart:RegionLuxembourg -1.514516 0.1326678341
## Treatment_bisMixt_smart:RegionLuxembourg 2.214528 0.0286431504summary(lmer(Time_in_pupa ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region, data = Data_AE))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 13.29467258 0.6281464 1.232235 21.164927
## TreatmentFull 0.63627573 0.2544695 117.358321 2.500401
## TreatmentSmart 0.40212521 0.2425852 117.534382 1.657666
## SexMale 0.52225754 0.1561309 128.237643 3.344998
## RegionLuxembourg 0.35161587 0.3005669 61.537701 1.169842
## TreatmentFull:RegionLuxembourg -0.72968955 0.3962549 121.447563 -1.841465
## TreatmentSmart:RegionLuxembourg 0.05641089 0.3615016 119.679804 0.156046
## Pr(>|t|)
## (Intercept) 0.015730646
## TreatmentFull 0.013785737
## TreatmentSmart 0.100051653
## SexMale 0.001079446
## RegionLuxembourg 0.246575418
## TreatmentFull:RegionLuxembourg 0.067993527
## TreatmentSmart:RegionLuxembourg 0.876259651Il faut garder treatment_bis
6.8.4 Résultats
Analysons les P-val
summary(LM_Time_in_pupa_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: 372.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4901 -0.6944 -0.1294 0.7102 2.8173
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.1034 0.3216
## Site (Intercept) 0.0000 0.0000
## Room (Intercept) 0.4739 0.6884
## Residual 0.7162 0.8463
## Number of obs: 141, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 13.2971 0.5286 1.2890 25.155
## Treatment_bisFull 0.6459 0.2429 115.6878 2.660
## Treatment_bisSmart 0.5220 0.3019 112.8818 1.729
## Treatment_bisMixt_smart 0.3398 0.2925 122.3506 1.162
## SexMale 0.5062 0.1495 125.3744 3.385
## RegionLuxembourg 0.3184 0.2917 59.9019 1.091
## Treatment_bisFull:RegionLuxembourg -0.7261 0.3782 119.2730 -1.920
## Treatment_bisSmart:RegionLuxembourg -0.6232 0.4115 113.7860 -1.515
## Treatment_bisMixt_smart:RegionLuxembourg 0.9441 0.4263 122.4362 2.215
## Pr(>|t|)
## (Intercept) 0.010804 *
## Treatment_bisFull 0.008934 **
## Treatment_bisSmart 0.086572 .
## Treatment_bisMixt_smart 0.247646
## SexMale 0.000951 ***
## RegionLuxembourg 0.279466
## Treatment_bisFull:RegionLuxembourg 0.057252 .
## Treatment_bisSmart:RegionLuxembourg 0.132668
## Treatment_bisMixt_smart:RegionLuxembourg 0.028643 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:RL T_S:RL
## Trtmnt_bsFl -0.215
## Trtmnt_bsSm -0.176 0.364
## Trtmnt_bsM_ -0.188 0.422 0.214
## SexMale -0.123 -0.050 0.059 -0.015
## ReginLxmbrg -0.245 0.397 0.335 0.305 -0.009
## Trtmnt_F:RL 0.141 -0.640 -0.241 -0.264 0.004 -0.582
## Trtmnt_S:RL 0.128 -0.275 -0.689 -0.212 -0.020 -0.543 0.416
## Trtmn_M_:RL 0.127 -0.277 -0.231 -0.582 -0.012 -0.536 0.415 0.374
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE_ref_full
##
## REML criterion at convergence: 372.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4901 -0.6944 -0.1294 0.7102 2.8173
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.1034 0.3216
## Site (Intercept) 0.0000 0.0000
## Room (Intercept) 0.4739 0.6884
## Residual 0.7162 0.8463
## Number of obs: 141, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 13.9430 0.5322 1.3244 26.198
## Treatment_bisDark -0.6459 0.2429 115.6878 -2.660
## Treatment_bisSmart -0.1239 0.3110 116.4622 -0.398
## Treatment_bisMixt_smart -0.3061 0.2909 115.4662 -1.052
## SexMale 0.5062 0.1495 125.3744 3.385
## RegionLuxembourg -0.4077 0.3159 64.9282 -1.291
## Treatment_bisDark:RegionLuxembourg 0.7261 0.3782 119.2730 1.920
## Treatment_bisSmart:RegionLuxembourg 0.1028 0.4276 117.2077 0.241
## Treatment_bisMixt_smart:RegionLuxembourg 1.6702 0.4369 118.2461 3.823
## Pr(>|t|)
## (Intercept) 0.009254 **
## Treatment_bisDark 0.008934 **
## Treatment_bisSmart 0.691105
## Treatment_bisMixt_smart 0.294963
## SexMale 0.000951 ***
## RegionLuxembourg 0.201414
## Treatment_bisDark:RegionLuxembourg 0.057252 .
## Treatment_bisSmart:RegionLuxembourg 0.810349
## Treatment_bisMixt_smart:RegionLuxembourg 0.000212 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_D:RL T_S:RL
## Trtmnt_bsDr -0.243
## Trtmnt_bsSm -0.198 0.427
## Trtmnt_bsM_ -0.197 0.411 0.234
## SexMale -0.145 0.050 0.096 0.027
## ReginLxmbrg -0.240 0.400 0.333 0.300 -0.004
## Trtmnt_D:RL 0.152 -0.640 -0.266 -0.269 -0.004 -0.660
## Trtmnt_S:RL 0.136 -0.302 -0.672 -0.222 -0.023 -0.587 0.484
## Trtmn_M_:RL 0.132 -0.284 -0.238 -0.579 -0.015 -0.570 0.460 0.412
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE_ref_smart
##
## REML criterion at convergence: 372.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4901 -0.6944 -0.1294 0.7102 2.8173
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.1034 0.3216
## Site (Intercept) 0.0000 0.0000
## Room (Intercept) 0.4739 0.6884
## Residual 0.7162 0.8463
## Number of obs: 141, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 13.8191 0.5609 1.6286 24.639
## Treatment_bisDark -0.5220 0.3019 112.8818 -1.729
## Treatment_bisFull 0.1239 0.3110 116.4622 0.398
## Treatment_bisMixt_smart -0.1822 0.3729 120.4413 -0.489
## SexMale 0.5062 0.1495 125.3744 3.385
## RegionLuxembourg -0.3048 0.3522 96.9262 -0.865
## Treatment_bisDark:RegionLuxembourg 0.6232 0.4115 113.7860 1.515
## Treatment_bisFull:RegionLuxembourg -0.1028 0.4276 117.2077 -0.241
## Treatment_bisMixt_smart:RegionLuxembourg 1.5673 0.4689 119.0301 3.343
## Pr(>|t|)
## (Intercept) 0.004344 **
## Treatment_bisDark 0.086572 .
## Treatment_bisFull 0.691105
## Treatment_bisMixt_smart 0.625973
## SexMale 0.000951 ***
## RegionLuxembourg 0.388932
## Treatment_bisDark:RegionLuxembourg 0.132668
## Treatment_bisFull:RegionLuxembourg 0.810349
## Treatment_bisMixt_smart:RegionLuxembourg 0.001110 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.373
## Trtmnt_bsFl -0.367 0.686
## Trtmnt_bsM_ -0.351 0.642 0.652
## SexMale -0.084 -0.059 -0.096 -0.059
## ReginLxmbrg -0.334 0.527 0.517 0.431 -0.031
## Trtmnt_D:RL 0.250 -0.689 -0.454 -0.392 0.020 -0.719
## Trtmnt_F:RL 0.243 -0.449 -0.672 -0.387 0.023 -0.688 0.594
## Trtmn_M_:RL 0.215 -0.394 -0.391 -0.589 0.007 -0.637 0.538 0.528
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_mixt_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE_ref_mixt_smart
##
## REML criterion at convergence: 372.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4901 -0.6944 -0.1294 0.7102 2.8173
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.1034 0.3216
## Site (Intercept) 0.0000 0.0000
## Room (Intercept) 0.4739 0.6884
## Residual 0.7162 0.8463
## Number of obs: 141, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 13.6369 0.5540 1.5497 24.617
## Treatment_bisDark -0.3398 0.2925 122.3506 -1.162
## Treatment_bisFull 0.3061 0.2909 115.4662 1.052
## Treatment_bisSmart 0.1822 0.3729 120.4413 0.489
## SexMale 0.5062 0.1495 125.3744 3.385
## RegionLuxembourg 1.2625 0.3653 95.3078 3.456
## Treatment_bisDark:RegionLuxembourg -0.9441 0.4263 122.4362 -2.215
## Treatment_bisFull:RegionLuxembourg -1.6702 0.4369 118.2461 -3.823
## Treatment_bisSmart:RegionLuxembourg -1.5673 0.4689 119.0301 -3.343
## Pr(>|t|)
## (Intercept) 0.005385 **
## Treatment_bisDark 0.247646
## Treatment_bisFull 0.294963
## Treatment_bisSmart 0.625973
## SexMale 0.000951 ***
## RegionLuxembourg 0.000820 ***
## Treatment_bisDark:RegionLuxembourg 0.028643 *
## Treatment_bisFull:RegionLuxembourg 0.000212 ***
## Treatment_bisSmart:RegionLuxembourg 0.001110 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.349
## Trtmnt_bsFl -0.336 0.654
## Trtmnt_bsSm -0.318 0.612 0.585
## SexMale -0.125 0.015 -0.027 0.059
## ReginLxmbrg -0.275 0.436 0.433 0.341 -0.021
## Trtmnt_D:RL 0.186 -0.582 -0.355 -0.270 0.012 -0.739
## Trtmnt_F:RL 0.178 -0.340 -0.579 -0.253 0.015 -0.703 0.616
## Trtmnt_S:RL 0.179 -0.344 -0.337 -0.589 -0.007 -0.669 0.581 0.556
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(LM_Time_in_pupa_AE)$coeff)[,]))
test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test4 <- data.frame(Reference = "Mixt_smart", as.data.frame(( summary(lmer(Time_in_pupa ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_mixt_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Time_in_pupa_AE <- rbind(test1,test2,test3,test4)
colnames(Results_Time_in_pupa_AE ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Time_in_pupa_AE , file = "output/Results_Time_in_pupa_AE.csv" )
kable(Results_Time_in_pupa_AE , caption = " Temps en chrysalide AE ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 13.2970982 | 0.5286168 | 1.288974 | 25.1545117 | 0.0108038 |
| Treatment_bisFull | Dark | 0.6459053 | 0.2428622 | 115.687832 | 2.6595543 | 0.0089340 |
| Treatment_bisSmart | Dark | 0.5220222 | 0.3019492 | 112.881842 | 1.7288410 | 0.0865716 |
| Treatment_bisMixt_smart | Dark | 0.3398202 | 0.2925367 | 122.350649 | 1.1616330 | 0.2476457 |
| SexMale | Dark | 0.5061546 | 0.1495354 | 125.374447 | 3.3848491 | 0.0009512 |
| RegionLuxembourg | Dark | 0.3184147 | 0.2917477 | 59.901894 | 1.0914042 | 0.2794655 |
| Treatment_bisFull:RegionLuxembourg | Dark | -0.7260823 | 0.3781777 | 119.272967 | -1.9199500 | 0.0572523 |
| Treatment_bisSmart:RegionLuxembourg | Dark | -0.6232444 | 0.4115138 | 113.785957 | -1.5145164 | 0.1326678 |
| Treatment_bisMixt_smart:RegionLuxembourg | Dark | 0.9440774 | 0.4263108 | 122.436231 | 2.2145285 | 0.0286432 |
| (Intercept)1 | Smart | 13.8191204 | 0.5608617 | 1.628619 | 24.6390891 | 0.0043440 |
| Treatment_bisDark | Smart | -0.5220222 | 0.3019492 | 112.881842 | -1.7288410 | 0.0865716 |
| Treatment_bisFull1 | Smart | 0.1238831 | 0.3109943 | 116.462188 | 0.3983453 | 0.6911050 |
| Treatment_bisMixt_smart1 | Smart | -0.1822019 | 0.3728628 | 120.441316 | -0.4886568 | 0.6259733 |
| SexMale1 | Smart | 0.5061546 | 0.1495354 | 125.374447 | 3.3848491 | 0.0009512 |
| RegionLuxembourg1 | Smart | -0.3048297 | 0.3522236 | 96.926205 | -0.8654435 | 0.3889324 |
| Treatment_bisDark:RegionLuxembourg | Smart | 0.6232444 | 0.4115138 | 113.785957 | 1.5145164 | 0.1326678 |
| Treatment_bisFull:RegionLuxembourg1 | Smart | -0.1028380 | 0.4275699 | 117.207725 | -0.2405173 | 0.8103494 |
| Treatment_bisMixt_smart:RegionLuxembourg1 | Smart | 1.5673217 | 0.4688945 | 119.030103 | 3.3425890 | 0.0011098 |
| (Intercept)2 | Full | 13.9430035 | 0.5322099 | 1.324387 | 26.1983164 | 0.0092543 |
| Treatment_bisDark1 | Full | -0.6459053 | 0.2428622 | 115.687832 | -2.6595543 | 0.0089340 |
| Treatment_bisSmart1 | Full | -0.1238831 | 0.3109943 | 116.462188 | -0.3983453 | 0.6911050 |
| Treatment_bisMixt_smart2 | Full | -0.3060851 | 0.2909353 | 115.466175 | -1.0520726 | 0.2949630 |
| SexMale2 | Full | 0.5061546 | 0.1495354 | 125.374447 | 3.3848491 | 0.0009512 |
| RegionLuxembourg2 | Full | -0.4076676 | 0.3158706 | 64.928238 | -1.2906160 | 0.2014139 |
| Treatment_bisDark:RegionLuxembourg1 | Full | 0.7260823 | 0.3781777 | 119.272967 | 1.9199500 | 0.0572523 |
| Treatment_bisSmart:RegionLuxembourg1 | Full | 0.1028380 | 0.4275699 | 117.207725 | 0.2405173 | 0.8103494 |
| Treatment_bisMixt_smart:RegionLuxembourg2 | Full | 1.6701597 | 0.4368948 | 118.246138 | 3.8227964 | 0.0002120 |
| (Intercept)3 | Mixt_smart | 13.6369185 | 0.5539699 | 1.549681 | 24.6167153 | 0.0053847 |
| Treatment_bisDark2 | Mixt_smart | -0.3398202 | 0.2925367 | 122.350649 | -1.1616330 | 0.2476457 |
| Treatment_bisFull2 | Mixt_smart | 0.3060851 | 0.2909353 | 115.466175 | 1.0520726 | 0.2949630 |
| Treatment_bisSmart2 | Mixt_smart | 0.1822019 | 0.3728628 | 120.441316 | 0.4886568 | 0.6259733 |
| SexMale3 | Mixt_smart | 0.5061546 | 0.1495354 | 125.374447 | 3.3848491 | 0.0009512 |
| RegionLuxembourg3 | Mixt_smart | 1.2624920 | 0.3652747 | 95.307810 | 3.4562809 | 0.0008197 |
| Treatment_bisDark:RegionLuxembourg2 | Mixt_smart | -0.9440774 | 0.4263108 | 122.436231 | -2.2145285 | 0.0286432 |
| Treatment_bisFull:RegionLuxembourg2 | Mixt_smart | -1.6701597 | 0.4368948 | 118.246138 | -3.8227964 | 0.0002120 |
| Treatment_bisSmart:RegionLuxembourg2 | Mixt_smart | -1.5673217 | 0.4688945 | 119.030103 | -3.3425890 | 0.0011098 |
Info_time_in_pupa_AE <- "
les individus du traitement Full passent significativement (p-val = 0.008934) plus de temps (0.6459 jours) en chrysalides que les individus du traitement Dark.
Les mâles passent significativement (p-val = 0.000951) plus de temps (0.51 jours) en chrysalides.
Les individus du traitement Mixt-smart en région luxembourgoise passe significativement plus de temps en chrysalide que l'effet de la région luxembourgeoise et du traitement mixt-smart additionnés.
"
Info_time_in_pupa_AE## [1] "\nles individus du traitement Full passent significativement (p-val = 0.008934) plus de temps (0.6459 jours) en chrysalides que les individus du traitement Dark.\nLes mâles passent significativement (p-val = 0.000951) plus de temps (0.51 jours) en chrysalides.\nLes individus du traitement Mixt-smart en région luxembourgoise passe significativement plus de temps en chrysalide que l'effet de la région luxembourgeoise et du traitement mixt-smart additionnés.\n"6.9 TT_emerge OP
6.9.1 Test
LM_TT_emerge_OP <- lmer(TT_emerge ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_OP)## boundary (singular) fit: see help('isSingular')summary(LM_TT_pupation_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_pupation ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room)
## Data: Data_OP
##
## REML criterion at convergence: 610.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3490 -0.5984 -0.1176 0.5181 2.6717
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.961 1.990
## Site (Intercept) 0.000 0.000
## Room (Intercept) 0.000 0.000
## Residual 4.092 2.023
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 14.8358 0.8848 9.9935 16.768 1.2e-08 ***
## Treatment_bisFull -0.1726 0.3832 123.9073 -0.450 0.6533
## Treatment_bisSmart 0.3867 0.5527 124.8872 0.700 0.4855
## SexMale -0.6684 0.3542 124.2542 -1.887 0.0615 .
## RegionLuxembourg 0.3129 1.2146 8.9037 0.258 0.8025
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal
## Trtmnt_bsFl -0.151
## Trtmnt_bsSm -0.086 0.296
## SexMale -0.144 -0.134 -0.089
## ReginLxmbrg -0.686 -0.014 -0.043 0.004
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification de la normalité
qqnorm(resid(LM_TT_emerge_OP))
qqline(resid(LM_TT_emerge_OP))
Homogénité des variances
plot(LM_TT_emerge_OP)
Distance de cook
plot(cooks.distance(LM_TT_emerge_OP))
6.9.2 Simplification du modèle
drop1(LM_TT_emerge_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## TT_emerge ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 1.6583 0.82915 2 103.74 0.1503 0.8607
## Treatment_bis:Region 1.6593 0.82963 2 101.61 0.1503 0.8606LM_TT_emerge1_OP <- update(LM_TT_emerge_OP, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_TT_emerge1_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## TT_emerge ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 0.22805 0.22805 1 107.50 0.0419 0.8381
## Treatment_bis:Region 1.59297 0.79649 2 103.62 0.1464 0.8640LM_TT_emerge2_OP <- update(LM_TT_emerge1_OP, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_TT_emerge2_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## TT_emerge ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room)
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.38304 0.191518 2 62.312 0.0358 0.9648
## Sex 0.21350 0.213497 1 109.226 0.0400 0.8419
## Region 0.00328 0.003276 1 8.025 0.0006 0.9808Nous n’avons plus d’interactions, nous pouvons nous arrêter ici
Regardons si les simplifications étaient utiles
AIC(LM_TT_emerge_OP)## [1] 581.3082AIC(LM_TT_emerge1_OP)## [1] 581.7585AIC(LM_TT_emerge2_OP)## [1] 582.1286Les simplifications n’ont pas étées utiles
6.9.3 Treatment VS Treatment_bis
AIC(lmer(TT_emerge ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] 581.3082AIC(lmer(TT_emerge ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex + Treatment:Region, data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] 579.298summary(lmer(TT_emerge ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 27.87557948 0.9030303 9.784419
## Treatment_bisFull 0.08411044 0.8444907 102.980079
## Treatment_bisSmart -0.42992325 1.2894288 91.591569
## SexMale 0.15250938 0.6486508 102.797281
## RegionLuxembourg -0.21574895 1.2042976 10.476720
## Treatment_bisFull:SexMale -0.53129757 0.9699534 103.582246
## Treatment_bisSmart:SexMale -0.27600600 1.3954280 104.066126
## Treatment_bisFull:RegionLuxembourg 0.32577994 0.9399401 101.045726
## Treatment_bisSmart:RegionLuxembourg 0.71090868 1.3994221 102.090842
## t value Pr(>|t|)
## (Intercept) 30.86892901 4.441528e-11
## Treatment_bisFull 0.09959901 9.208563e-01
## Treatment_bisSmart -0.33342146 7.395783e-01
## SexMale 0.23511783 8.145850e-01
## RegionLuxembourg -0.17914920 8.612380e-01
## Treatment_bisFull:SexMale -0.54775574 5.850381e-01
## Treatment_bisSmart:SexMale -0.19779308 8.435928e-01
## Treatment_bisFull:RegionLuxembourg 0.34659648 7.296152e-01
## Treatment_bisSmart:RegionLuxembourg 0.50800163 6.125481e-01summary(lmer(TT_emerge ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex + Treatment:Region, data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 27.5589015 1.0112227 13.96590 27.2530479
## TreatmentFull 0.4432732 0.9089710 101.34304 0.4876649
## TreatmentSmart 0.4384482 0.8804013 102.88955 0.4980095
## SexMale 1.1827119 0.8089739 104.00154 1.4619902
## RegionLuxembourg -0.7805045 1.3431321 14.06289 -0.5811078
## TreatmentFull:SexMale -1.6165231 1.0907931 104.18586 -1.4819703
## TreatmentSmart:SexMale -1.8886943 1.1044772 101.30492 -1.7100347
## TreatmentFull:RegionLuxembourg 0.9070555 1.0462572 100.79839 0.8669527
## TreatmentSmart:RegionLuxembourg 1.1224347 1.0822820 101.85066 1.0371001
## Pr(>|t|)
## (Intercept) 1.651104e-13
## TreatmentFull 6.268406e-01
## TreatmentSmart 6.195402e-01
## SexMale 1.467590e-01
## RegionLuxembourg 5.703647e-01
## TreatmentFull:SexMale 1.413665e-01
## TreatmentSmart:SexMale 9.032062e-02
## TreatmentFull:RegionLuxembourg 3.880270e-01
## TreatmentSmart:RegionLuxembourg 3.021452e-01Treatment serait à privilégier au vu des AIC
6.9.4 Résultats
Analysons les P-val
summary(LM_TT_emerge_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_emerge ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_OP
##
## REML criterion at convergence: 555.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.86427 -0.52797 -0.02408 0.59660 3.01729
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.05194 1.7470
## Site (Intercept) 0.00000 0.0000
## Room (Intercept) 0.09577 0.3095
## Residual 5.51833 2.3491
## Number of obs: 122, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 27.87558 0.90303 9.78442 30.869
## Treatment_bisFull 0.08411 0.84449 102.98008 0.100
## Treatment_bisSmart -0.42992 1.28943 91.59157 -0.333
## SexMale 0.15251 0.64865 102.79728 0.235
## RegionLuxembourg -0.21575 1.20430 10.47672 -0.179
## Treatment_bisFull:SexMale -0.53130 0.96995 103.58225 -0.548
## Treatment_bisSmart:SexMale -0.27601 1.39543 104.06613 -0.198
## Treatment_bisFull:RegionLuxembourg 0.32578 0.93994 101.04573 0.347
## Treatment_bisSmart:RegionLuxembourg 0.71091 1.39942 102.09084 0.508
## Pr(>|t|)
## (Intercept) 4.44e-11 ***
## Treatment_bisFull 0.921
## Treatment_bisSmart 0.740
## SexMale 0.815
## RegionLuxembourg 0.861
## Treatment_bisFull:SexMale 0.585
## Treatment_bisSmart:SexMale 0.844
## Treatment_bisFull:RegionLuxembourg 0.730
## Treatment_bisSmart:RegionLuxembourg 0.613
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm T_F:SM T_S:SM T_F:RL
## Trtmnt_bsFl -0.322
## Trtmnt_bsSm -0.212 0.232
## SexMale -0.263 0.267 0.218
## ReginLxmbrg -0.646 0.166 0.091 -0.018
## Trtmnt_F:SM 0.183 -0.569 -0.143 -0.661 0.026
## Trtmnt_S:SM 0.123 -0.127 -0.526 -0.482 0.034 0.324
## Trtmnt_F:RL 0.207 -0.610 -0.133 0.040 -0.342 0.027 -0.028
## Trtmnt_S:RL 0.131 -0.134 -0.589 0.017 -0.235 -0.033 -0.091 0.294
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(TT_emerge ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex + Treatment:Region, data = Data_OP_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_emerge ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment:Sex + Treatment:Region
## Data: Data_OP_ref_full
##
## REML criterion at convergence: 553.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.87514 -0.58549 -0.06971 0.55940 2.74663
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.434e+00 1.853e+00
## Site (Intercept) 1.248e-09 3.532e-05
## Room (Intercept) 1.271e-01 3.565e-01
## Residual 5.282e+00 2.298e+00
## Number of obs: 122, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 28.002175 1.047210 16.111424 26.740
## TreatmentDark -0.443273 0.908971 101.343037 -0.488
## TreatmentSmart -0.004825 0.927026 103.820955 -0.005
## SexMale -0.433811 0.712715 103.125540 -0.609
## RegionLuxembourg 0.126551 1.290239 12.010919 0.098
## TreatmentDark:SexMale 1.616523 1.090793 104.185860 1.482
## TreatmentSmart:SexMale -0.272171 1.027290 102.041561 -0.265
## TreatmentDark:RegionLuxembourg -0.907055 1.046257 100.798393 -0.867
## TreatmentSmart:RegionLuxembourg 0.215379 1.020885 102.098748 0.211
## Pr(>|t|)
## (Intercept) 8.89e-15 ***
## TreatmentDark 0.627
## TreatmentSmart 0.996
## SexMale 0.544
## RegionLuxembourg 0.923
## TreatmentDark:SexMale 0.141
## TreatmentSmart:SexMale 0.792
## TreatmentDark:RegionLuxembourg 0.388
## TreatmentSmart:RegionLuxembourg 0.833
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnS SexMal RgnLxm TrD:SM TrS:SM TrD:RL
## TreatmntDrk -0.473
## TretmntSmrt -0.458 0.540
## SexMale -0.403 0.483 0.460
## ReginLxmbrg -0.660 0.257 0.248 0.068
## TrtmntDr:SM 0.269 -0.561 -0.301 -0.671 -0.039
## TrtmntSm:SM 0.265 -0.321 -0.562 -0.671 -0.033 0.457
## TrtmntDr:RL 0.266 -0.561 -0.307 -0.058 -0.354 -0.066 0.033
## TrtmntSm:RL 0.282 -0.329 -0.657 -0.081 -0.363 0.043 0.077 0.452
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(TT_emerge ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex + Treatment:Region, data = Data_OP_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: TT_emerge ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment:Sex + Treatment:Region
## Data: Data_OP_ref_smart
##
## REML criterion at convergence: 553.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.87514 -0.58549 -0.06971 0.55940 2.74663
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 3.434e+00 1.853e+00
## Site (Intercept) 1.248e-09 3.532e-05
## Room (Intercept) 1.271e-01 3.565e-01
## Residual 5.282e+00 2.298e+00
## Number of obs: 122, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 27.997350 1.033172 14.548382 27.098
## TreatmentDark -0.438448 0.880401 102.889551 -0.498
## TreatmentFull 0.004825 0.927026 103.820955 0.005
## SexMale -0.705982 0.762476 102.738009 -0.926
## RegionLuxembourg 0.341930 1.323532 13.090840 0.258
## TreatmentDark:SexMale 1.888694 1.104477 101.304916 1.710
## TreatmentFull:SexMale 0.272171 1.027290 102.041561 0.265
## TreatmentDark:RegionLuxembourg -1.122435 1.082282 101.850655 -1.037
## TreatmentFull:RegionLuxembourg -0.215379 1.020885 102.098748 -0.211
## Pr(>|t|)
## (Intercept) 7.35e-14 ***
## TreatmentDark 0.6195
## TreatmentFull 0.9959
## SexMale 0.3567
## RegionLuxembourg 0.8002
## TreatmentDark:SexMale 0.0903 .
## TreatmentFull:SexMale 0.7916
## TreatmentDark:RegionLuxembourg 0.3021
## TreatmentFull:RegionLuxembourg 0.8333
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnF SexMal RgnLxm TrD:SM TrF:SM TrD:RL
## TreatmntDrk -0.451
## TreatmntFll -0.433 0.495
## SexMale -0.314 0.365 0.328
## ReginLxmbrg -0.670 0.275 0.265 0.041
## TrtmntDr:SM 0.222 -0.501 -0.225 -0.681 -0.029
## TrtmntFl:SM 0.236 -0.261 -0.562 -0.721 -0.027 0.478
## TrtmntDr:RL 0.280 -0.579 -0.322 -0.036 -0.391 -0.066 0.040
## TrtmntFl:RL 0.304 -0.352 -0.657 -0.028 -0.418 0.029 0.077 0.506
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(LM_TT_emerge_OP)$coeff)[,]))
test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(TT_emerge ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex + Treatment:Region, data = Data_OP_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(TT_emerge ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex + Treatment:Region, data = Data_OP_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_TT_emerge_OP <- rbind(test1,test2,test3)
colnames(Results_TT_emerge_OP ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_TT_emerge_OP , file = "output/Results_TT_emerge_OP.csv" )
kable(Results_TT_emerge_OP, caption = " Temps pour sortir de chrysalide OP ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 27.8755795 | 0.9030303 | 9.784419 | 30.8689290 | 0.0000000 |
| Treatment_bisFull | Dark | 0.0841104 | 0.8444907 | 102.980079 | 0.0995990 | 0.9208563 |
| Treatment_bisSmart | Dark | -0.4299232 | 1.2894288 | 91.591569 | -0.3334215 | 0.7395783 |
| SexMale | Dark | 0.1525094 | 0.6486508 | 102.797281 | 0.2351178 | 0.8145850 |
| RegionLuxembourg | Dark | -0.2157489 | 1.2042976 | 10.476720 | -0.1791492 | 0.8612380 |
| Treatment_bisFull:SexMale | Dark | -0.5312976 | 0.9699534 | 103.582246 | -0.5477557 | 0.5850381 |
| Treatment_bisSmart:SexMale | Dark | -0.2760060 | 1.3954280 | 104.066125 | -0.1977931 | 0.8435928 |
| Treatment_bisFull:RegionLuxembourg | Dark | 0.3257799 | 0.9399401 | 101.045726 | 0.3465965 | 0.7296152 |
| Treatment_bisSmart:RegionLuxembourg | Dark | 0.7109087 | 1.3994221 | 102.090842 | 0.5080016 | 0.6125481 |
| (Intercept)1 | Smart | 27.9973497 | 1.0331725 | 14.548382 | 27.0984273 | 0.0000000 |
| TreatmentDark | Smart | -0.4384482 | 0.8804013 | 102.889551 | -0.4980095 | 0.6195402 |
| TreatmentFull | Smart | 0.0048250 | 0.9270259 | 103.820955 | 0.0052048 | 0.9958571 |
| SexMale1 | Smart | -0.7059824 | 0.7624760 | 102.738009 | -0.9259078 | 0.3566638 |
| RegionLuxembourg1 | Smart | 0.3419302 | 1.3235316 | 13.090840 | 0.2583468 | 0.8001565 |
| TreatmentDark:SexMale | Smart | 1.8886943 | 1.1044772 | 101.304917 | 1.7100347 | 0.0903206 |
| TreatmentFull:SexMale | Smart | 0.2721713 | 1.0272899 | 102.041561 | 0.2649410 | 0.7915893 |
| TreatmentDark:RegionLuxembourg | Smart | -1.1224347 | 1.0822820 | 101.850655 | -1.0371001 | 0.3021452 |
| TreatmentFull:RegionLuxembourg | Smart | -0.2153793 | 1.0208849 | 102.098748 | -0.2109731 | 0.8333288 |
| (Intercept)2 | Full | 28.0021747 | 1.0472095 | 16.111424 | 26.7398008 | 0.0000000 |
| TreatmentDark1 | Full | -0.4432732 | 0.9089710 | 101.343037 | -0.4876649 | 0.6268406 |
| TreatmentSmart | Full | -0.0048250 | 0.9270259 | 103.820955 | -0.0052048 | 0.9958571 |
| SexMale2 | Full | -0.4338112 | 0.7127152 | 103.125540 | -0.6086740 | 0.5440790 |
| RegionLuxembourg2 | Full | 0.1265509 | 1.2902387 | 12.010919 | 0.0980834 | 0.9234839 |
| TreatmentDark:SexMale1 | Full | 1.6165231 | 1.0907931 | 104.185860 | 1.4819703 | 0.1413665 |
| TreatmentSmart:SexMale | Full | -0.2721713 | 1.0272899 | 102.041561 | -0.2649410 | 0.7915893 |
| TreatmentDark:RegionLuxembourg1 | Full | -0.9070555 | 1.0462572 | 100.798393 | -0.8669527 | 0.3880270 |
| TreatmentSmart:RegionLuxembourg | Full | 0.2153793 | 1.0208849 | 102.098748 | 0.2109731 | 0.8333288 |
Infos_TT_emerge_OP <- "
RIEN DU TOUT de significatif
"
Infos_TT_emerge_OP## [1] "\nRIEN DU TOUT de significatif\n"6.10 TT_emerge AE
6.10.1 Test
LM_TT_emerge_AE <- lmer(TT_emerge ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)
summary(LM_TT_pupation_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_pupation) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: 20.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7966 -0.7170 -0.1319 0.4654 3.4962
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.004651 0.0682
## Site (Intercept) 0.016315 0.1277
## Room (Intercept) 0.000000 0.0000
## Residual 0.048352 0.2199
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 3.730223 0.072678 15.927558
## Treatment_bisFull -0.025347 0.057426 141.055825
## Treatment_bisSmart -0.071770 0.070289 140.342406
## Treatment_bisMixt_smart -0.055765 0.068962 142.481416
## SexMale 0.004833 0.036243 147.534799
## RegionLuxembourg 0.141065 0.101426 17.484790
## Treatment_bisFull:RegionLuxembourg 0.083329 0.088995 144.914259
## Treatment_bisSmart:RegionLuxembourg -0.156871 0.101294 140.771354
## Treatment_bisMixt_smart:RegionLuxembourg 0.234982 0.105533 144.897884
## t value Pr(>|t|)
## (Intercept) 51.325 <2e-16 ***
## Treatment_bisFull -0.441 0.6596
## Treatment_bisSmart -1.021 0.3090
## Treatment_bisMixt_smart -0.809 0.4201
## SexMale 0.133 0.8941
## RegionLuxembourg 1.391 0.1817
## Treatment_bisFull:RegionLuxembourg 0.936 0.3507
## Treatment_bisSmart:RegionLuxembourg -1.549 0.1237
## Treatment_bisMixt_smart:RegionLuxembourg 2.227 0.0275 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:RL T_S:RL
## Trtmnt_bsFl -0.391
## Trtmnt_bsSm -0.323 0.411
## Trtmnt_bsM_ -0.335 0.425 0.345
## SexMale -0.198 -0.047 0.035 -0.021
## ReginLxmbrg -0.684 0.288 0.226 0.244 -0.024
## Trtmnt_F:RL 0.255 -0.645 -0.266 -0.274 0.018 -0.447
## Trtmnt_S:RL 0.219 -0.287 -0.693 -0.240 0.001 -0.382 0.445
## Trtmn_M_:RL 0.225 -0.277 -0.226 -0.653 -0.016 -0.376 0.446 0.374
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification de la normalité
qqnorm(resid(LM_TT_emerge_AE))
qqline(resid(LM_TT_emerge_AE))
Cela pourrait encore aller peut-être mais on peut tenter en faisant des
modifications
LM_TT_emerge_AE <- lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)Vérification de la normalité
qqnorm(resid(LM_TT_emerge_AE))
qqline(resid(LM_TT_emerge_AE))
C’est déjà beaucoup mieux
Homogénité des variances
plot(LM_TT_emerge_AE)
Distance de cook
plot(cooks.distance(LM_TT_emerge_AE))
Je pense que je vais retirer le point outlier
Data_TT_emerge_AE <- (Data_AE %>% filter(TT_emerge != "NA"))[unname(cooks.distance(LM_TT_emerge_AE) != max(cooks.distance(LM_TT_emerge_AE))),]
Data_TT_emerge_AE_ref_smart <- Data_TT_emerge_AE
Data_TT_emerge_AE_ref_smart$Treatment_bis <- relevel(Data_TT_emerge_AE$Treatment_bis, ref = "Smart")
Data_TT_emerge_AE_ref_full <- Data_TT_emerge_AE
Data_TT_emerge_AE_ref_full$Treatment_bis <- relevel(Data_TT_emerge_AE$Treatment_bis, ref = "Full")
Data_TT_emerge_AE_ref_mixt_smart <- Data_TT_emerge_AE
Data_TT_emerge_AE_ref_mixt_smart$Treatment_bis <- relevel(Data_TT_emerge_AE$Treatment_bis, ref = "Mixt_smart")LM_TT_emerge_AE <- lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_TT_emerge_AE)Vérification de la normalité
qqnorm(resid(LM_TT_emerge_AE))
qqline(resid(LM_TT_emerge_AE))
Homogénité des variances
plot(LM_TT_emerge_AE)
Distance de cook
plot(cooks.distance(LM_TT_emerge_AE))
6.10.2 Simplification du modèle
drop1(LM_TT_emerge_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.044494 0.014831 3 119.83 0.8600 0.463986
## Treatment_bis:Region 0.214083 0.071361 3 114.15 4.1378 0.007971 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_TT_emerge1_AE <- update(LM_TT_emerge_AE, . ~ . - Treatment_bis:Sex)
drop1(LM_TT_emerge1_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 0.042638 0.042638 1 120.64 2.4921 0.117040
## Treatment_bis:Region 0.208287 0.069429 3 116.98 4.0580 0.008764 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Nous n’avons plus d’interactions non significatives, nous pouvons nous arrêter ici
Regardons si les simplifications étaient utiles
AIC(LM_TT_emerge_AE)## [1] -70.3028AIC(LM_TT_emerge1_AE)## [1] -85.00483Les simplifications ont étées utiles
6.10.3 Treatment VS Treatment_bis
AIC(lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_TT_emerge_AE))## [1] -85.00483AIC(lmer(log(TT_emerge) ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region, data = Data_TT_emerge_AE))## [1] -79.83351summary(lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_TT_emerge_AE))$coeff## Estimate Std. Error df
## (Intercept) 3.937831986 0.05372966 6.667809
## Treatment_bisFull 0.019440282 0.03779753 114.687830
## Treatment_bisSmart 0.005527079 0.04643601 112.131751
## Treatment_bisMixt_smart 0.008068429 0.04509883 112.949573
## SexMale 0.037320542 0.02364111 120.643665
## RegionLuxembourg 0.113469549 0.06359356 18.246683
## Treatment_bisFull:RegionLuxembourg 0.045158762 0.05915378 116.783455
## Treatment_bisSmart:RegionLuxembourg -0.103791097 0.06412734 113.990567
## Treatment_bisMixt_smart:RegionLuxembourg 0.146465280 0.06692477 119.669046
## t value Pr(>|t|)
## (Intercept) 73.2897210 6.073881e-11
## Treatment_bisFull 0.5143268 6.080132e-01
## Treatment_bisSmart 0.1190257 9.054680e-01
## Treatment_bisMixt_smart 0.1789055 8.583324e-01
## SexMale 1.5786291 1.170396e-01
## RegionLuxembourg 1.7842931 9.101423e-02
## Treatment_bisFull:RegionLuxembourg 0.7634129 4.467567e-01
## Treatment_bisSmart:RegionLuxembourg -1.6185156 1.083152e-01
## Treatment_bisMixt_smart:RegionLuxembourg 2.1885062 3.057481e-02summary(lmer(log(TT_emerge) ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region, data = Data_TT_emerge_AE))$coeff## Estimate Std. Error df t value
## (Intercept) 3.936687035 0.06868135 3.108999 57.31813673
## TreatmentFull 0.017837237 0.03974452 115.152611 0.44879743
## TreatmentSmart 0.003287872 0.03788359 116.458328 0.08678883
## SexMale 0.042133206 0.02483477 121.849161 1.69654067
## RegionLuxembourg 0.119150273 0.06540721 19.413236 1.82166876
## TreatmentFull:RegionLuxembourg 0.042732448 0.06227982 117.757038 0.68613640
## TreatmentSmart:RegionLuxembourg -0.001941170 0.05688847 117.471008 -0.03412238
## Pr(>|t|)
## (Intercept) 8.317383e-06
## TreatmentFull 6.544212e-01
## TreatmentSmart 9.309884e-01
## SexMale 9.233677e-02
## RegionLuxembourg 8.395123e-02
## TreatmentFull:RegionLuxembourg 4.939758e-01
## TreatmentSmart:RegionLuxembourg 9.728375e-01Treatment_bis serait à privilégier au vu des AIC
6.10.4 Résultats
Analysons les P-val
summary(lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_TT_emerge_AE))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_TT_emerge_AE
##
## REML criterion at convergence: -111
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.17988 -0.69424 -0.08191 0.51398 2.39915
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.002616 0.05115
## Site (Intercept) 0.005481 0.07403
## Room (Intercept) 0.001508 0.03884
## Residual 0.017109 0.13080
## Number of obs: 140, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 3.937832 0.053730 6.667809
## Treatment_bisFull 0.019440 0.037798 114.687830
## Treatment_bisSmart 0.005527 0.046436 112.131751
## Treatment_bisMixt_smart 0.008068 0.045099 112.949573
## SexMale 0.037321 0.023641 120.643665
## RegionLuxembourg 0.113470 0.063594 18.246683
## Treatment_bisFull:RegionLuxembourg 0.045159 0.059154 116.783455
## Treatment_bisSmart:RegionLuxembourg -0.103791 0.064127 113.990567
## Treatment_bisMixt_smart:RegionLuxembourg 0.146465 0.066925 119.669046
## t value Pr(>|t|)
## (Intercept) 73.290 6.07e-11 ***
## Treatment_bisFull 0.514 0.6080
## Treatment_bisSmart 0.119 0.9055
## Treatment_bisMixt_smart 0.179 0.8583
## SexMale 1.579 0.1170
## RegionLuxembourg 1.784 0.0910 .
## Treatment_bisFull:RegionLuxembourg 0.763 0.4468
## Treatment_bisSmart:RegionLuxembourg -1.619 0.1083
## Treatment_bisMixt_smart:RegionLuxembourg 2.189 0.0306 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:RL T_S:RL
## Trtmnt_bsFl -0.346
## Trtmnt_bsSm -0.269 0.368
## Trtmnt_bsM_ -0.314 0.432 0.237
## SexMale -0.199 -0.050 0.052 -0.005
## ReginLxmbrg -0.590 0.299 0.234 0.247 0.004
## Trtmnt_F:RL 0.229 -0.637 -0.239 -0.273 -0.010 -0.434
## Trtmnt_S:RL 0.195 -0.273 -0.686 -0.218 -0.023 -0.396 0.421
## Trtmn_M_:RL 0.213 -0.280 -0.226 -0.593 -0.033 -0.398 0.424 0.375summary(lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_TT_emerge_AE_ref_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_TT_emerge_AE_ref_smart
##
## REML criterion at convergence: -111
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.17988 -0.69424 -0.08191 0.51398 2.39915
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.002616 0.05115
## Site (Intercept) 0.005481 0.07403
## Room (Intercept) 0.001508 0.03884
## Residual 0.017109 0.13080
## Number of obs: 140, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 3.943359 0.060840 10.061802
## Treatment_bisDark -0.005527 0.046436 112.131751
## Treatment_bisFull 0.013913 0.047889 112.461609
## Treatment_bisMixt_smart 0.002541 0.056538 84.869958
## SexMale 0.037321 0.023641 120.643665
## RegionLuxembourg 0.009678 0.070178 26.669949
## Treatment_bisDark:RegionLuxembourg 0.103791 0.064127 113.990567
## Treatment_bisFull:RegionLuxembourg 0.148950 0.066449 116.966510
## Treatment_bisMixt_smart:RegionLuxembourg 0.250256 0.073270 117.544237
## t value Pr(>|t|)
## (Intercept) 64.815 1.59e-14 ***
## Treatment_bisDark -0.119 0.905468
## Treatment_bisFull 0.291 0.771944
## Treatment_bisMixt_smart 0.045 0.964253
## SexMale 1.579 0.117040
## RegionLuxembourg 0.138 0.891345
## Treatment_bisDark:RegionLuxembourg 1.619 0.108315
## Treatment_bisFull:RegionLuxembourg 2.242 0.026876 *
## Treatment_bisMixt_smart:RegionLuxembourg 3.416 0.000875 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.526
## Trtmnt_bsFl -0.530 0.679
## Trtmnt_bsM_ -0.509 0.632 0.646
## SexMale -0.136 -0.052 -0.090 -0.047
## ReginLxmbrg -0.631 0.415 0.419 0.359 -0.017
## Trtmnt_D:RL 0.351 -0.686 -0.450 -0.389 0.023 -0.555
## Trtmnt_F:RL 0.357 -0.449 -0.675 -0.395 0.013 -0.543 0.590
## Trtmn_M_:RL 0.321 -0.394 -0.395 -0.603 -0.010 -0.501 0.532 0.531summary(lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_TT_emerge_AE_ref_full))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_TT_emerge_AE_ref_full
##
## REML criterion at convergence: -111
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.17988 -0.69424 -0.08191 0.51398 2.39915
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.002616 0.05115
## Site (Intercept) 0.005481 0.07403
## Room (Intercept) 0.001508 0.03884
## Residual 0.017109 0.13080
## Number of obs: 140, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.95727 0.05393 6.87689 73.380
## Treatment_bisDark -0.01944 0.03780 114.68783 -0.514
## Treatment_bisSmart -0.01391 0.04789 112.46161 -0.291
## Treatment_bisMixt_smart -0.01137 0.04460 112.05571 -0.255
## SexMale 0.03732 0.02364 120.64366 1.579
## RegionLuxembourg 0.15863 0.06542 20.90884 2.425
## Treatment_bisDark:RegionLuxembourg -0.04516 0.05915 116.78346 -0.763
## Treatment_bisSmart:RegionLuxembourg -0.14895 0.06645 116.96651 -2.242
## Treatment_bisMixt_smart:RegionLuxembourg 0.10131 0.06795 117.18579 1.491
## Pr(>|t|)
## (Intercept) 3.28e-11 ***
## Treatment_bisDark 0.6080
## Treatment_bisSmart 0.7719
## Treatment_bisMixt_smart 0.7992
## SexMale 0.1170
## RegionLuxembourg 0.0245 *
## Treatment_bisDark:RegionLuxembourg 0.4468
## Treatment_bisSmart:RegionLuxembourg 0.0269 *
## Treatment_bisMixt_smart:RegionLuxembourg 0.1387
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_D:RL T_S:RL
## Trtmnt_bsDr -0.356
## Trtmnt_bsSm -0.290 0.432
## Trtmnt_bsM_ -0.312 0.410 0.254
## SexMale -0.233 0.050 0.090 0.037
## ReginLxmbrg -0.565 0.285 0.236 0.234 -0.005
## Trtmnt_D:RL 0.218 -0.637 -0.270 -0.263 0.010 -0.483
## Trtmnt_S:RL 0.197 -0.303 -0.675 -0.224 -0.013 -0.434 0.484
## Trtmn_M_:RL 0.205 -0.279 -0.234 -0.586 -0.024 -0.423 0.453 0.406summary(lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_TT_emerge_AE_ref_mixt_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_TT_emerge_AE_ref_mixt_smart
##
## REML criterion at convergence: -111
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.17988 -0.69424 -0.08191 0.51398 2.39915
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.002616 0.05115
## Site (Intercept) 0.005481 0.07403
## Room (Intercept) 0.001508 0.03884
## Residual 0.017109 0.13080
## Number of obs: 140, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.945900 0.058291 8.667662 67.693
## Treatment_bisDark -0.008068 0.045099 112.949573 -0.179
## Treatment_bisFull 0.011372 0.044602 112.055707 0.255
## Treatment_bisSmart -0.002541 0.056538 84.869958 -0.045
## SexMale 0.037321 0.023641 120.643665 1.579
## RegionLuxembourg 0.259935 0.071678 28.774745 3.626
## Treatment_bisDark:RegionLuxembourg -0.146465 0.066925 119.669046 -2.189
## Treatment_bisFull:RegionLuxembourg -0.101307 0.067954 117.185793 -1.491
## Treatment_bisSmart:RegionLuxembourg -0.250256 0.073270 117.544237 -3.416
## Pr(>|t|)
## (Intercept) 4.13e-13 ***
## Treatment_bisDark 0.858332
## Treatment_bisFull 0.799217
## Treatment_bisSmart 0.964253
## SexMale 0.117040
## RegionLuxembourg 0.001101 **
## Treatment_bisDark:RegionLuxembourg 0.030575 *
## Treatment_bisFull:RegionLuxembourg 0.138701
## Treatment_bisSmart:RegionLuxembourg 0.000875 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.484
## Trtmnt_bsFl -0.477 0.645
## Trtmnt_bsSm -0.439 0.603 0.574
## SexMale -0.187 0.005 -0.037 0.047
## ReginLxmbrg -0.559 0.335 0.342 0.265 -0.027
## Trtmnt_D:RL 0.263 -0.593 -0.363 -0.287 0.033 -0.581
## Trtmnt_F:RL 0.259 -0.346 -0.586 -0.264 0.024 -0.562 0.615
## Trtmnt_S:RL 0.250 -0.350 -0.340 -0.603 0.010 -0.531 0.585 0.559test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_TT_emerge_AE))$coeff)[,]))
test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_TT_emerge_AE_ref_smart))$coeff)[,]))
test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_TT_emerge_AE_ref_full))$coeff)[,]))
test4 <- data.frame(Reference = "Mixt_smart", as.data.frame(( summary(lmer(log(TT_emerge) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_TT_emerge_AE_ref_mixt_smart))$coeff)[,]))
Results_TT_emerge_AE <- rbind(test1,test2,test3,test4)
colnames(Results_TT_emerge_AE ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_TT_emerge_AE , file = "output/Results_TT_emerge_AE.csv" )
kable(Results_TT_emerge_AE , caption = " Temps pour sortir de chrysalide AE ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 3.9378320 | 0.0537297 | 6.667809 | 73.2897210 | 0.0000000 |
| Treatment_bisFull | Dark | 0.0194403 | 0.0377975 | 114.687830 | 0.5143268 | 0.6080132 |
| Treatment_bisSmart | Dark | 0.0055271 | 0.0464360 | 112.131751 | 0.1190257 | 0.9054680 |
| Treatment_bisMixt_smart | Dark | 0.0080684 | 0.0450988 | 112.949573 | 0.1789055 | 0.8583324 |
| SexMale | Dark | 0.0373205 | 0.0236411 | 120.643665 | 1.5786291 | 0.1170396 |
| RegionLuxembourg | Dark | 0.1134695 | 0.0635936 | 18.246682 | 1.7842931 | 0.0910142 |
| Treatment_bisFull:RegionLuxembourg | Dark | 0.0451588 | 0.0591538 | 116.783455 | 0.7634129 | 0.4467567 |
| Treatment_bisSmart:RegionLuxembourg | Dark | -0.1037911 | 0.0641273 | 113.990567 | -1.6185156 | 0.1083152 |
| Treatment_bisMixt_smart:RegionLuxembourg | Dark | 0.1464653 | 0.0669248 | 119.669046 | 2.1885062 | 0.0305748 |
| (Intercept)1 | Smart | 3.9433591 | 0.0608399 | 10.061802 | 64.8153565 | 0.0000000 |
| Treatment_bisDark | Smart | -0.0055271 | 0.0464360 | 112.131751 | -0.1190257 | 0.9054680 |
| Treatment_bisFull1 | Smart | 0.0139132 | 0.0478887 | 112.461609 | 0.2905323 | 0.7719441 |
| Treatment_bisMixt_smart1 | Smart | 0.0025413 | 0.0565384 | 84.869958 | 0.0449491 | 0.9642535 |
| SexMale1 | Smart | 0.0373205 | 0.0236411 | 120.643665 | 1.5786291 | 0.1170396 |
| RegionLuxembourg1 | Smart | 0.0096785 | 0.0701777 | 26.669949 | 0.1379135 | 0.8913448 |
| Treatment_bisDark:RegionLuxembourg | Smart | 0.1037911 | 0.0641273 | 113.990567 | 1.6185156 | 0.1083152 |
| Treatment_bisFull:RegionLuxembourg1 | Smart | 0.1489499 | 0.0664491 | 116.966510 | 2.2415643 | 0.0268758 |
| Treatment_bisMixt_smart:RegionLuxembourg1 | Smart | 0.2502564 | 0.0732697 | 117.544237 | 3.4155500 | 0.0008746 |
| (Intercept)2 | Full | 3.9572723 | 0.0539287 | 6.876888 | 73.3797668 | 0.0000000 |
| Treatment_bisDark1 | Full | -0.0194403 | 0.0377975 | 114.687830 | -0.5143268 | 0.6080132 |
| Treatment_bisSmart1 | Full | -0.0139132 | 0.0478887 | 112.461609 | -0.2905323 | 0.7719441 |
| Treatment_bisMixt_smart2 | Full | -0.0113719 | 0.0446016 | 112.055707 | -0.2549652 | 0.7992174 |
| SexMale2 | Full | 0.0373205 | 0.0236411 | 120.643665 | 1.5786291 | 0.1170396 |
| RegionLuxembourg2 | Full | 0.1586283 | 0.0654200 | 20.908844 | 2.4247693 | 0.0244662 |
| Treatment_bisDark:RegionLuxembourg1 | Full | -0.0451588 | 0.0591538 | 116.783455 | -0.7634129 | 0.4467567 |
| Treatment_bisSmart:RegionLuxembourg1 | Full | -0.1489499 | 0.0664491 | 116.966510 | -2.2415643 | 0.0268758 |
| Treatment_bisMixt_smart:RegionLuxembourg2 | Full | 0.1013065 | 0.0679544 | 117.185793 | 1.4908013 | 0.1387006 |
| (Intercept)3 | Mixt_smart | 3.9459004 | 0.0582909 | 8.667662 | 67.6932828 | 0.0000000 |
| Treatment_bisDark2 | Mixt_smart | -0.0080684 | 0.0450988 | 112.949573 | -0.1789055 | 0.8583324 |
| Treatment_bisFull2 | Mixt_smart | 0.0113719 | 0.0446016 | 112.055707 | 0.2549652 | 0.7992174 |
| Treatment_bisSmart2 | Mixt_smart | -0.0025413 | 0.0565384 | 84.869958 | -0.0449491 | 0.9642535 |
| SexMale3 | Mixt_smart | 0.0373205 | 0.0236411 | 120.643665 | 1.5786291 | 0.1170396 |
| RegionLuxembourg3 | Mixt_smart | 0.2599348 | 0.0716780 | 28.774745 | 3.6264258 | 0.0011006 |
| Treatment_bisDark:RegionLuxembourg2 | Mixt_smart | -0.1464653 | 0.0669248 | 119.669046 | -2.1885062 | 0.0305748 |
| Treatment_bisFull:RegionLuxembourg2 | Mixt_smart | -0.1013065 | 0.0679544 | 117.185793 | -1.4908013 | 0.1387006 |
| Treatment_bisSmart:RegionLuxembourg2 | Mixt_smart | -0.2502564 | 0.0732697 | 117.544237 | -3.4155500 | 0.0008746 |
Infos_TT_emerge_AE <- "
Le traitement mixt-smart en région luxembourgoise est significativement plus lent que l'effet de la région luxembourgeoise et du traitement mixt-smart additionné sauf quand on le compare au traitement full où là, la région luxembourg est elle même significativement plus lente.
Les individus du traitement full mettent significativements (p-val = 0.0245) plus de temps (1.17 jours) à atteindre le stade adulte si ils descendent d'une mère qui provient du luxembourg.
Le traitement full en région luxembourgoise est significativement plus lent que l'effet de la région luxembourgeoise et du traitement full additionné qaund ils sont comparés au traitement smart.
"
Infos_TT_emerge_AE## [1] "\nLe traitement mixt-smart en région luxembourgoise est significativement plus lent que l'effet de la région luxembourgeoise et du traitement mixt-smart additionné sauf quand on le compare au traitement full où là, la région luxembourg est elle même significativement plus lente.\nLes individus du traitement full mettent significativements (p-val = 0.0245) plus de temps (1.17 jours) à atteindre le stade adulte si ils descendent d'une mère qui provient du luxembourg.\nLe traitement full en région luxembourgoise est significativement plus lent que l'effet de la région luxembourgeoise et du traitement full additionné qaund ils sont comparés au traitement smart.\n"6.11 Pupa_mass OP
6.11.1 Test
LM_Pupa_mass_OP <- lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_OP)## boundary (singular) fit: see help('isSingular')summary(LM_Pupa_mass_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_OP
##
## REML criterion at convergence: -613.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.68459 -0.51981 -0.03472 0.58713 2.23727
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.924e-04 0.013871
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 1.742e-05 0.004173
## Residual 2.196e-04 0.014820
## Number of obs: 127, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 1.537e-01 7.083e-03 9.633e+00 21.705
## Treatment_bisFull 6.617e-03 4.990e-03 1.093e+02 1.326
## Treatment_bisSmart -1.545e-03 7.544e-03 1.107e+02 -0.205
## SexMale -1.263e-03 3.811e-03 1.106e+02 -0.331
## RegionLuxembourg -4.800e-03 9.179e-03 1.221e+01 -0.523
## Treatment_bisFull:SexMale -3.901e-03 5.950e-03 1.098e+02 -0.656
## Treatment_bisSmart:SexMale 2.254e-02 8.942e-03 1.136e+02 2.520
## Treatment_bisFull:RegionLuxembourg -6.839e-04 5.870e-03 1.094e+02 -0.117
## Treatment_bisSmart:RegionLuxembourg -5.974e-03 8.843e-03 1.128e+02 -0.676
## Pr(>|t|)
## (Intercept) 1.67e-09 ***
## Treatment_bisFull 0.1876
## Treatment_bisSmart 0.8381
## SexMale 0.7410
## RegionLuxembourg 0.6103
## Treatment_bisFull:SexMale 0.5134
## Treatment_bisSmart:SexMale 0.0131 *
## Treatment_bisFull:RegionLuxembourg 0.9075
## Treatment_bisSmart:RegionLuxembourg 0.5007
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm T_F:SM T_S:SM T_F:RL
## Trtmnt_bsFl -0.249
## Trtmnt_bsSm -0.162 0.252
## SexMale -0.203 0.295 0.240
## ReginLxmbrg -0.592 0.114 0.036 -0.063
## Trtmnt_F:SM 0.139 -0.588 -0.164 -0.642 0.051
## Trtmnt_S:SM 0.082 -0.136 -0.516 -0.448 0.084 0.301
## Trtmnt_F:RL 0.140 -0.525 -0.103 0.062 -0.274 -0.038 -0.053
## Trtmnt_S:RL 0.086 -0.116 -0.495 0.041 -0.208 -0.048 -0.177 0.297
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_Pupa_mass_OP))
qqline(resid(LM_Pupa_mass_OP))
Homogénité des variances
plot(LM_Pupa_mass_OP)
Distance de cook
plot(cooks.distance(LM_Pupa_mass_OP))
6.11.2 Simplification du modèle
drop1(LM_Pupa_mass_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.00187894 0.00093947 2 111.5 4.2775 0.01622 *
## Treatment_bis:Region 0.00010196 0.00005098 2 110.9 0.2321 0.79323
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass1_OP <- update(LM_Pupa_mass_OP, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_Pupa_mass1_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Region 0.00010102 0.00010102 1 10.197 0.4656 0.51024
## Treatment_bis:Sex 0.00178994 0.00089497 2 113.059 4.1247 0.01866 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Il n’y a plus aucune interaction non significative, nous arrêtons la simplification du modèle
Regardons si les simplifications étaient utiles
AIC(LM_Pupa_mass1_OP)## [1] -606.8376AIC(LM_Pupa_mass_OP)## [1] -587.1425Elle l’a été
LM_Pupa_mass <- LM_Pupa_mass1_OP6.11.3 Treatment VS Treatment_bis
AIC(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] -606.8376AIC(lmer(Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] -608.3169summary(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 0.154060690 0.006944391 9.198834 22.1849084
## Treatment_bisFull 0.006456355 0.004216502 111.784885 1.5312110
## Treatment_bisSmart -0.004095014 0.006506692 115.348376 -0.6293542
## SexMale -0.001174378 0.003779701 112.697540 -0.3107067
## RegionLuxembourg -0.005899060 0.008645588 10.197294 -0.6823202
## Treatment_bisFull:SexMale -0.004085283 0.005905066 111.790778 -0.6918269
## Treatment_bisSmart:SexMale 0.021472735 0.008746241 114.718190 2.4550814
## Pr(>|t|)
## (Intercept) 2.661037e-09
## Treatment_bisFull 1.285424e-01
## Treatment_bisSmart 5.303617e-01
## SexMale 7.565975e-01
## RegionLuxembourg 5.102381e-01
## Treatment_bisFull:SexMale 4.904804e-01
## Treatment_bisSmart:SexMale 1.558609e-02summary(lmer(Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 0.151867449 0.006893828 13.59328 22.0294804
## TreatmentFull 0.008451858 0.004585248 111.14771 1.8432717
## TreatmentSmart 0.003882641 0.004424789 112.44766 0.8774748
## SexMale -0.002138311 0.004517490 112.73565 -0.4733405
## RegionLuxembourg -0.005874209 0.008869863 10.24985 -0.6622661
## TreatmentFull:SexMale -0.002890346 0.006435103 112.30863 -0.4491530
## TreatmentSmart:SexMale 0.012373029 0.006717551 111.55568 1.8418958
## Pr(>|t|)
## (Intercept) 4.988168e-12
## TreatmentFull 6.795368e-02
## TreatmentSmart 3.820997e-01
## SexMale 6.368855e-01
## RegionLuxembourg 5.224121e-01
## TreatmentFull:SexMale 6.541868e-01
## TreatmentSmart:SexMale 6.814661e-02Treatment à l’air d’être meilleur
6.11.4 Résultats
Analyse des p-val
summary(lmer(Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment:Sex
## Data: Data_OP
##
## REML criterion at convergence: -630.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.5331 -0.5876 -0.0413 0.7036 2.3827
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.002e-04 0.014151
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 5.938e-06 0.002437
## Residual 2.124e-04 0.014573
## Number of obs: 127, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.151867 0.006894 13.593281 22.029 4.99e-12 ***
## TreatmentFull 0.008452 0.004585 111.147714 1.843 0.0680 .
## TreatmentSmart 0.003883 0.004425 112.447660 0.877 0.3821
## SexMale -0.002138 0.004517 112.735651 -0.473 0.6369
## RegionLuxembourg -0.005874 0.008870 10.249851 -0.662 0.5224
## TreatmentFull:SexMale -0.002890 0.006435 112.308634 -0.449 0.6542
## TreatmentSmart:SexMale 0.012373 0.006718 111.555678 1.842 0.0681 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnF TrtmnS SexMal RgnLxm TrF:SM
## TreatmntFll -0.299
## TretmntSmrt -0.296 0.496
## SexMale -0.284 0.476 0.480
## ReginLxmbrg -0.597 -0.034 -0.049 -0.058
## TrtmntFl:SM 0.213 -0.727 -0.362 -0.717 0.048
## TrtmntSm:SM 0.196 -0.343 -0.664 -0.674 0.057 0.499
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment:Sex
## Data: Data_OP_ref_smart
##
## REML criterion at convergence: -630.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.5331 -0.5876 -0.0413 0.7036 2.3827
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.002e-04 0.014151
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 5.938e-06 0.002437
## Residual 2.124e-04 0.014573
## Number of obs: 127, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.155750 0.007003 14.260607 22.239 1.79e-12 ***
## TreatmentDark -0.003883 0.004425 112.447660 -0.877 0.3821
## TreatmentFull 0.004569 0.004523 111.573392 1.010 0.3146
## SexMale 0.010235 0.004961 112.329307 2.063 0.0414 *
## RegionLuxembourg -0.005874 0.008870 10.249851 -0.662 0.5224
## TreatmentDark:SexMale -0.012373 0.006718 111.555678 -1.842 0.0681 .
## TreatmentFull:SexMale -0.015263 0.006586 110.955659 -2.318 0.0223 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnF SexMal RgnLxm TrD:SM
## TreatmntDrk -0.340
## TreatmntFll -0.314 0.475
## SexMale -0.285 0.462 0.421
## ReginLxmbrg -0.618 0.049 0.013 0.024
## TrtmntDr:SM 0.226 -0.664 -0.302 -0.740 -0.057
## TrtmntFl:SM 0.212 -0.324 -0.682 -0.733 -0.011 0.532
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment:Sex
## Data: Data_OP_ref_full
##
## REML criterion at convergence: -630.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.5331 -0.5876 -0.0413 0.7036 2.3827
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.002e-04 0.014151
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 5.938e-06 0.002437
## Residual 2.124e-04 0.014573
## Number of obs: 127, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.160319 0.007044 14.818028 22.760 6.13e-13 ***
## TreatmentDark -0.008452 0.004585 111.147714 -1.843 0.0680 .
## TreatmentSmart -0.004569 0.004523 111.573392 -1.010 0.3146
## SexMale -0.005029 0.004485 111.265633 -1.121 0.2646
## RegionLuxembourg -0.005874 0.008870 10.249851 -0.662 0.5224
## TreatmentDark:SexMale 0.002890 0.006435 112.308634 0.449 0.6542
## TreatmentSmart:SexMale 0.015263 0.006586 110.955659 2.318 0.0223 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TrtmnD TrtmnS SexMal RgnLxm TrD:SM
## TreatmntDrk -0.358
## TretmntSmrt -0.330 0.528
## SexMale -0.348 0.563 0.536
## ReginLxmbrg -0.606 0.034 -0.013 0.011
## TrtmntDr:SM 0.265 -0.727 -0.382 -0.712 -0.048
## TrtmntSm:SM 0.227 -0.360 -0.682 -0.658 0.011 0.468
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Pupa_mass_OP <- rbind(test1,test2,test3)
colnames(Results_Pupa_mass_OP ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Pupa_mass_OP , file = "output/Results_Pupa_mass_OP.csv" )
kable(Results_Pupa_mass_OP , caption = " Poids des chrysalides OP ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 0.1518674 | 0.0068938 | 13.59328 | 22.0294804 | 0.0000000 |
| TreatmentFull | Dark | 0.0084519 | 0.0045852 | 111.14771 | 1.8432717 | 0.0679537 |
| TreatmentSmart | Dark | 0.0038826 | 0.0044248 | 112.44766 | 0.8774748 | 0.3820997 |
| SexMale | Dark | -0.0021383 | 0.0045175 | 112.73565 | -0.4733405 | 0.6368855 |
| RegionLuxembourg | Dark | -0.0058742 | 0.0088699 | 10.24985 | -0.6622661 | 0.5224121 |
| TreatmentFull:SexMale | Dark | -0.0028903 | 0.0064351 | 112.30863 | -0.4491530 | 0.6541868 |
| TreatmentSmart:SexMale | Dark | 0.0123730 | 0.0067176 | 111.55568 | 1.8418958 | 0.0681466 |
| (Intercept)1 | Smart | 0.1557501 | 0.0070034 | 14.26061 | 22.2390888 | 0.0000000 |
| TreatmentDark | Smart | -0.0038826 | 0.0044248 | 112.44766 | -0.8774748 | 0.3820997 |
| TreatmentFull1 | Smart | 0.0045692 | 0.0045230 | 111.57339 | 1.0102160 | 0.3145776 |
| SexMale1 | Smart | 0.0102347 | 0.0049607 | 112.32931 | 2.0631748 | 0.0414011 |
| RegionLuxembourg1 | Smart | -0.0058742 | 0.0088699 | 10.24985 | -0.6622661 | 0.5224121 |
| TreatmentDark:SexMale | Smart | -0.0123730 | 0.0067176 | 111.55568 | -1.8418958 | 0.0681466 |
| TreatmentFull:SexMale1 | Smart | -0.0152634 | 0.0065856 | 110.95566 | -2.3176776 | 0.0223008 |
| (Intercept)2 | Full | 0.1603193 | 0.0070438 | 14.81803 | 22.7602580 | 0.0000000 |
| TreatmentDark1 | Full | -0.0084519 | 0.0045852 | 111.14771 | -1.8432717 | 0.0679537 |
| TreatmentSmart1 | Full | -0.0045692 | 0.0045230 | 111.57339 | -1.0102160 | 0.3145776 |
| SexMale2 | Full | -0.0050287 | 0.0044845 | 111.26563 | -1.1213405 | 0.2645572 |
| RegionLuxembourg2 | Full | -0.0058742 | 0.0088699 | 10.24985 | -0.6622661 | 0.5224121 |
| TreatmentDark:SexMale1 | Full | 0.0028903 | 0.0064351 | 112.30863 | 0.4491530 | 0.6541868 |
| TreatmentSmart:SexMale1 | Full | 0.0152634 | 0.0065856 | 110.95566 | 2.3176776 | 0.0223008 |
Info_Pupa_mass_OP <- "
Les chrysalides du traitement Full sont quasiment significativement (p-val = 0.0680) plus légères (0.0085 g) que celels du traitement Dark.
Les chrysalides des individus mâles du traitement Smart sont significativement (p-val = 0.0223) plus lourdes (0.015 g) que l'effet de mâle et du traitement Smart additioné comparé au traitement Full.
Les mâles sont significativements (p-val = 0.041) plus lourd (0.010 g) que les femelles dans le traitement Smart.
"
Info_Pupa_mass_OP## [1] "\nLes chrysalides du traitement Full sont quasiment significativement (p-val = 0.0680) plus légères (0.0085 g) que celels du traitement Dark.\nLes chrysalides des individus mâles du traitement Smart sont significativement (p-val = 0.0223) plus lourdes (0.015 g) que l'effet de mâle et du traitement Smart additioné comparé au traitement Full.\nLes mâles sont significativements (p-val = 0.041) plus lourd (0.010 g) que les femelles dans le traitement Smart.\n"6.12 Pupa_mass AE
6.12.1 Test
LM_Pupa_mass_AE <- lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)## boundary (singular) fit: see help('isSingular')summary(LM_Pupa_mass_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: -371.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3033 -0.6809 -0.1277 0.6045 2.4322
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0004491 0.02119
## Site (Intercept) 0.0009460 0.03076
## Room (Intercept) 0.0000000 0.00000
## Residual 0.0033237 0.05765
## Number of obs: 161, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 0.325002 0.019798 19.931133
## Treatment_bisFull 0.013028 0.018470 135.678533
## Treatment_bisSmart 0.012277 0.021295 135.491562
## Treatment_bisMixt_smart 0.057756 0.021882 136.517747
## SexMale 0.028060 0.017182 139.948127
## RegionLuxembourg 0.003959 0.026362 18.609779
## Treatment_bisFull:SexMale -0.001725 0.023850 138.111303
## Treatment_bisSmart:SexMale -0.057238 0.028821 143.074150
## Treatment_bisMixt_smart:SexMale -0.065912 0.028524 140.043272
## Treatment_bisFull:RegionLuxembourg 0.018949 0.023788 136.126736
## Treatment_bisSmart:RegionLuxembourg 0.015090 0.026825 133.114322
## Treatment_bisMixt_smart:RegionLuxembourg 0.050850 0.027983 138.087984
## t value Pr(>|t|)
## (Intercept) 16.416 4.8e-13 ***
## Treatment_bisFull 0.705 0.48179
## Treatment_bisSmart 0.577 0.56523
## Treatment_bisMixt_smart 2.639 0.00927 **
## SexMale 1.633 0.10469
## RegionLuxembourg 0.150 0.88223
## Treatment_bisFull:SexMale -0.072 0.94244
## Treatment_bisSmart:SexMale -1.986 0.04894 *
## Treatment_bisMixt_smart:SexMale -2.311 0.02231 *
## Treatment_bisFull:RegionLuxembourg 0.797 0.42709
## Treatment_bisSmart:RegionLuxembourg 0.563 0.57470
## Treatment_bisMixt_smart:RegionLuxembourg 1.817 0.07136 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM T_M_:S
## Trtmnt_bsFl -0.462
## Trtmnt_bsSm -0.403 0.431
## Trtmnt_bsM_ -0.394 0.421 0.371
## SexMale -0.356 0.380 0.334 0.331
## ReginLxmbrg -0.640 0.233 0.198 0.192 -0.046
## Trtmnt_F:SM 0.248 -0.569 -0.239 -0.240 -0.716 0.031
## Trtmnt_S:SM 0.226 -0.234 -0.491 -0.215 -0.602 0.019 0.431
## Trtmn_M_:SM 0.201 -0.227 -0.205 -0.553 -0.611 0.041 0.440 0.384
## Trtmnt_F:RL 0.247 -0.511 -0.224 -0.213 0.030 -0.459 -0.025 -0.020 -0.032
## Trtmnt_S:RL 0.206 -0.224 -0.575 -0.186 0.041 -0.403 -0.029 -0.050 -0.033
## Trtmn_M_:RL 0.211 -0.219 -0.178 -0.511 0.036 -0.396 -0.026 -0.046 -0.057
## T_F:RL T_S:RL
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_F:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## Trtmnt_F:RL
## Trtmnt_S:RL 0.447
## Trtmn_M_:RL 0.446 0.386
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_Pupa_mass_AE))
qqline(resid(LM_Pupa_mass_AE))
Homogénité des variances
plot(LM_Pupa_mass_AE)
Distance de cook
plot(cooks.distance(LM_Pupa_mass_AE))
6.12.2 Simplification du modèle
drop1(LM_Pupa_mass_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.029970 0.0099900 3 140.26 3.0057 0.03251 *
## Treatment_bis:Region 0.011055 0.0036849 3 135.03 1.1087 0.34794
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass1_AE <- update(LM_Pupa_mass_AE, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_Pupa_mass1_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Region 0.0034995 0.0034995 1 9.672 1.0424 0.33211
## Treatment_bis:Sex 0.0279772 0.0093257 3 143.934 2.7780 0.04341 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Il n’y a plus aucune interaction non significative, nous arrêtons la simplification du modèle
Regardons si les simplifications étaient utiles
AIC(LM_Pupa_mass1_AE)## [1] -359.5025AIC(LM_Pupa_mass_AE)## [1] -339.9384Elle l’a été
LM_Pupa_mass <- LM_Pupa_mass1_AE6.12.3 Treatment VS Treatment_bis
AIC(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE))## boundary (singular) fit: see help('isSingular')## [1] -359.5025AIC(lmer(Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_AE))## [1] -365.9949summary(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 0.3176877678 0.01867902 17.465600 17.00773048
## Treatment_bisFull 0.0202478780 0.01594034 139.663529 1.27022903
## Treatment_bisSmart 0.0173217169 0.01744408 141.721782 0.99298516
## Treatment_bisMixt_smart 0.0780836889 0.01887122 142.688894 4.13771246
## SexMale 0.0269688312 0.01722325 143.882597 1.56583867
## RegionLuxembourg 0.0221783122 0.02172206 9.672011 1.02100416
## Treatment_bisFull:SexMale -0.0004494336 0.02392421 141.913220 -0.01878572
## Treatment_bisSmart:SexMale -0.0545609755 0.02884039 146.305545 -1.89182534
## Treatment_bisMixt_smart:SexMale -0.0627545333 0.02857574 143.939336 -2.19607694
## Pr(>|t|)
## (Intercept) 2.614820e-12
## Treatment_bisFull 2.061151e-01
## Treatment_bisSmart 3.224096e-01
## Treatment_bisMixt_smart 5.967512e-05
## SexMale 1.195831e-01
## RegionLuxembourg 3.321110e-01
## Treatment_bisFull:SexMale 9.850384e-01
## Treatment_bisSmart:SexMale 6.049034e-02
## Treatment_bisMixt_smart:SexMale 2.968718e-02summary(lmer(Pupa_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_AE))$coeff## Estimate Std. Error df t value
## (Intercept) 0.321391127 0.02258020 6.286076 14.2333174
## TreatmentFull 0.014566306 0.01633438 141.411446 0.8917577
## TreatmentSmart 0.041384586 0.01545358 144.527372 2.6779938
## SexMale 0.023161649 0.01758617 145.440882 1.3170375
## RegionLuxembourg 0.022531502 0.02155884 9.489238 1.0451166
## TreatmentFull:SexMale 0.009449579 0.02461249 144.079375 0.3839342
## TreatmentSmart:SexMale -0.051189438 0.02418489 147.588893 -2.1165874
## Pr(>|t|)
## (Intercept) 5.110065e-06
## TreatmentFull 3.740377e-01
## TreatmentSmart 8.264155e-03
## SexMale 1.898974e-01
## RegionLuxembourg 3.218609e-01
## TreatmentFull:SexMale 7.015932e-01
## TreatmentSmart:SexMale 3.597253e-02Treatment à l’air d’être meilleur pour expliquer les données (AIc) mais le traitement Mixt Smart est fort significatif donc je préfère garder Treatment_bis
6.12.4 Résultats
Analyse des p-val
summary(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex
## Data: Data_AE
##
## REML criterion at convergence: -385.5
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.29190 -0.55172 -0.09124 0.58741 2.52972
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0003927 0.01982
## Site (Intercept) 0.0009053 0.03009
## Room (Intercept) 0.0000000 0.00000
## Residual 0.0033570 0.05794
## Number of obs: 161, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.177e-01 1.868e-02 1.747e+01 17.008
## Treatment_bisFull 2.025e-02 1.594e-02 1.397e+02 1.270
## Treatment_bisSmart 1.732e-02 1.744e-02 1.417e+02 0.993
## Treatment_bisMixt_smart 7.808e-02 1.887e-02 1.427e+02 4.138
## SexMale 2.697e-02 1.722e-02 1.439e+02 1.566
## RegionLuxembourg 2.218e-02 2.172e-02 9.672e+00 1.021
## Treatment_bisFull:SexMale -4.494e-04 2.392e-02 1.419e+02 -0.019
## Treatment_bisSmart:SexMale -5.456e-02 2.884e-02 1.463e+02 -1.892
## Treatment_bisMixt_smart:SexMale -6.275e-02 2.858e-02 1.439e+02 -2.196
## Pr(>|t|)
## (Intercept) 2.61e-12 ***
## Treatment_bisFull 0.2061
## Treatment_bisSmart 0.3224
## Treatment_bisMixt_smart 5.97e-05 ***
## SexMale 0.1196
## RegionLuxembourg 0.3321
## Treatment_bisFull:SexMale 0.9850
## Treatment_bisSmart:SexMale 0.0605 .
## Treatment_bisMixt_smart:SexMale 0.0297 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM
## Trtmnt_bsFl -0.418
## Trtmnt_bsSm -0.383 0.455
## Trtmnt_bsM_ -0.359 0.429 0.408
## SexMale -0.392 0.460 0.437 0.407
## ReginLxmbrg -0.597 0.002 -0.023 -0.006 -0.026
## Trtmnt_F:SM 0.274 -0.676 -0.311 -0.294 -0.715 0.014
## Trtmnt_S:SM 0.254 -0.284 -0.636 -0.277 -0.602 -0.008 0.430
## Trtmn_M_:SM 0.230 -0.282 -0.271 -0.678 -0.610 0.017 0.439 0.382
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex
## Data: Data_AE_ref_smart
##
## REML criterion at convergence: -385.5
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.29190 -0.55172 -0.09124 0.58741 2.52972
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0003927 0.01982
## Site (Intercept) 0.0009053 0.03009
## Room (Intercept) 0.0000000 0.00000
## Residual 0.0033570 0.05794
## Number of obs: 161, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 0.335009 0.020083 23.820039 16.681
## Treatment_bisDark -0.017322 0.017444 141.721782 -0.993
## Treatment_bisFull 0.002926 0.017482 140.618688 0.167
## Treatment_bisMixt_smart 0.060762 0.019801 138.188503 3.069
## SexMale -0.027592 0.023038 146.896488 -1.198
## RegionLuxembourg 0.022178 0.021722 9.672011 1.021
## Treatment_bisDark:SexMale 0.054561 0.028840 146.305545 1.892
## Treatment_bisFull:SexMale 0.054112 0.028477 145.207243 1.900
## Treatment_bisMixt_smart:SexMale -0.008194 0.031910 143.692041 -0.257
## Pr(>|t|)
## (Intercept) 1.22e-14 ***
## Treatment_bisDark 0.32241
## Treatment_bisFull 0.86731
## Treatment_bisMixt_smart 0.00259 **
## SexMale 0.23296
## RegionLuxembourg 0.33211
## Treatment_bisDark:SexMale 0.06049 .
## Treatment_bisFull:SexMale 0.05939 .
## Treatment_bisMixt_smart:SexMale 0.79772
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_D:SM T_F:SM
## Trtmnt_bsDr -0.512
## Trtmnt_bsFl -0.506 0.583
## Trtmnt_bsM_ -0.432 0.493 0.499
## SexMale -0.384 0.469 0.458 0.373
## ReginLxmbrg -0.575 0.023 0.024 0.015 -0.029
## Trtmnt_D:SM 0.316 -0.636 -0.376 -0.296 -0.802 0.008
## Trtmnt_F:SM 0.307 -0.383 -0.638 -0.306 -0.809 0.020 0.652
## Trtmn_M_:SM 0.266 -0.332 -0.328 -0.633 -0.705 0.022 0.561 0.573
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex
## Data: Data_AE_ref_full
##
## REML criterion at convergence: -385.5
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.29190 -0.55172 -0.09124 0.58741 2.52972
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0003927 0.01982
## Site (Intercept) 0.0009053 0.03009
## Room (Intercept) 0.0000000 0.00000
## Residual 0.0033570 0.05794
## Number of obs: 161, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.379e-01 1.881e-02 1.828e+01 17.963
## Treatment_bisDark -2.025e-02 1.594e-02 1.397e+02 -1.270
## Treatment_bisSmart -2.926e-03 1.748e-02 1.406e+02 -0.167
## Treatment_bisMixt_smart 5.784e-02 1.877e-02 1.401e+02 3.082
## SexMale 2.652e-02 1.673e-02 1.403e+02 1.586
## RegionLuxembourg 2.218e-02 2.172e-02 9.672e+00 1.021
## Treatment_bisDark:SexMale 4.494e-04 2.392e-02 1.419e+02 0.019
## Treatment_bisSmart:SexMale -5.411e-02 2.848e-02 1.452e+02 -1.900
## Treatment_bisMixt_smart:SexMale -6.231e-02 2.808e-02 1.412e+02 -2.219
## Pr(>|t|)
## (Intercept) 4.57e-13 ***
## Treatment_bisDark 0.20612
## Treatment_bisSmart 0.86731
## Treatment_bisMixt_smart 0.00248 **
## SexMale 0.11510
## RegionLuxembourg 0.33211
## Treatment_bisDark:SexMale 0.98504
## Treatment_bisSmart:SexMale 0.05939 .
## Treatment_bisMixt_smart:SexMale 0.02809 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_D:SM T_S:SM
## Trtmnt_bsDr -0.432
## Trtmnt_bsSm -0.390 0.458
## Trtmnt_bsM_ -0.361 0.418 0.405
## SexMale -0.430 0.494 0.455 0.417
## ReginLxmbrg -0.592 -0.002 -0.024 -0.007 -0.006
## Trtmnt_D:SM 0.301 -0.676 -0.306 -0.278 -0.694 -0.014
## Trtmnt_S:SM 0.265 -0.280 -0.638 -0.271 -0.588 -0.020 0.405
## Trtmn_M_:SM 0.245 -0.289 -0.274 -0.687 -0.591 0.005 0.405 0.363
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_mixt_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex
## Data: Data_AE_ref_mixt_smart
##
## REML criterion at convergence: -385.5
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.29190 -0.55172 -0.09124 0.58741 2.52972
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0003927 0.01982
## Site (Intercept) 0.0009053 0.03009
## Room (Intercept) 0.0000000 0.00000
## Residual 0.0033570 0.05794
## Number of obs: 161, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.395771 0.021251 28.473561 18.624 < 2e-16
## Treatment_bisDark -0.078084 0.018871 142.688894 -4.138 5.97e-05
## Treatment_bisFull -0.057836 0.018769 140.139050 -3.082 0.00248
## Treatment_bisSmart -0.060762 0.019801 138.188503 -3.069 0.00259
## SexMale -0.035786 0.022648 143.319886 -1.580 0.11630
## RegionLuxembourg 0.022178 0.021722 9.672011 1.021 0.33211
## Treatment_bisDark:SexMale 0.062755 0.028576 143.939336 2.196 0.02969
## Treatment_bisFull:SexMale 0.062305 0.028079 141.212963 2.219 0.02809
## Treatment_bisSmart:SexMale 0.008194 0.031910 143.692041 0.257 0.79772
##
## (Intercept) ***
## Treatment_bisDark ***
## Treatment_bisFull **
## Treatment_bisSmart **
## SexMale
## RegionLuxembourg
## Treatment_bisDark:SexMale *
## Treatment_bisFull:SexMale *
## Treatment_bisSmart:SexMale
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_D:SM T_F:SM
## Trtmnt_bsDr -0.572
## Trtmnt_bsFl -0.564 0.641
## Trtmnt_bsSm -0.523 0.594 0.590
## SexMale -0.492 0.546 0.543 0.512
## ReginLxmbrg -0.530 0.006 0.007 -0.015 0.002
## Trtmnt_D:SM 0.400 -0.678 -0.442 -0.407 -0.798 -0.017
## Trtmnt_F:SM 0.390 -0.439 -0.687 -0.409 -0.803 -0.005 0.643
## Trtmnt_S:SM 0.338 -0.357 -0.362 -0.633 -0.692 -0.022 0.550 0.556
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test4 <- data.frame(Reference = "Mixt_smart", as.data.frame(( summary(lmer(Pupa_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_mixt_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Pupa_mass_AE <- rbind(test1,test2,test3,test4)
colnames(Results_Pupa_mass_AE ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Pupa_mass_AE , file = "output/Results_Pupa_mass_AE.csv" )
kable(Results_Pupa_mass_AE , caption = " Poids des chrysalides AE ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 0.3176878 | 0.0186790 | 17.465600 | 17.0077305 | 0.0000000 |
| Treatment_bisFull | Dark | 0.0202479 | 0.0159403 | 139.663529 | 1.2702290 | 0.2061151 |
| Treatment_bisSmart | Dark | 0.0173217 | 0.0174441 | 141.721782 | 0.9929852 | 0.3224096 |
| Treatment_bisMixt_smart | Dark | 0.0780837 | 0.0188712 | 142.688894 | 4.1377125 | 0.0000597 |
| SexMale | Dark | 0.0269688 | 0.0172233 | 143.882597 | 1.5658387 | 0.1195831 |
| RegionLuxembourg | Dark | 0.0221783 | 0.0217221 | 9.672011 | 1.0210042 | 0.3321110 |
| Treatment_bisFull:SexMale | Dark | -0.0004494 | 0.0239242 | 141.913220 | -0.0187857 | 0.9850384 |
| Treatment_bisSmart:SexMale | Dark | -0.0545610 | 0.0288404 | 146.305545 | -1.8918253 | 0.0604903 |
| Treatment_bisMixt_smart:SexMale | Dark | -0.0627545 | 0.0285757 | 143.939336 | -2.1960769 | 0.0296872 |
| (Intercept)1 | Smart | 0.3350095 | 0.0200830 | 23.820039 | 16.6812224 | 0.0000000 |
| Treatment_bisDark | Smart | -0.0173217 | 0.0174441 | 141.721782 | -0.9929852 | 0.3224096 |
| Treatment_bisFull1 | Smart | 0.0029262 | 0.0174816 | 140.618688 | 0.1673856 | 0.8673072 |
| Treatment_bisMixt_smart1 | Smart | 0.0607620 | 0.0198012 | 138.188503 | 3.0685988 | 0.0025890 |
| SexMale1 | Smart | -0.0275921 | 0.0230377 | 146.896488 | -1.1976961 | 0.2329643 |
| RegionLuxembourg1 | Smart | 0.0221783 | 0.0217221 | 9.672011 | 1.0210042 | 0.3321110 |
| Treatment_bisDark:SexMale | Smart | 0.0545610 | 0.0288404 | 146.305545 | 1.8918253 | 0.0604903 |
| Treatment_bisFull:SexMale1 | Smart | 0.0541115 | 0.0284773 | 145.207243 | 1.9001668 | 0.0593935 |
| Treatment_bisMixt_smart:SexMale1 | Smart | -0.0081936 | 0.0319098 | 143.692041 | -0.2567722 | 0.7977219 |
| (Intercept)2 | Full | 0.3379356 | 0.0188129 | 18.283861 | 17.9629383 | 0.0000000 |
| Treatment_bisDark1 | Full | -0.0202479 | 0.0159403 | 139.663529 | -1.2702290 | 0.2061151 |
| Treatment_bisSmart1 | Full | -0.0029262 | 0.0174816 | 140.618688 | -0.1673856 | 0.8673072 |
| Treatment_bisMixt_smart2 | Full | 0.0578358 | 0.0187687 | 140.139050 | 3.0815079 | 0.0024800 |
| SexMale2 | Full | 0.0265194 | 0.0167261 | 140.309076 | 1.5855137 | 0.1151009 |
| RegionLuxembourg2 | Full | 0.0221783 | 0.0217221 | 9.672011 | 1.0210042 | 0.3321110 |
| Treatment_bisDark:SexMale1 | Full | 0.0004494 | 0.0239242 | 141.913220 | 0.0187857 | 0.9850384 |
| Treatment_bisSmart:SexMale1 | Full | -0.0541115 | 0.0284773 | 145.207243 | -1.9001668 | 0.0593935 |
| Treatment_bisMixt_smart:SexMale2 | Full | -0.0623051 | 0.0280787 | 141.212963 | -2.2189457 | 0.0280862 |
| (Intercept)3 | Mixt_smart | 0.3957715 | 0.0212510 | 28.473561 | 18.6236682 | 0.0000000 |
| Treatment_bisDark2 | Mixt_smart | -0.0780837 | 0.0188712 | 142.688894 | -4.1377125 | 0.0000597 |
| Treatment_bisFull2 | Mixt_smart | -0.0578358 | 0.0187687 | 140.139050 | -3.0815079 | 0.0024800 |
| Treatment_bisSmart2 | Mixt_smart | -0.0607620 | 0.0198012 | 138.188503 | -3.0685988 | 0.0025890 |
| SexMale3 | Mixt_smart | -0.0357857 | 0.0226485 | 143.319886 | -1.5800490 | 0.1163001 |
| RegionLuxembourg3 | Mixt_smart | 0.0221783 | 0.0217221 | 9.672011 | 1.0210042 | 0.3321110 |
| Treatment_bisDark:SexMale2 | Mixt_smart | 0.0627545 | 0.0285757 | 143.939335 | 2.1960769 | 0.0296872 |
| Treatment_bisFull:SexMale2 | Mixt_smart | 0.0623051 | 0.0280787 | 141.212963 | 2.2189457 | 0.0280862 |
| Treatment_bisSmart:SexMale2 | Mixt_smart | 0.0081936 | 0.0319098 | 143.692041 | 0.2567722 | 0.7977219 |
Info_Pupa_mass_AE <- "
Les individus du traitement Mixt-smart sont significfativement (p-val = 5.97e-05) plus lourds (0.078 g) que ceux du traitement Dark mais les mâles (toujours comparé au traitement Dark) le sont significativvement (p-val = 0.0297) moins que les femelles (0.063 g).
Les chrysalides des individus du traitement Mixt smart sont significativements (p-val = 0.00259) plus lourd (0.061 g) que celles du traitement Smart.
Les chrysalides du traitement Mixt-smart sont significfativements (p-val = 0.00248) plus lourdes (0.058 g) que celles du traitement Full mais les mâles le sont significativvement (p-val = 0.02809) moins (0.062 g) que les femelles.
"
Info_Pupa_mass_AE## [1] "\nLes individus du traitement Mixt-smart sont significfativement (p-val = 5.97e-05) plus lourds (0.078 g) que ceux du traitement Dark mais les mâles (toujours comparé au traitement Dark) le sont significativvement (p-val = 0.0297) moins que les femelles (0.063 g).\nLes chrysalides des individus du traitement Mixt smart sont significativements (p-val = 0.00259) plus lourd (0.061 g) que celles du traitement Smart.\nLes chrysalides du traitement Mixt-smart sont significfativements (p-val = 0.00248) plus lourdes (0.058 g) que celles du traitement Full mais les mâles le sont significativvement (p-val = 0.02809) moins (0.062 g) que les femelles.\n"6.13 Adult_mass OP
6.13.1 Test
LM_Adult_mass_OP <- lmer(Adult_mass ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_OP)## boundary (singular) fit: see help('isSingular')summary(LM_Adult_mass_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_OP
##
## REML criterion at convergence: -639
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.27013 -0.67303 -0.03053 0.59709 2.14744
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.062e-05 0.003259
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 4.081e-06 0.002020
## Residual 1.760e-04 0.013267
## Number of obs: 124, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 9.058e-02 3.357e-03 6.257e+00 26.981
## Treatment_bisFull 7.122e-03 4.693e-03 1.107e+02 1.518
## Treatment_bisSmart -9.629e-04 7.156e-03 1.002e+02 -0.135
## SexMale -1.526e-02 3.540e-03 1.132e+02 -4.309
## RegionLuxembourg -2.841e-03 3.952e-03 2.062e+01 -0.719
## Treatment_bisFull:SexMale -5.211e-04 5.362e-03 1.140e+02 -0.097
## Treatment_bisSmart:SexMale 1.269e-02 7.702e-03 1.140e+02 1.648
## Treatment_bisFull:RegionLuxembourg -2.176e-03 5.233e-03 1.082e+02 -0.416
## Treatment_bisSmart:RegionLuxembourg -2.187e-03 7.752e-03 1.112e+02 -0.282
## Pr(>|t|)
## (Intercept) 1.03e-07 ***
## Treatment_bisFull 0.132
## Treatment_bisSmart 0.893
## SexMale 3.51e-05 ***
## RegionLuxembourg 0.480
## Treatment_bisFull:SexMale 0.923
## Treatment_bisSmart:SexMale 0.102
## Treatment_bisFull:RegionLuxembourg 0.678
## Treatment_bisSmart:RegionLuxembourg 0.778
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm T_F:SM T_S:SM T_F:RL
## Trtmnt_bsFl -0.466
## Trtmnt_bsSm -0.321 0.233
## SexMale -0.392 0.276 0.208
## ReginLxmbrg -0.529 0.268 0.163 -0.059
## Trtmnt_F:SM 0.267 -0.571 -0.139 -0.663 0.048
## Trtmnt_S:SM 0.183 -0.129 -0.520 -0.472 0.042 0.315
## Trtmnt_F:RL 0.290 -0.607 -0.130 0.046 -0.561 0.025 -0.026
## Trtmnt_S:RL 0.190 -0.134 -0.588 0.032 -0.382 -0.030 -0.093 0.287
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_Adult_mass_OP))
qqline(resid(LM_Adult_mass_OP))
Homogénité des variances
plot(LM_Adult_mass_OP)
Distance de cook
plot(cooks.distance(LM_Adult_mass_OP))
6.13.2 Simplification du modèle
drop1(LM_Adult_mass_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.00055209 2.7605e-04 2 113.34 1.5683 0.2129
## Treatment_bis:Region 0.00003552 1.7758e-05 2 109.68 0.1009 0.9041LM_Adult_mass1_OP <- update(LM_Adult_mass_OP, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_Adult_mass1_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Region 0.00027388 0.00027388 1 8.98 1.5808 0.2404
## Treatment_bis:Sex 0.00053783 0.00026891 2 115.36 1.5521 0.2162LM_Adult_mass2_OP <- update(LM_Adult_mass1_OP, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_Adult_mass2_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room)
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 0.0008031 0.0004015 2 81.241 2.3105 0.1057
## Sex 0.0054632 0.0054632 1 115.801 31.4368 1.42e-07 ***
## Region 0.0002609 0.0002609 1 9.082 1.5012 0.2513
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Nous n’avons plus d’interaction, nous arrêtons la simplification du modèle.
Est ce que la simplification a été utile ?
AIC(LM_Adult_mass2_OP)## [1] -651.0048AIC(LM_Adult_mass_OP)## [1] -612.9728Oui
LM_Adult_mass_OP <- LM_Adult_mass2_OP6.13.3 Treatment VS Treatment_bis
AIC(lmer(Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] -651.0048AIC(lmer(Adult_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] -649.7452summary(lmer(Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.090445370 0.003144128 4.350699 28.766444 3.941422e-06
## Treatment_bisFull 0.005501308 0.002646817 112.218247 2.078462 3.994684e-02
## Treatment_bisSmart 0.004970301 0.004038420 63.579302 1.230754 2.229487e-01
## SexMale -0.013680069 0.002439882 115.800568 -5.606856 1.420160e-07
## RegionLuxembourg -0.003958525 0.003230779 9.082217 -1.225254 2.513039e-01summary(lmer(Adult_mass ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.090346601 0.003081258 30.294326 29.3213389 8.472131e-24
## TreatmentFull 0.005370691 0.002983401 111.919560 1.8001906 7.452427e-02
## TreatmentSmart 0.001977442 0.003044249 114.410902 0.6495665 5.172743e-01
## SexMale -0.013576680 0.002435780 115.786226 -5.5738543 1.649671e-07
## RegionLuxembourg -0.003685080 0.003187152 9.096545 -1.1562298 2.770500e-01On va continuer avec treatment_bis
6.13.4 Résultats
Analyse des P-val
summary(lmer(Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room)
## Data: Data_OP
##
## REML criterion at convergence: -669
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.36138 -0.66854 -0.04749 0.65191 2.14515
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.249e-05 0.003534
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 4.830e-06 0.002198
## Residual 1.738e-04 0.013183
## Number of obs: 124, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.090445 0.003144 4.350699 28.766 3.94e-06 ***
## Treatment_bisFull 0.005501 0.002647 112.218247 2.078 0.0399 *
## Treatment_bisSmart 0.004970 0.004038 63.579302 1.231 0.2229
## SexMale -0.013680 0.002440 115.800568 -5.607 1.42e-07 ***
## RegionLuxembourg -0.003959 0.003231 9.082217 -1.225 0.2513
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal
## Trtmnt_bsFl -0.286
## Trtmnt_bsSm -0.206 0.344
## SexMale -0.304 -0.142 -0.085
## ReginLxmbrg -0.492 -0.071 -0.087 0.008
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room)
## Data: Data_OP_ref_smart
##
## REML criterion at convergence: -669
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.36138 -0.66854 -0.04749 0.65191 2.14515
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.249e-05 0.003534
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 4.830e-06 0.002198
## Residual 1.738e-04 0.013183
## Number of obs: 124, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.095416 0.004579 15.194148 20.840 1.36e-12 ***
## Treatment_bisDark -0.004970 0.004038 63.579302 -1.231 0.223
## Treatment_bisFull 0.000531 0.003994 96.473719 0.133 0.895
## SexMale -0.013680 0.002440 115.800568 -5.607 1.42e-07 ***
## RegionLuxembourg -0.003959 0.003231 9.082217 -1.225 0.251
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F SexMal
## Trtmnt_bsDr -0.741
## Trtmnt_bsFl -0.678 0.783
## SexMale -0.283 0.085 -0.008
## ReginLxmbrg -0.415 0.087 0.041 0.008
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room)
## Data: Data_OP_ref_full
##
## REML criterion at convergence: -669
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.36138 -0.66854 -0.04749 0.65191 2.14515
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.249e-05 0.003534
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 4.830e-06 0.002198
## Residual 1.738e-04 0.013183
## Number of obs: 124, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.095947 0.003482 6.940186 27.557 2.39e-08 ***
## Treatment_bisDark -0.005501 0.002647 112.218248 -2.078 0.0399 *
## Treatment_bisSmart -0.000531 0.003994 96.473719 -0.133 0.8945
## SexMale -0.013680 0.002440 115.800568 -5.607 1.42e-07 ***
## RegionLuxembourg -0.003959 0.003231 9.082217 -1.225 0.2513
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S SexMal
## Trtmnt_bsDr -0.501
## Trtmnt_bsSm -0.256 0.315
## SexMale -0.382 0.142 0.008
## ReginLxmbrg -0.498 0.071 -0.041 0.008
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_OP_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Adult_mass_OP <- rbind(test1,test2,test3)
colnames(Results_Adult_mass_OP ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Adult_mass_OP , file = "output/Results_Adult_mass_OP.csv" )
kable(Results_Adult_mass_OP , caption = " Poids des adultes OP ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 0.0904454 | 0.0031441 | 4.350699 | 28.7664437 | 0.0000039 |
| Treatment_bisFull | Dark | 0.0055013 | 0.0026468 | 112.218248 | 2.0784621 | 0.0399468 |
| Treatment_bisSmart | Dark | 0.0049703 | 0.0040384 | 63.579302 | 1.2307539 | 0.2229487 |
| SexMale | Dark | -0.0136801 | 0.0024399 | 115.800568 | -5.6068558 | 0.0000001 |
| RegionLuxembourg | Dark | -0.0039585 | 0.0032308 | 9.082217 | -1.2252542 | 0.2513039 |
| (Intercept)1 | Smart | 0.0954157 | 0.0045785 | 15.194148 | 20.8397696 | 0.0000000 |
| Treatment_bisDark | Smart | -0.0049703 | 0.0040384 | 63.579302 | -1.2307539 | 0.2229487 |
| Treatment_bisFull1 | Smart | 0.0005310 | 0.0039942 | 96.473719 | 0.1329458 | 0.8945132 |
| SexMale1 | Smart | -0.0136801 | 0.0024399 | 115.800568 | -5.6068558 | 0.0000001 |
| RegionLuxembourg1 | Smart | -0.0039585 | 0.0032308 | 9.082217 | -1.2252542 | 0.2513039 |
| (Intercept)2 | Full | 0.0959467 | 0.0034818 | 6.940186 | 27.5568391 | 0.0000000 |
| Treatment_bisDark1 | Full | -0.0055013 | 0.0026468 | 112.218248 | -2.0784621 | 0.0399468 |
| Treatment_bisSmart1 | Full | -0.0005310 | 0.0039942 | 96.473719 | -0.1329458 | 0.8945132 |
| SexMale2 | Full | -0.0136801 | 0.0024399 | 115.800568 | -5.6068558 | 0.0000001 |
| RegionLuxembourg2 | Full | -0.0039585 | 0.0032308 | 9.082217 | -1.2252542 | 0.2513039 |
Info_Adult_mass_OP <- "
Les adultes du traitement Full sont significativement plus lourd que ceux du traitement Dark.
Les mâles sont significativement plus légers que les femelles
"
Info_Adult_mass_OP## [1] "\nLes adultes du traitement Full sont significativement plus lourd que ceux du traitement Dark.\nLes mâles sont significativement plus légers que les femelles\n"6.14 Adult_mass AE
6.14.1 Test
LM_Adult_mass_AE <- lmer(Adult_mass ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)
summary(LM_Adult_mass_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Adult_mass ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: -428.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4461 -0.5775 0.0190 0.4564 3.2066
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.363e-04 0.011677
## Site (Intercept) 3.368e-04 0.018353
## Room (Intercept) 4.388e-05 0.006624
## Residual 1.523e-03 0.039022
## Number of obs: 143, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 1.918e-01 1.375e-02 1.202e+01
## Treatment_bisFull 2.063e-02 1.361e-02 1.200e+02
## Treatment_bisSmart 1.620e-02 1.554e-02 1.128e+02
## Treatment_bisMixt_smart 4.187e-02 1.575e-02 1.052e+02
## SexMale -1.758e-02 1.214e-02 1.237e+02
## RegionLuxembourg 9.095e-03 1.694e-02 2.165e+01
## Treatment_bisFull:SexMale 4.164e-03 1.736e-02 1.235e+02
## Treatment_bisSmart:SexMale -1.817e-02 2.092e-02 1.254e+02
## Treatment_bisMixt_smart:SexMale -4.214e-02 2.034e-02 1.253e+02
## Treatment_bisFull:RegionLuxembourg -3.526e-04 1.717e-02 1.186e+02
## Treatment_bisSmart:RegionLuxembourg -6.535e-03 1.939e-02 1.146e+02
## Treatment_bisMixt_smart:RegionLuxembourg 2.333e-02 1.978e-02 1.209e+02
## t value Pr(>|t|)
## (Intercept) 13.950 8.75e-09 ***
## Treatment_bisFull 1.516 0.13220
## Treatment_bisSmart 1.042 0.29964
## Treatment_bisMixt_smart 2.658 0.00908 **
## SexMale -1.448 0.15006
## RegionLuxembourg 0.537 0.59677
## Treatment_bisFull:SexMale 0.240 0.81081
## Treatment_bisSmart:SexMale -0.868 0.38678
## Treatment_bisMixt_smart:SexMale -2.072 0.04033 *
## Treatment_bisFull:RegionLuxembourg -0.021 0.98365
## Treatment_bisSmart:RegionLuxembourg -0.337 0.73668
## Treatment_bisMixt_smart:RegionLuxembourg 1.179 0.24073
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM T_M_:S
## Trtmnt_bsFl -0.458
## Trtmnt_bsSm -0.389 0.380
## Trtmnt_bsM_ -0.420 0.435 0.310
## SexMale -0.360 0.369 0.317 0.340
## ReginLxmbrg -0.599 0.245 0.226 0.218 -0.035
## Trtmnt_F:SM 0.234 -0.586 -0.200 -0.259 -0.698 0.046
## Trtmnt_S:SM 0.214 -0.217 -0.418 -0.208 -0.584 0.009 0.403
## Trtmn_M_:SM 0.206 -0.227 -0.200 -0.551 -0.615 0.031 0.438 0.375
## Trtmnt_F:RL 0.265 -0.523 -0.222 -0.229 0.004 -0.486 0.009 0.001 -0.005
## Trtmnt_S:RL 0.213 -0.212 -0.596 -0.178 0.019 -0.423 -0.018 -0.102 -0.011
## Trtmn_M_:RL 0.234 -0.218 -0.187 -0.484 0.019 -0.436 -0.025 -0.026 -0.044
## T_F:RL T_S:RL
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_F:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## Trtmnt_F:RL
## Trtmnt_S:RL 0.417
## Trtmn_M_:RL 0.431 0.364Vérification des hypothèses
qqnorm(resid(LM_Adult_mass_AE))
qqline(resid(LM_Adult_mass_AE))
On va insérer un logarythme dans les données quand même
LM_Adult_mass_AE <- lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)Vérification des hypothèses
qqnorm(resid(LM_Adult_mass_AE))
qqline(resid(LM_Adult_mass_AE))
Homogénité des variances
plot(LM_Adult_mass_AE)
Distance de cook
plot(cooks.distance(LM_Adult_mass_AE))
6.14.2 Simplification du modèle
drop1(LM_Adult_mass_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Adult_mass) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.185699 0.061900 3 121.91 1.5975 0.1935
## Treatment_bis:Region 0.093063 0.031021 3 117.82 0.8006 0.4959LM_Adult_mass1_AE <- update(LM_Adult_mass_AE, . ~ . - Treatment_bis:Region)
drop1(LM_Adult_mass1_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Adult_mass) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Region 0.039206 0.039206 1 10.226 1.0097 0.3382
## Treatment_bis:Sex 0.179712 0.059904 3 125.546 1.5427 0.2068Nous n’avons plus d’interaction à retirer, nous arrêtons la simplification du modèle.
Est ce que la simplification a été utile ?
AIC(LM_Adult_mass1_AE)## [1] 13.5903AIC(LM_Adult_mass_AE)## [1] 26.29923Oui
LM_Adult_mass_AE <- LM_Adult_mass1_AE6.14.3 Treatment VS Treatment_bis
AIC(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE))## boundary (singular) fit: see help('isSingular')## [1] 3.161663AIC(lmer(log(Adult_mass) ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE))## [1] 1.791244summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) -1.68367188 0.05380158 17.99265 -31.294100
## Treatment_bisFull 0.13592965 0.04308590 126.39365 3.154853
## Treatment_bisSmart 0.03944971 0.04902320 122.04083 0.804715
## Treatment_bisMixt_smart 0.19144309 0.04947199 128.49503 3.869727
## SexMale -0.13503554 0.03528278 130.43816 -3.827237
## RegionLuxembourg 0.06481243 0.06265904 10.56742 1.034367
## Pr(>|t|)
## (Intercept) 3.843221e-17
## Treatment_bisFull 2.007076e-03
## Treatment_bisSmart 4.225490e-01
## Treatment_bisMixt_smart 1.724180e-04
## SexMale 2.001719e-04
## RegionLuxembourg 3.240559e-01summary(lmer(log(Adult_mass) ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE))$coeff## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.67804327 0.06578375 5.726785 -25.5084752 4.064884e-07
## TreatmentFull 0.12971461 0.04329543 125.599733 2.9960348 3.296326e-03
## TreatmentSmart 0.10831693 0.04087224 124.131258 2.6501345 9.093434e-03
## SexMale -0.12746733 0.03532718 129.602262 -3.6081948 4.389807e-04
## RegionLuxembourg 0.06155811 0.06392561 10.296531 0.9629648 3.576352e-01On va continuer avec treatment_bis car même si l’AIC préfère le modèle Treatment , Mixt smart a un effet significatif avec Treatment_bis
6.14.4 Résultats
Analyse des P-val
summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_AE
##
## REML criterion at convergence: -12.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.1636 -0.5865 0.0686 0.5200 2.6310
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0032149 0.05670
## Site (Intercept) 0.0072751 0.08529
## Room (Intercept) 0.0002591 0.01610
## Residual 0.0388314 0.19706
## Number of obs: 143, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.70140 0.06049 13.18179 -28.128 3.71e-13
## Treatment_bisFull 0.12438 0.05823 120.58211 2.136 0.034705
## Treatment_bisSmart 0.07786 0.06214 92.49497 1.253 0.213415
## Treatment_bisMixt_smart 0.26692 0.06781 50.02743 3.936 0.000256
## SexMale -0.08843 0.06112 127.63335 -1.447 0.150407
## RegionLuxembourg 0.06641 0.06609 10.22644 1.005 0.338170
## Treatment_bisFull:SexMale 0.01268 0.08696 122.87809 0.146 0.884270
## Treatment_bisSmart:SexMale -0.09682 0.10472 129.28245 -0.925 0.356892
## Treatment_bisMixt_smart:SexMale -0.18314 0.10232 129.07500 -1.790 0.075813
##
## (Intercept) ***
## Treatment_bisFull *
## Treatment_bisSmart
## Treatment_bisMixt_smart ***
## SexMale
## RegionLuxembourg
## Treatment_bisFull:SexMale
## Treatment_bisSmart:SexMale
## Treatment_bisMixt_smart:SexMale .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM
## Trtmnt_bsFl -0.432
## Trtmnt_bsSm -0.396 0.414
## Trtmnt_bsM_ -0.399 0.418 0.357
## SexMale -0.418 0.435 0.419 0.403
## ReginLxmbrg -0.560 -0.005 -0.024 0.007 -0.030
## Trtmnt_F:SM 0.271 -0.679 -0.284 -0.296 -0.699 0.045
## Trtmnt_S:SM 0.262 -0.257 -0.609 -0.259 -0.586 -0.023 0.406
## Trtmn_M_:SM 0.246 -0.270 -0.259 -0.668 -0.615 0.021 0.438 0.376summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE_ref_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_AE_ref_smart
##
## REML criterion at convergence: -12.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.1636 -0.5865 0.0686 0.5200 2.6310
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0032149 0.05670
## Site (Intercept) 0.0072751 0.08529
## Room (Intercept) 0.0002591 0.01610
## Residual 0.0388314 0.19706
## Number of obs: 143, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.62355 0.06741 12.87270 -24.084 4.34e-12
## Treatment_bisDark -0.07786 0.06214 92.49497 -1.253 0.2134
## Treatment_bisFull 0.04652 0.06526 39.67268 0.713 0.4801
## Treatment_bisMixt_smart 0.18906 0.07381 12.50088 2.561 0.0243
## SexMale -0.18525 0.08483 130.18960 -2.184 0.0308
## RegionLuxembourg 0.06641 0.06609 10.22644 1.005 0.3382
## Treatment_bisDark:SexMale 0.09682 0.10472 129.28245 0.925 0.3569
## Treatment_bisFull:SexMale 0.10951 0.10556 128.54859 1.037 0.3015
## Treatment_bisMixt_smart:SexMale -0.08632 0.11566 127.53174 -0.746 0.4569
##
## (Intercept) ***
## Treatment_bisDark
## Treatment_bisFull
## Treatment_bisMixt_smart *
## SexMale *
## RegionLuxembourg
## Treatment_bisDark:SexMale
## Treatment_bisFull:SexMale
## Treatment_bisMixt_smart:SexMale
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_D:SM T_F:SM
## Trtmnt_bsDr -0.567
## Trtmnt_bsFl -0.545 0.583
## Trtmnt_bsM_ -0.503 0.514 0.521
## SexMale -0.394 0.450 0.425 0.352
## ReginLxmbrg -0.524 0.024 0.018 0.026 -0.051
## Trtmnt_D:SM 0.326 -0.609 -0.351 -0.275 -0.812 0.023
## Trtmnt_F:SM 0.308 -0.370 -0.625 -0.300 -0.808 0.060 0.658
## Trtmn_M_:SM 0.279 -0.322 -0.313 -0.599 -0.717 0.040 0.573 0.585summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE_ref_full))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_AE_ref_full
##
## REML criterion at convergence: -12.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.1636 -0.5865 0.0686 0.5200 2.6310
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0032149 0.05670
## Site (Intercept) 0.0072751 0.08529
## Room (Intercept) 0.0002591 0.01610
## Residual 0.0388314 0.19706
## Number of obs: 143, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.57703 0.06332 15.14825 -24.906 1.04e-13
## Treatment_bisDark -0.12438 0.05823 120.58211 -2.136 0.0347
## Treatment_bisSmart -0.04652 0.06526 39.67268 -0.713 0.4801
## Treatment_bisMixt_smart 0.14254 0.06847 107.59342 2.082 0.0397
## SexMale -0.07574 0.06221 117.90424 -1.217 0.2259
## RegionLuxembourg 0.06641 0.06609 10.22644 1.005 0.3382
## Treatment_bisDark:SexMale -0.01268 0.08696 122.87809 -0.146 0.8843
## Treatment_bisSmart:SexMale -0.10951 0.10556 128.54859 -1.037 0.3015
## Treatment_bisMixt_smart:SexMale -0.19582 0.10119 124.01958 -1.935 0.0552
##
## (Intercept) ***
## Treatment_bisDark *
## Treatment_bisSmart
## Treatment_bisMixt_smart *
## SexMale
## RegionLuxembourg
## Treatment_bisDark:SexMale
## Treatment_bisSmart:SexMale
## Treatment_bisMixt_smart:SexMale .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_D:SM T_S:SM
## Trtmnt_bsDr -0.507
## Trtmnt_bsSm -0.451 0.498
## Trtmnt_bsM_ -0.428 0.436 0.391
## SexMale -0.510 0.522 0.480 0.426
## ReginLxmbrg -0.539 0.005 -0.018 0.011 0.033
## Trtmnt_D:SM 0.366 -0.679 -0.336 -0.285 -0.711 -0.045
## Trtmnt_S:SM 0.316 -0.305 -0.625 -0.272 -0.595 -0.060 0.422
## Trtmn_M_:SM 0.300 -0.311 -0.294 -0.682 -0.603 -0.018 0.417 0.375summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE_ref_mixt_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex +
## (1 | Mother) + (1 | Site) + (1 | Room)
## Data: Data_AE_ref_mixt_smart
##
## REML criterion at convergence: -12.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.1636 -0.5865 0.0686 0.5200 2.6310
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0032149 0.05670
## Site (Intercept) 0.0072751 0.08529
## Room (Intercept) 0.0002591 0.01610
## Residual 0.0388314 0.19706
## Number of obs: 143, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.43448 0.07061 14.51590 -20.317 4.56e-12 ***
## Treatment_bisDark -0.26692 0.06781 50.02743 -3.936 0.000256 ***
## Treatment_bisFull -0.14254 0.06847 107.59342 -2.082 0.039735 *
## Treatment_bisSmart -0.18906 0.07381 12.50088 -2.561 0.024281 *
## SexMale -0.27157 0.08070 127.31270 -3.365 0.001011 **
## RegionLuxembourg 0.06641 0.06609 10.22644 1.005 0.338170
## Treatment_bisDark:SexMale 0.18314 0.10232 129.07500 1.790 0.075813 .
## Treatment_bisFull:SexMale 0.19582 0.10119 124.01958 1.935 0.055244 .
## Treatment_bisSmart:SexMale 0.08632 0.11566 127.53174 0.746 0.456864
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_D:SM T_F:SM
## Trtmnt_bsDr -0.619
## Trtmnt_bsFl -0.586 0.635
## Trtmnt_bsSm -0.565 0.618 0.582
## SexMale -0.525 0.543 0.526 0.489
## ReginLxmbrg -0.473 -0.007 -0.011 -0.026 0.003
## Trtmnt_D:SM 0.431 -0.668 -0.432 -0.396 -0.802 -0.021
## Trtmnt_F:SM 0.392 -0.422 -0.682 -0.372 -0.789 0.018 0.635
## Trtmnt_S:SM 0.360 -0.357 -0.348 -0.599 -0.680 -0.040 0.544 0.533test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE))$coeff)[,]))
test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE_ref_smart))$coeff)[,]))
test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE_ref_full))$coeff)[,]))
test4 <- data.frame(Reference = "Mixt_smart", as.data.frame(( summary(lmer(log(Adult_mass) ~ Treatment_bis + Sex + Region + Treatment_bis:Sex + (1 | Mother) + (1 | Site) + (1 | Room), data = Data_AE_ref_mixt_smart))$coeff)[,]))
Results_Adult_mass_AE <- rbind(test1,test2,test3,test4)
colnames(Results_Adult_mass_AE ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Adult_mass_AE , file = "output/Results_Adult_mass_AE.csv" )
kable(Results_Adult_mass_AE , caption = " Poids des adultes AE ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | -1.7014022 | 0.0604881 | 13.18179 | -28.1278797 | 0.0000000 |
| Treatment_bisFull | Dark | 0.1243766 | 0.0582301 | 120.58211 | 2.1359503 | 0.0347052 |
| Treatment_bisSmart | Dark | 0.0778551 | 0.0621420 | 92.49497 | 1.2528592 | 0.2134151 |
| Treatment_bisMixt_smart | Dark | 0.2669182 | 0.0678116 | 50.02743 | 3.9361726 | 0.0002562 |
| SexMale | Dark | -0.0884291 | 0.0611208 | 127.63335 | -1.4467924 | 0.1504066 |
| RegionLuxembourg | Dark | 0.0664067 | 0.0660886 | 10.22644 | 1.0048136 | 0.3381697 |
| Treatment_bisFull:SexMale | Dark | 0.0126844 | 0.0869623 | 122.87809 | 0.1458614 | 0.8842698 |
| Treatment_bisSmart:SexMale | Dark | -0.0968221 | 0.1047168 | 129.28245 | -0.9246090 | 0.3568919 |
| Treatment_bisMixt_smart:SexMale | Dark | -0.1831390 | 0.1023176 | 129.07500 | -1.7899066 | 0.0758135 |
| (Intercept)1 | Smart | -1.6235471 | 0.0674129 | 12.87270 | -24.0836352 | 0.0000000 |
| Treatment_bisDark | Smart | -0.0778551 | 0.0621420 | 92.49497 | -1.2528592 | 0.2134151 |
| Treatment_bisFull1 | Smart | 0.0465214 | 0.0652567 | 39.67268 | 0.7128989 | 0.4800807 |
| Treatment_bisMixt_smart1 | Smart | 0.1890631 | 0.0738146 | 12.50088 | 2.5613230 | 0.0242814 |
| SexMale1 | Smart | -0.1852512 | 0.0848312 | 130.18960 | -2.1837634 | 0.0307716 |
| RegionLuxembourg1 | Smart | 0.0664067 | 0.0660886 | 10.22644 | 1.0048136 | 0.3381697 |
| Treatment_bisDark:SexMale | Smart | 0.0968221 | 0.1047168 | 129.28245 | 0.9246090 | 0.3568919 |
| Treatment_bisFull:SexMale1 | Smart | 0.1095066 | 0.1055570 | 128.54859 | 1.0374165 | 0.3014893 |
| Treatment_bisMixt_smart:SexMale1 | Smart | -0.0863169 | 0.1156610 | 127.53174 | -0.7462922 | 0.4568644 |
| (Intercept)2 | Full | -1.5770256 | 0.0633180 | 15.14825 | -24.9064178 | 0.0000000 |
| Treatment_bisDark1 | Full | -0.1243766 | 0.0582301 | 120.58211 | -2.1359503 | 0.0347052 |
| Treatment_bisSmart1 | Full | -0.0465214 | 0.0652567 | 39.67268 | -0.7128989 | 0.4800807 |
| Treatment_bisMixt_smart2 | Full | 0.1425416 | 0.0684711 | 107.59342 | 2.0817770 | 0.0397352 |
| SexMale2 | Full | -0.0757447 | 0.0622145 | 117.90424 | -1.2174758 | 0.2258543 |
| RegionLuxembourg2 | Full | 0.0664067 | 0.0660886 | 10.22644 | 1.0048136 | 0.3381697 |
| Treatment_bisDark:SexMale1 | Full | -0.0126844 | 0.0869623 | 122.87809 | -0.1458614 | 0.8842698 |
| Treatment_bisSmart:SexMale1 | Full | -0.1095066 | 0.1055570 | 128.54859 | -1.0374165 | 0.3014893 |
| Treatment_bisMixt_smart:SexMale2 | Full | -0.1958234 | 0.1011910 | 124.01958 | -1.9351871 | 0.0552438 |
| (Intercept)3 | Mixt_smart | -1.4344840 | 0.0706055 | 14.51590 | -20.3169001 | 0.0000000 |
| Treatment_bisDark2 | Mixt_smart | -0.2669182 | 0.0678116 | 50.02743 | -3.9361726 | 0.0002562 |
| Treatment_bisFull2 | Mixt_smart | -0.1425416 | 0.0684711 | 107.59342 | -2.0817770 | 0.0397352 |
| Treatment_bisSmart2 | Mixt_smart | -0.1890631 | 0.0738146 | 12.50088 | -2.5613230 | 0.0242814 |
| SexMale3 | Mixt_smart | -0.2715681 | 0.0806965 | 127.31270 | -3.3653004 | 0.0010110 |
| RegionLuxembourg3 | Mixt_smart | 0.0664067 | 0.0660886 | 10.22644 | 1.0048136 | 0.3381697 |
| Treatment_bisDark:SexMale2 | Mixt_smart | 0.1831390 | 0.1023176 | 129.07500 | 1.7899066 | 0.0758135 |
| Treatment_bisFull:SexMale2 | Mixt_smart | 0.1958234 | 0.1011910 | 124.01958 | 1.9351871 | 0.0552438 |
| Treatment_bisSmart:SexMale2 | Mixt_smart | 0.0863169 | 0.1156610 | 127.53174 | 0.7462922 | 0.4568644 |
Info_Adult_mass_AE <- "
Les individus du traitement Full sont significativement plus lourds que ceux du traitement Dark.
Les individus du traitement Mixt-smart sont significativement plus lourd que ceux de n'importe quel autre traitement.
Les mâles significativement plus léger que les femelles dans le traitement Smart.
"
Info_Adult_mass_AE## [1] "\nLes individus du traitement Full sont significativement plus lourds que ceux du traitement Dark.\nLes individus du traitement Mixt-smart sont significativement plus lourd que ceux de n'importe quel autre traitement.\nLes mâles significativement plus léger que les femelles dans le traitement Smart.\n"6.15 M0 OP
6.15.1 Test
LM_M0_OP <- lmer(M0 ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_OP)## boundary (singular) fit: see help('isSingular')summary(LM_M0_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_OP
##
## REML criterion at convergence: -726.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7192 -0.6855 -0.1027 0.6434 3.5627
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 8.482e-05 0.00921
## Site (Intercept) 0.000e+00 0.00000
## Room (Intercept) 0.000e+00 0.00000
## Residual 1.567e-04 0.01252
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.569e-02 4.503e-03 1.090e+01 7.927
## Treatment_bisFull 1.920e-03 4.103e-03 1.198e+02 0.468
## Treatment_bisSmart -9.400e-03 6.010e-03 1.203e+02 -1.564
## SexMale -1.093e-03 3.048e-03 1.188e+02 -0.359
## RegionLuxembourg -2.325e-03 6.224e-03 9.969e+00 -0.373
## Treatment_bisFull:SexMale 9.446e-04 4.796e-03 1.201e+02 0.197
## Treatment_bisSmart:SexMale 1.006e-02 6.945e-03 1.228e+02 1.448
## Treatment_bisFull:RegionLuxembourg -4.604e-03 4.705e-03 1.191e+02 -0.978
## Treatment_bisSmart:RegionLuxembourg 1.544e-03 6.959e-03 1.209e+02 0.222
## Pr(>|t|)
## (Intercept) 7.55e-06 ***
## Treatment_bisFull 0.641
## Treatment_bisSmart 0.120
## SexMale 0.721
## RegionLuxembourg 0.717
## Treatment_bisFull:SexMale 0.844
## Treatment_bisSmart:SexMale 0.150
## Treatment_bisFull:RegionLuxembourg 0.330
## Treatment_bisSmart:RegionLuxembourg 0.825
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm T_F:SM T_S:SM T_F:RL
## Trtmnt_bsFl -0.310
## Trtmnt_bsSm -0.190 0.224
## SexMale -0.243 0.270 0.198
## ReginLxmbrg -0.672 0.156 0.085 -0.034
## Trtmnt_F:SM 0.165 -0.568 -0.128 -0.635 0.032
## Trtmnt_S:SM 0.101 -0.123 -0.486 -0.457 0.046 0.297
## Trtmnt_F:RL 0.199 -0.591 -0.140 0.038 -0.317 0.010 -0.021
## Trtmnt_S:RL 0.121 -0.128 -0.598 0.030 -0.221 -0.038 -0.124 0.278
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_M0_OP))
qqline(resid(LM_M0_OP))
Je pense que ca va
Homogénité des variances
plot(LM_M0_OP)
Distance de cook
plot(cooks.distance(LM_M0_OP))
6.15.2 Simplification du modèle
drop1(LM_M0_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.00033807 1.6904e-04 2 121.39 1.0786 0.3433
## Treatment_bis:Region 0.00019141 9.5704e-05 2 120.11 0.6107 0.5447LM_M0_1_OP <- update(LM_M0_OP, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_M0_1_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Region 0.00006655 6.6549e-05 1 7.754 0.4275 0.5321
## Treatment_bis:Sex 0.00035972 1.7986e-04 2 123.130 1.1554 0.31836.15.3 Résultats
summary(LM_M0_1_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment_bis:Sex
## Data: Data_OP
##
## REML criterion at convergence: -742.7
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8514 -0.6524 -0.1601 0.5753 3.6332
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 8.538e-05 0.00924
## Site (Intercept) 0.000e+00 0.00000
## Room (Intercept) 0.000e+00 0.00000
## Residual 1.557e-04 0.01248
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 3.642e-02 4.409e-03 9.956e+00 8.260 9.14e-06
## Treatment_bisFull -5.351e-04 3.295e-03 1.218e+02 -0.162 0.8713
## Treatment_bisSmart -8.413e-03 4.801e-03 1.255e+02 -1.753 0.0821
## SexMale -1.009e-03 3.035e-03 1.206e+02 -0.332 0.7401
## RegionLuxembourg -3.826e-03 5.852e-03 7.754e+00 -0.654 0.5321
## Treatment_bisFull:SexMale 1.097e-03 4.775e-03 1.220e+02 0.230 0.8186
## Treatment_bisSmart:SexMale 1.033e-02 6.868e-03 1.244e+02 1.504 0.1352
##
## (Intercept) ***
## Treatment_bisFull
## Treatment_bisSmart .
## SexMale
## RegionLuxembourg
## Treatment_bisFull:SexMale
## Treatment_bisSmart:SexMale
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm T_F:SM
## Trtmnt_bsFl -0.247
## Trtmnt_bsSm -0.156 0.253
## SexMale -0.256 0.362 0.268
## ReginLxmbrg -0.655 -0.035 -0.054 -0.021
## Trtmnt_F:SM 0.169 -0.696 -0.190 -0.635 0.031
## Trtmnt_S:SM 0.117 -0.164 -0.705 -0.457 0.024 0.295
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_OP_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment_bis:Sex
## Data: Data_OP_ref_smart
##
## REML criterion at convergence: -742.7
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8514 -0.6524 -0.1601 0.5753 3.6332
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 8.538e-05 9.240e-03
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 3.853e-21 6.207e-11
## Residual 1.557e-04 1.248e-02
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.028005 0.005990 30.692049 4.675 5.55e-05 ***
## Treatment_bisDark 0.008413 0.004801 125.473009 1.753 0.0821 .
## Treatment_bisFull 0.007878 0.005089 124.449688 1.548 0.1242
## SexMale 0.009318 0.006109 124.377624 1.525 0.1297
## RegionLuxembourg -0.003826 0.005852 7.753922 -0.654 0.5321
## Treatment_bisDark:SexMale -0.010327 0.006868 124.352313 -1.504 0.1352
## Treatment_bisFull:SexMale -0.009229 0.007115 123.630243 -1.297 0.1970
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F SexMal RgnLxm T_D:SM
## Trtmnt_bsDr -0.687
## Trtmnt_bsFl -0.634 0.779
## SexMale -0.526 0.660 0.619
## ReginLxmbrg -0.525 0.054 0.028 0.017
## Trtmnt_D:SM 0.479 -0.705 -0.559 -0.897 -0.024
## Trtmnt_F:SM 0.444 -0.554 -0.722 -0.855 -0.002 0.767
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_OP_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment_bis:Sex
## Data: Data_OP_ref_full
##
## REML criterion at convergence: -742.7
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8514 -0.6524 -0.1601 0.5753 3.6332
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 8.538e-05 9.240e-03
## Site (Intercept) 0.000e+00 0.000e+00
## Room (Intercept) 2.676e-21 5.173e-11
## Residual 1.557e-04 1.248e-02
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 3.588e-02 4.809e-03 1.419e+01 7.462 2.82e-06
## Treatment_bisDark 5.351e-04 3.295e-03 1.218e+02 0.162 0.871
## Treatment_bisSmart -7.878e-03 5.089e-03 1.244e+02 -1.548 0.124
## SexMale 8.828e-05 3.687e-03 1.231e+02 0.024 0.981
## RegionLuxembourg -3.826e-03 5.852e-03 7.754e+00 -0.654 0.532
## Treatment_bisDark:SexMale -1.097e-03 4.775e-03 1.220e+02 -0.230 0.819
## Treatment_bisSmart:SexMale 9.229e-03 7.115e-03 1.236e+02 1.297 0.197
##
## (Intercept) ***
## Treatment_bisDark
## Treatment_bisSmart
## SexMale
## RegionLuxembourg
## Treatment_bisDark:SexMale
## Treatment_bisSmart:SexMale
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S SexMal RgnLxm T_D:SM
## Trtmnt_bsDr -0.459
## Trtmnt_bsSm -0.268 0.409
## SexMale -0.407 0.604 0.368
## ReginLxmbrg -0.624 0.035 -0.028 0.024
## Trtmnt_D:SM 0.322 -0.696 -0.272 -0.772 -0.031
## Trtmnt_S:SM 0.211 -0.309 -0.722 -0.513 0.002 0.386
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(LM_M0_1_OP)$coeff)[,]))
test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_OP_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_OP_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_M0_OP <- rbind(test1,test2,test3)
colnames(Results_M0_OP ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_M0_OP , file = "output/Results_M0_OP.csv" )
kable(Results_M0_OP , caption = " Poids initial OP ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 0.0364184 | 0.0044089 | 9.955682 | 8.2601491 | 0.0000091 |
| Treatment_bisFull | Dark | -0.0005351 | 0.0032952 | 121.757241 | -0.1623803 | 0.8712756 |
| Treatment_bisSmart | Dark | -0.0084130 | 0.0048005 | 125.473009 | -1.7525267 | 0.0821260 |
| SexMale | Dark | -0.0010091 | 0.0030352 | 120.636410 | -0.3324473 | 0.7401285 |
| RegionLuxembourg | Dark | -0.0038264 | 0.0058521 | 7.753922 | -0.6538441 | 0.5321193 |
| Treatment_bisFull:SexMale | Dark | 0.0010973 | 0.0047754 | 121.972295 | 0.2297892 | 0.8186405 |
| Treatment_bisSmart:SexMale | Dark | 0.0103267 | 0.0068679 | 124.352313 | 1.5036232 | 0.1352139 |
| (Intercept)1 | Smart | 0.0280054 | 0.0059903 | 30.692049 | 4.6751021 | 0.0000555 |
| Treatment_bisDark | Smart | 0.0084130 | 0.0048005 | 125.473009 | 1.7525267 | 0.0821260 |
| Treatment_bisFull1 | Smart | 0.0078780 | 0.0050890 | 124.449688 | 1.5480472 | 0.1241502 |
| SexMale1 | Smart | 0.0093177 | 0.0061091 | 124.377624 | 1.5252227 | 0.1297424 |
| RegionLuxembourg1 | Smart | -0.0038264 | 0.0058521 | 7.753922 | -0.6538441 | 0.5321193 |
| Treatment_bisDark:SexMale | Smart | -0.0103267 | 0.0068679 | 124.352313 | -1.5036232 | 0.1352139 |
| Treatment_bisFull:SexMale1 | Smart | -0.0092294 | 0.0071154 | 123.630244 | -1.2970967 | 0.1970133 |
| (Intercept)2 | Full | 0.0358833 | 0.0048090 | 14.187000 | 7.4616463 | 0.0000028 |
| Treatment_bisDark1 | Full | 0.0005351 | 0.0032952 | 121.757241 | 0.1623803 | 0.8712756 |
| Treatment_bisSmart1 | Full | -0.0078780 | 0.0050890 | 124.449688 | -1.5480472 | 0.1241502 |
| SexMale2 | Full | 0.0000883 | 0.0036875 | 123.086873 | 0.0239394 | 0.9809397 |
| RegionLuxembourg2 | Full | -0.0038264 | 0.0058521 | 7.753922 | -0.6538441 | 0.5321193 |
| Treatment_bisDark:SexMale1 | Full | -0.0010973 | 0.0047754 | 121.972295 | -0.2297892 | 0.8186405 |
| Treatment_bisSmart:SexMale1 | Full | 0.0092294 | 0.0071154 | 123.630244 | 1.2970967 | 0.1970133 |
Aucune différence significative de poids initial en fonction des traitements ou région ou sexe
6.16 M0 AE
6.16.1 Test
LM_M0_AE <- lmer(M0 ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)
summary(LM_M0_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: -1077
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0225 -0.6040 -0.1758 0.6000 2.7818
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 4.833e-06 0.0021985
## Site (Intercept) 7.789e-06 0.0027909
## Room (Intercept) 9.016e-07 0.0009495
## Residual 3.571e-05 0.0059755
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 1.398e-02 2.013e-03 1.319e+01
## Treatment_bisFull -1.788e-03 1.899e-03 1.422e+02
## Treatment_bisSmart -5.464e-04 2.216e-03 1.355e+02
## Treatment_bisMixt_smart -4.359e-04 2.309e-03 1.169e+02
## SexMale 1.663e-03 1.752e-03 1.451e+02
## RegionLuxembourg -1.691e-04 2.551e-03 2.511e+01
## Treatment_bisFull:SexMale 1.930e-04 2.462e-03 1.402e+02
## Treatment_bisSmart:SexMale -3.854e-03 2.961e-03 1.472e+02
## Treatment_bisMixt_smart:SexMale 9.994e-04 2.935e-03 1.444e+02
## Treatment_bisFull:RegionLuxembourg 5.616e-04 2.422e-03 1.416e+02
## Treatment_bisSmart:RegionLuxembourg 6.085e-04 2.758e-03 1.374e+02
## Treatment_bisMixt_smart:RegionLuxembourg -2.249e-03 2.875e-03 1.417e+02
## t value Pr(>|t|)
## (Intercept) 6.946 9.36e-06 ***
## Treatment_bisFull -0.942 0.348
## Treatment_bisSmart -0.247 0.806
## Treatment_bisMixt_smart -0.189 0.851
## SexMale 0.949 0.344
## RegionLuxembourg -0.066 0.948
## Treatment_bisFull:SexMale 0.078 0.938
## Treatment_bisSmart:SexMale -1.302 0.195
## Treatment_bisMixt_smart:SexMale 0.340 0.734
## Treatment_bisFull:RegionLuxembourg 0.232 0.817
## Treatment_bisSmart:RegionLuxembourg 0.221 0.826
## Treatment_bisMixt_smart:RegionLuxembourg -0.782 0.435
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM T_M_:S
## Trtmnt_bsFl -0.446
## Trtmnt_bsSm -0.370 0.392
## Trtmnt_bsM_ -0.373 0.423 0.302
## SexMale -0.338 0.373 0.302 0.327
## ReginLxmbrg -0.593 0.231 0.205 0.178 -0.051
## Trtmnt_F:SM 0.240 -0.568 -0.198 -0.260 -0.717 0.040
## Trtmnt_S:SM 0.210 -0.225 -0.472 -0.203 -0.595 0.023 0.426
## Trtmn_M_:SM 0.191 -0.220 -0.186 -0.541 -0.606 0.046 0.436 0.376
## Trtmnt_F:RL 0.242 -0.528 -0.220 -0.206 0.027 -0.481 -0.004 -0.020 -0.032
## Trtmnt_S:RL 0.201 -0.219 -0.579 -0.171 0.036 -0.414 -0.030 -0.048 -0.031
## Trtmn_M_:RL 0.204 -0.213 -0.178 -0.496 0.032 -0.407 -0.028 -0.043 -0.055
## T_F:RL T_S:RL
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_F:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## Trtmnt_F:RL
## Trtmnt_S:RL 0.446
## Trtmn_M_:RL 0.446 0.376Vérification des hypothèses
qqnorm(resid(LM_M0_AE))
qqline(resid(LM_M0_AE))
Je pense que ca va
Homogénité des variances
plot(LM_M0_AE)
Distance de cook
plot(cooks.distance(LM_M0_AE))
6.16.2 Simplification du modèle
drop1(LM_M0_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 9.5697e-05 3.1899e-05 3 144.28 0.8934 0.4463
## Treatment_bis:Region 4.1519e-05 1.3840e-05 3 139.00 0.3876 0.7621LM_M0_1_AE <- update(LM_M0_AE, . ~ . - Treatment_bis:Region)
drop1(LM_M0_1_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Region 5.1800e-07 5.1800e-07 1 12.597 0.0147 0.9053
## Treatment_bis:Sex 9.6857e-05 3.2286e-05 3 146.957 0.9189 0.43346.16.3 Résultats
summary(LM_M0_1_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment_bis:Sex
## Data: Data_AE
##
## REML criterion at convergence: -1106.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0462 -0.6640 -0.1532 0.6146 2.9586
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.149e-06 0.002269
## Site (Intercept) 7.787e-06 0.002790
## Room (Intercept) 8.910e-07 0.000944
## Residual 3.513e-05 0.005927
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 1.402e-02 1.934e-03 1.140e+01 7.247
## Treatment_bisFull -1.515e-03 1.599e-03 1.447e+02 -0.947
## Treatment_bisSmart -1.921e-04 1.789e-03 1.362e+02 -0.107
## Treatment_bisMixt_smart -1.360e-03 1.989e-03 9.589e+01 -0.684
## SexMale 1.678e-03 1.738e-03 1.481e+02 0.966
## RegionLuxembourg -2.586e-04 2.130e-03 1.260e+01 -0.121
## Treatment_bisFull:SexMale 1.482e-04 2.442e-03 1.430e+02 0.061
## Treatment_bisSmart:SexMale -3.943e-03 2.936e-03 1.500e+02 -1.343
## Treatment_bisMixt_smart:SexMale 8.966e-04 2.909e-03 1.472e+02 0.308
## Pr(>|t|)
## (Intercept) 1.35e-05 ***
## Treatment_bisFull 0.345
## Treatment_bisSmart 0.915
## Treatment_bisMixt_smart 0.496
## SexMale 0.336
## RegionLuxembourg 0.905
## Treatment_bisFull:SexMale 0.952
## Treatment_bisSmart:SexMale 0.181
## Treatment_bisMixt_smart:SexMale 0.758
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM
## Trtmnt_bsFl -0.391
## Trtmnt_bsSm -0.334 0.413
## Trtmnt_bsM_ -0.328 0.442 0.316
## SexMale -0.360 0.456 0.396 0.395
## ReginLxmbrg -0.552 -0.021 -0.023 -0.023 -0.036
## Trtmnt_F:SM 0.254 -0.671 -0.264 -0.316 -0.717 0.033
## Trtmnt_S:SM 0.230 -0.277 -0.614 -0.259 -0.594 -0.001 0.424
## Trtmn_M_:SM 0.211 -0.278 -0.249 -0.656 -0.606 0.024 0.436 0.375summary(lmer(M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment_bis:Sex
## Data: Data_AE_ref_smart
##
## REML criterion at convergence: -1106.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0462 -0.6640 -0.1532 0.6146 2.9586
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.149e-06 0.002269
## Site (Intercept) 7.787e-06 0.002790
## Room (Intercept) 8.910e-07 0.000944
## Residual 3.513e-05 0.005927
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 1.383e-02 2.152e-03 1.419e+01 6.426
## Treatment_bisDark 1.921e-04 1.789e-03 1.362e+02 0.107
## Treatment_bisFull -1.323e-03 1.843e-03 8.697e+01 -0.718
## Treatment_bisMixt_smart -1.168e-03 2.215e-03 4.146e+01 -0.527
## SexMale -2.265e-03 2.361e-03 1.508e+02 -0.959
## RegionLuxembourg -2.586e-04 2.130e-03 1.260e+01 -0.121
## Treatment_bisDark:SexMale 3.943e-03 2.936e-03 1.500e+02 1.343
## Treatment_bisFull:SexMale 4.091e-03 2.915e-03 1.499e+02 1.403
## Treatment_bisMixt_smart:SexMale 4.839e-03 3.267e-03 1.467e+02 1.481
## Pr(>|t|)
## (Intercept) 1.48e-05 ***
## Treatment_bisDark 0.915
## Treatment_bisFull 0.475
## Treatment_bisMixt_smart 0.601
## SexMale 0.339
## RegionLuxembourg 0.905
## Treatment_bisDark:SexMale 0.181
## Treatment_bisFull:SexMale 0.163
## Treatment_bisMixt_smart:SexMale 0.141
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_D:SM T_F:SM
## Trtmnt_bsDr -0.531
## Trtmnt_bsFl -0.523 0.612
## Trtmnt_bsM_ -0.457 0.523 0.564
## SexMale -0.375 0.473 0.452 0.353
## ReginLxmbrg -0.515 0.023 0.003 -0.002 -0.028
## Trtmnt_D:SM 0.304 -0.614 -0.356 -0.263 -0.806 0.001
## Trtmnt_F:SM 0.314 -0.397 -0.632 -0.324 -0.812 0.028 0.652
## Trtmn_M_:SM 0.258 -0.331 -0.320 -0.582 -0.706 0.022 0.565 0.574summary(lmer(M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_full))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment_bis:Sex
## Data: Data_AE_ref_full
##
## REML criterion at convergence: -1106.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0462 -0.6640 -0.1532 0.6146 2.9586
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.149e-06 0.002269
## Site (Intercept) 7.787e-06 0.002790
## Room (Intercept) 8.910e-07 0.000944
## Residual 3.513e-05 0.005927
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 1.250e-02 1.970e-03 1.214e+01 6.347
## Treatment_bisDark 1.515e-03 1.599e-03 1.447e+02 0.947
## Treatment_bisSmart 1.323e-03 1.843e-03 8.697e+01 0.718
## Treatment_bisMixt_smart 1.554e-04 1.924e-03 1.354e+02 0.081
## SexMale 1.826e-03 1.701e-03 1.425e+02 1.074
## RegionLuxembourg -2.586e-04 2.130e-03 1.260e+01 -0.121
## Treatment_bisDark:SexMale -1.482e-04 2.442e-03 1.430e+02 -0.061
## Treatment_bisSmart:SexMale -4.091e-03 2.915e-03 1.499e+02 -1.403
## Treatment_bisMixt_smart:SexMale 7.484e-04 2.870e-03 1.449e+02 0.261
## Pr(>|t|)
## (Intercept) 3.49e-05 ***
## Treatment_bisDark 0.345
## Treatment_bisSmart 0.475
## Treatment_bisMixt_smart 0.936
## SexMale 0.285
## RegionLuxembourg 0.905
## Treatment_bisDark:SexMale 0.952
## Treatment_bisSmart:SexMale 0.163
## Treatment_bisMixt_smart:SexMale 0.795
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_D:SM T_S:SM
## Trtmnt_bsDr -0.428
## Trtmnt_bsSm -0.365 0.467
## Trtmnt_bsM_ -0.317 0.374 0.309
## SexMale -0.407 0.497 0.456 0.362
## ReginLxmbrg -0.559 0.021 -0.003 -0.006 0.011
## Trtmnt_D:SM 0.295 -0.671 -0.326 -0.232 -0.703 -0.033
## Trtmnt_S:SM 0.248 -0.284 -0.632 -0.232 -0.587 -0.028 0.410
## Trtmn_M_:SM 0.232 -0.289 -0.277 -0.650 -0.591 -0.004 0.409 0.362summary(lmer(M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_mixt_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) +
## (1 | Room) + Treatment_bis:Sex
## Data: Data_AE_ref_mixt_smart
##
## REML criterion at convergence: -1106.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0462 -0.6640 -0.1532 0.6146 2.9586
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.149e-06 0.002269
## Site (Intercept) 7.787e-06 0.002790
## Room (Intercept) 8.910e-07 0.000944
## Residual 3.513e-05 0.005927
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.266e-02 2.275e-03 1.668e+01 5.565 3.67e-05
## Treatment_bisDark 1.360e-03 1.989e-03 9.589e+01 0.684 0.496
## Treatment_bisFull -1.554e-04 1.924e-03 1.354e+02 -0.081 0.936
## Treatment_bisSmart 1.168e-03 2.215e-03 4.146e+01 0.527 0.601
## SexMale 2.575e-03 2.315e-03 1.455e+02 1.112 0.268
## RegionLuxembourg -2.586e-04 2.130e-03 1.260e+01 -0.121 0.905
## Treatment_bisDark:SexMale -8.966e-04 2.909e-03 1.472e+02 -0.308 0.758
## Treatment_bisFull:SexMale -7.484e-04 2.870e-03 1.449e+02 -0.261 0.795
## Treatment_bisSmart:SexMale -4.839e-03 3.267e-03 1.467e+02 -1.481 0.141
##
## (Intercept) ***
## Treatment_bisDark
## Treatment_bisFull
## Treatment_bisSmart
## SexMale
## RegionLuxembourg
## Treatment_bisDark:SexMale
## Treatment_bisFull:SexMale
## Treatment_bisSmart:SexMale
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_D:SM T_F:SM
## Trtmnt_bsDr -0.596
## Trtmnt_bsFl -0.571 0.666
## Trtmnt_bsSm -0.541 0.643 0.611
## SexMale -0.466 0.528 0.540 0.462
## ReginLxmbrg -0.490 0.023 0.006 0.002 0.003
## Trtmnt_D:SM 0.394 -0.656 -0.447 -0.388 -0.802 -0.024
## Trtmnt_F:SM 0.349 -0.396 -0.650 -0.334 -0.805 0.004 0.643
## Trtmnt_S:SM 0.323 -0.351 -0.364 -0.582 -0.691 -0.022 0.553 0.555test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(LM_M0_1_AE)$coeff)[,]))
test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_smart))$coeff)[,]))
test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_full))$coeff)[,]))
test4 <- data.frame(Reference = "Mixt_smart", as.data.frame(( summary(lmer(M0 ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_AE_ref_mixt_smart))$coeff)[,]))
Results_M0_AE <- rbind(test1,test2,test3,test4)
colnames(Results_M0_AE ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_M0_AE , file = "output/Results_M0_AE.csv" )
kable(Results_M0_AE , caption = " Poids inital AE ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 0.0140190 | 0.0019344 | 11.40235 | 7.2472755 | 0.0000135 |
| Treatment_bisFull | Dark | -0.0015153 | 0.0015994 | 144.67510 | -0.9473976 | 0.3450159 |
| Treatment_bisSmart | Dark | -0.0001921 | 0.0017889 | 136.15414 | -0.1073595 | 0.9146619 |
| Treatment_bisMixt_smart | Dark | -0.0013599 | 0.0019894 | 95.88649 | -0.6835834 | 0.4958869 |
| SexMale | Dark | 0.0016783 | 0.0017376 | 148.07944 | 0.9658657 | 0.3356861 |
| RegionLuxembourg | Dark | -0.0002586 | 0.0021302 | 12.59660 | -0.1214121 | 0.9052800 |
| Treatment_bisFull:SexMale | Dark | 0.0001482 | 0.0024419 | 142.96874 | 0.0606870 | 0.9516933 |
| Treatment_bisSmart:SexMale | Dark | -0.0039427 | 0.0029363 | 149.98292 | -1.3427458 | 0.1813829 |
| Treatment_bisMixt_smart:SexMale | Dark | 0.0008966 | 0.0029094 | 147.15856 | 0.3081664 | 0.7583915 |
| (Intercept)1 | Smart | 0.0138269 | 0.0021517 | 14.19444 | 6.4260484 | 0.0000148 |
| Treatment_bisDark | Smart | 0.0001921 | 0.0017889 | 136.15414 | 0.1073595 | 0.9146619 |
| Treatment_bisFull1 | Smart | -0.0013232 | 0.0018430 | 86.96799 | -0.7179751 | 0.4746969 |
| Treatment_bisMixt_smart1 | Smart | -0.0011679 | 0.0022148 | 41.46048 | -0.5272976 | 0.6007974 |
| SexMale1 | Smart | -0.0022645 | 0.0023612 | 150.76195 | -0.9590214 | 0.3390834 |
| RegionLuxembourg1 | Smart | -0.0002586 | 0.0021302 | 12.59660 | -0.1214121 | 0.9052800 |
| Treatment_bisDark:SexMale | Smart | 0.0039427 | 0.0029363 | 149.98292 | 1.3427458 | 0.1813829 |
| Treatment_bisFull:SexMale1 | Smart | 0.0040909 | 0.0029153 | 149.94530 | 1.4032438 | 0.1626116 |
| Treatment_bisMixt_smart:SexMale1 | Smart | 0.0048393 | 0.0032674 | 146.68311 | 1.4810871 | 0.1407282 |
| (Intercept)2 | Full | 0.0125037 | 0.0019699 | 12.14206 | 6.3473321 | 0.0000349 |
| Treatment_bisDark1 | Full | 0.0015153 | 0.0015994 | 144.67510 | 0.9473976 | 0.3450159 |
| Treatment_bisSmart1 | Full | 0.0013232 | 0.0018430 | 86.96799 | 0.7179751 | 0.4746969 |
| Treatment_bisMixt_smart2 | Full | 0.0001554 | 0.0019236 | 135.43643 | 0.0807628 | 0.9357498 |
| SexMale2 | Full | 0.0018265 | 0.0017013 | 142.48312 | 1.0735920 | 0.2848204 |
| RegionLuxembourg2 | Full | -0.0002586 | 0.0021302 | 12.59660 | -0.1214121 | 0.9052800 |
| Treatment_bisDark:SexMale1 | Full | -0.0001482 | 0.0024419 | 142.96874 | -0.0606870 | 0.9516933 |
| Treatment_bisSmart:SexMale1 | Full | -0.0040909 | 0.0029153 | 149.94530 | -1.4032438 | 0.1626116 |
| Treatment_bisMixt_smart:SexMale2 | Full | 0.0007484 | 0.0028697 | 144.87347 | 0.2607928 | 0.7946226 |
| (Intercept)3 | Mixt_smart | 0.0126591 | 0.0022748 | 16.68104 | 5.5648871 | 0.0000367 |
| Treatment_bisDark2 | Mixt_smart | 0.0013599 | 0.0019894 | 95.88649 | 0.6835834 | 0.4958869 |
| Treatment_bisFull2 | Mixt_smart | -0.0001554 | 0.0019236 | 135.43643 | -0.0807628 | 0.9357498 |
| Treatment_bisSmart2 | Mixt_smart | 0.0011679 | 0.0022148 | 41.46048 | 0.5272976 | 0.6007974 |
| SexMale3 | Mixt_smart | 0.0025749 | 0.0023145 | 145.47190 | 1.1124769 | 0.2677682 |
| RegionLuxembourg3 | Mixt_smart | -0.0002586 | 0.0021302 | 12.59660 | -0.1214121 | 0.9052800 |
| Treatment_bisDark:SexMale2 | Mixt_smart | -0.0008966 | 0.0029094 | 147.15856 | -0.3081664 | 0.7583915 |
| Treatment_bisFull:SexMale2 | Mixt_smart | -0.0007484 | 0.0028697 | 144.87347 | -0.2607928 | 0.7946226 |
| Treatment_bisSmart:SexMale2 | Mixt_smart | -0.0048393 | 0.0032674 | 146.68311 | -1.4810871 | 0.1407282 |
Aucune différence significative de poids initial en fonction des traitements ou région ou sexe
6.17 Total_eaten OP
6.17.1 Test
LM_Total_eaten_OP <- lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_OP)## boundary (singular) fit: see help('isSingular')summary(LM_Total_eaten_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_OP
##
## REML criterion at convergence: 718
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.24866 -0.69967 -0.09318 0.53341 2.88674
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 8.449 2.907
## Site (Intercept) 0.000 0.000
## Room (Intercept) 0.000 0.000
## Residual 10.237 3.200
## Number of obs: 139, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 18.15357 1.34723 11.01082 13.475
## Treatment_bisFull -0.06889 1.04989 120.14787 -0.066
## Treatment_bisSmart 1.69339 1.53830 120.44026 1.101
## SexMale -1.32241 0.77954 119.40243 -1.696
## RegionLuxembourg -0.97306 1.87361 10.31823 -0.519
## Treatment_bisFull:SexMale 0.30329 1.22740 120.29875 0.247
## Treatment_bisSmart:SexMale -0.05799 1.78031 122.24385 -0.033
## Treatment_bisFull:RegionLuxembourg 1.07805 1.20346 119.65951 0.896
## Treatment_bisSmart:RegionLuxembourg -0.27879 1.78171 120.86496 -0.156
## Pr(>|t|)
## (Intercept) 3.47e-08 ***
## Treatment_bisFull 0.9478
## Treatment_bisSmart 0.2732
## SexMale 0.0924 .
## RegionLuxembourg 0.6145
## Treatment_bisFull:SexMale 0.8053
## Treatment_bisSmart:SexMale 0.9741
## Treatment_bisFull:RegionLuxembourg 0.3722
## Treatment_bisSmart:RegionLuxembourg 0.8759
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm T_F:SM T_S:SM T_F:RL
## Trtmnt_bsFl -0.267
## Trtmnt_bsSm -0.162 0.224
## SexMale -0.206 0.269 0.198
## ReginLxmbrg -0.682 0.133 0.070 -0.030
## Trtmnt_F:SM 0.140 -0.568 -0.129 -0.634 0.029
## Trtmnt_S:SM 0.085 -0.123 -0.487 -0.456 0.042 0.298
## Trtmnt_F:RL 0.171 -0.591 -0.140 0.038 -0.270 0.010 -0.022
## Trtmnt_S:RL 0.103 -0.127 -0.595 0.031 -0.189 -0.040 -0.126 0.277
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_Total_eaten_OP))
qqline(resid(LM_Total_eaten_OP))
C’est très bon.
Homogénité des variances
plot(LM_Total_eaten_OP)
c’est correcte
Distance de cook
plot(cooks.distance(LM_Total_eaten_OP))
Un point semble énormément influencer le modèle, je pense qu’il est
préférable de le retirer
Data_Total_eaten_OP <- (Data_OP %>% filter(Sex != "NA"))[unname(cooks.distance(LM_Total_eaten_OP) != max(cooks.distance(LM_Total_eaten_OP))),]
Data_Total_eaten_OP_ref_smart <- Data_Total_eaten_OP
Data_Total_eaten_OP_ref_smart$Treatment_bis <- relevel(Data_Total_eaten_OP$Treatment_bis, ref = "Smart")
Data_Total_eaten_OP_ref_full <- Data_Total_eaten_OP
Data_Total_eaten_OP_ref_full$Treatment_bis <- relevel(Data_Total_eaten_OP$Treatment_bis, ref = "Full")et on refait les test
LM_Total_eaten_OP <- lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_Total_eaten_OP)## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_Total_eaten_OP))
qqline(resid(LM_Total_eaten_OP))
C’est très bon.
Homogénité des variances
plot(LM_Total_eaten_OP)
c’est correcte
Distance de cook
plot(cooks.distance(LM_Total_eaten_OP))
6.17.2 Simplification du modèle
drop1(LM_Total_eaten_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 3.314 1.6570 2 119.70 0.1724 0.8418
## Treatment_bis:Region 17.383 8.6915 2 118.91 0.9045 0.4075LM_Total_eaten1_OP <- update(LM_Total_eaten_OP, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_Total_eaten1_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 39.242 39.242 1 121.11 4.1325 0.04425 *
## Treatment_bis:Region 16.000 8.000 2 120.90 0.8425 0.43316
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Total_eaten2_OP <- update(LM_Total_eaten1_OP, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_Total_eaten2_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room)
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis 16.298 8.149 2 123.072 0.8574 0.4268
## Sex 43.838 43.838 1 123.084 4.6126 0.0337 *
## Region 4.002 4.002 1 5.133 0.4211 0.5443
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1On arrête la simplification de modèle.
Est-ce qu’elle a été utile ?
AIC(LM_Total_eaten2_OP)## [1] 731.8259AIC(LM_Total_eaten_OP)## [1] 727.7808Non
6.17.3 Treatment VS Treatment_bis
AIC(lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_Total_eaten_OP))## boundary (singular) fit: see help('isSingular')## [1] 727.7808AIC(lmer(Total_eaten ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex + Treatment:Region, data = Data_Total_eaten_OP))## boundary (singular) fit: see help('isSingular')## [1] 727.7255summary(lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_Total_eaten_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 18.12733331 1.1619093 11.04065
## Treatment_bisFull -0.03363087 1.0163663 119.06383
## Treatment_bisSmart 1.19332307 1.4962120 119.11142
## SexMale -1.31715659 0.7549267 118.12777
## RegionLuxembourg -1.14003702 1.6094219 10.17740
## Treatment_bisFull:SexMale 0.25236977 1.1881265 119.34712
## Treatment_bisSmart:SexMale 1.02761472 1.7549765 120.24537
## Treatment_bisFull:RegionLuxembourg 1.00691238 1.1653922 118.42889
## Treatment_bisSmart:RegionLuxembourg -1.32092535 1.7534389 119.29191
## t value Pr(>|t|)
## (Intercept) 15.60133184 7.191011e-09
## Treatment_bisFull -0.03308932 9.736588e-01
## Treatment_bisSmart 0.79756280 4.267114e-01
## SexMale -1.74474768 8.362955e-02
## RegionLuxembourg -0.70835188 4.946308e-01
## Treatment_bisFull:SexMale 0.21240985 8.321497e-01
## Treatment_bisSmart:SexMale 0.58554330 5.592798e-01
## Treatment_bisFull:RegionLuxembourg 0.86401163 3.893281e-01
## Treatment_bisSmart:RegionLuxembourg -0.75333412 4.527334e-01summary(lmer(Total_eaten ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex + Treatment:Region, data = Data_Total_eaten_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 18.971512683 1.2007564 10.330774 15.799634397
## TreatmentFull -0.919164001 1.1104822 118.825677 -0.827716090
## TreatmentSmart -1.636353887 1.0711662 119.013783 -1.527637718
## SexMale -1.036123613 0.9343839 118.358743 -1.108884238
## RegionLuxembourg -2.439095317 1.6491080 8.200123 -1.479039133
## TreatmentFull:SexMale -0.030326341 1.3198484 119.903849 -0.022977140
## TreatmentSmart:SexMale -0.005207723 1.3571577 118.632932 -0.003837227
## TreatmentFull:RegionLuxembourg 2.269954540 1.2923172 117.918351 1.756499504
## TreatmentSmart:RegionLuxembourg 2.360201515 1.3366530 118.335528 1.765754840
## Pr(>|t|)
## (Intercept) 1.432869e-08
## TreatmentFull 4.094906e-01
## TreatmentSmart 1.292559e-01
## SexMale 2.697282e-01
## RegionLuxembourg 1.764858e-01
## TreatmentFull:SexMale 9.817067e-01
## TreatmentSmart:SexMale 9.969448e-01
## TreatmentFull:RegionLuxembourg 8.159913e-02
## TreatmentSmart:RegionLuxembourg 8.001608e-02Aucun des 2 ne se justifie tellement par rapport à l’autre donc je vais continuer avec treatment_bis qui est plus fréquemment repris dans les autres modèles et plus rigoureux scientifiquement parlant.
6.17.4 Résultats
Analyse des P-val
summary(lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_Total_eaten_OP))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_Total_eaten_OP
##
## REML criterion at convergence: 701.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3037 -0.7174 -0.0551 0.5424 2.5491
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.833e+00 2.4151344
## Site (Intercept) 1.966e-07 0.0004434
## Room (Intercept) 0.000e+00 0.0000000
## Residual 9.609e+00 3.0998386
## Number of obs: 138, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 18.12733 1.16191 11.04065 15.601
## Treatment_bisFull -0.03363 1.01637 119.06383 -0.033
## Treatment_bisSmart 1.19332 1.49621 119.11142 0.798
## SexMale -1.31716 0.75493 118.12777 -1.745
## RegionLuxembourg -1.14004 1.60942 10.17740 -0.708
## Treatment_bisFull:SexMale 0.25237 1.18813 119.34712 0.212
## Treatment_bisSmart:SexMale 1.02761 1.75498 120.24537 0.586
## Treatment_bisFull:RegionLuxembourg 1.00691 1.16539 118.42889 0.864
## Treatment_bisSmart:RegionLuxembourg -1.32093 1.75344 119.29191 -0.753
## Pr(>|t|)
## (Intercept) 7.19e-09 ***
## Treatment_bisFull 0.9737
## Treatment_bisSmart 0.4267
## SexMale 0.0836 .
## RegionLuxembourg 0.4946
## Treatment_bisFull:SexMale 0.8321
## Treatment_bisSmart:SexMale 0.5593
## Treatment_bisFull:RegionLuxembourg 0.3893
## Treatment_bisSmart:RegionLuxembourg 0.4527
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S SexMal RgnLxm T_F:SM T_S:SM T_F:RL
## Trtmnt_bsFl -0.298
## Trtmnt_bsSm -0.181 0.222
## SexMale -0.233 0.270 0.197
## ReginLxmbrg -0.675 0.149 0.082 -0.033
## Trtmnt_F:SM 0.158 -0.568 -0.127 -0.634 0.032
## Trtmnt_S:SM 0.094 -0.119 -0.494 -0.448 0.039 0.289
## Trtmnt_F:RL 0.191 -0.591 -0.138 0.038 -0.304 0.010 -0.023
## Trtmnt_S:RL 0.114 -0.127 -0.566 0.030 -0.204 -0.036 -0.156 0.275
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_Total_eaten_OP_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_Total_eaten_OP_ref_smart
##
## REML criterion at convergence: 701.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3037 -0.7174 -0.0551 0.5424 2.5491
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.833e+00 2.4151344
## Site (Intercept) 1.966e-07 0.0004434
## Room (Intercept) 0.000e+00 0.0000000
## Residual 9.609e+00 3.0998386
## Number of obs: 138, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 19.3207 1.7200 45.5666 11.233
## Treatment_bisDark -1.1933 1.4962 119.1114 -0.798
## Treatment_bisFull -1.2270 1.6111 119.3468 -0.762
## SexMale -0.2895 1.5695 119.9648 -0.184
## RegionLuxembourg -2.4610 2.1240 29.5655 -1.159
## Treatment_bisDark:SexMale -1.0276 1.7550 120.2454 -0.586
## Treatment_bisFull:SexMale -0.7752 1.8127 119.6454 -0.428
## Treatment_bisDark:RegionLuxembourg 1.3209 1.7534 119.2919 0.753
## Treatment_bisFull:RegionLuxembourg 2.3278 1.8189 119.2619 1.280
## Pr(>|t|)
## (Intercept) 1.01e-14 ***
## Treatment_bisDark 0.427
## Treatment_bisFull 0.448
## SexMale 0.854
## RegionLuxembourg 0.256
## Treatment_bisDark:SexMale 0.559
## Treatment_bisFull:SexMale 0.670
## Treatment_bisDark:RegionLuxembourg 0.453
## Treatment_bisFull:RegionLuxembourg 0.203
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F SexMal RgnLxm T_D:SM T_F:SM T_D:RL
## Trtmnt_bsDr -0.747
## Trtmnt_bsFl -0.699 0.788
## SexMale -0.403 0.458 0.423
## ReginLxmbrg -0.634 0.405 0.381 -0.111
## Trtmnt_D:SM 0.366 -0.494 -0.384 -0.903 0.099
## Trtmnt_F:SM 0.352 -0.396 -0.530 -0.862 0.092 0.779
## Trtmnt_D:RL 0.415 -0.566 -0.445 0.160 -0.671 -0.156 -0.128
## Trtmnt_F:RL 0.406 -0.457 -0.586 0.149 -0.648 -0.135 -0.104 0.788
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_Total_eaten_OP_ref_full ))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_Total_eaten_OP_ref_full
##
## REML criterion at convergence: 701.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3037 -0.7174 -0.0551 0.5424 2.5491
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.833e+00 2.4151344
## Site (Intercept) 1.966e-07 0.0004434
## Room (Intercept) 0.000e+00 0.0000000
## Residual 9.609e+00 3.0998386
## Number of obs: 138, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 18.09370 1.29568 17.24936 13.965
## Treatment_bisDark 0.03363 1.01637 119.06383 0.033
## Treatment_bisSmart 1.22695 1.61114 119.34677 0.762
## SexMale -1.06479 0.91835 120.30814 -1.159
## RegionLuxembourg -0.13312 1.67622 12.09664 -0.079
## Treatment_bisDark:SexMale -0.25237 1.18813 119.34712 -0.212
## Treatment_bisSmart:SexMale 0.77524 1.81269 119.64544 0.428
## Treatment_bisDark:RegionLuxembourg -1.00691 1.16539 118.42889 -0.864
## Treatment_bisSmart:RegionLuxembourg -2.32784 1.81890 119.26195 -1.280
## Pr(>|t|)
## (Intercept) 7.8e-11 ***
## Treatment_bisDark 0.974
## Treatment_bisSmart 0.448
## SexMale 0.249
## RegionLuxembourg 0.938
## Treatment_bisDark:SexMale 0.832
## Treatment_bisSmart:SexMale 0.670
## Treatment_bisDark:RegionLuxembourg 0.389
## Treatment_bisSmart:RegionLuxembourg 0.203
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S SexMal RgnLxm T_D:SM T_S:SM T_D:RL
## Trtmnt_bsDr -0.517
## Trtmnt_bsSm -0.315 0.424
## SexMale -0.391 0.513 0.322
## ReginLxmbrg -0.672 0.268 0.153 0.044
## Trtmnt_D:SM 0.304 -0.568 -0.241 -0.772 -0.037
## Trtmnt_S:SM 0.191 -0.257 -0.530 -0.500 -0.004 0.376
## Trtmnt_D:RL 0.292 -0.591 -0.245 -0.044 -0.404 0.010 0.029
## Trtmnt_S:RL 0.190 -0.256 -0.586 -0.049 -0.263 0.041 -0.104 0.376
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_Total_eaten_OP))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_Total_eaten_OP_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_Total_eaten_OP_ref_full ))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Total_eaten_OP <- rbind(test1,test2,test3)
colnames(Results_Total_eaten_OP ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Total_eaten_OP , file = "output/Results_Total_eaten_OP.csv" )
kable(Results_Total_eaten_OP , caption = " Quantité mangée OP ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 18.1273333 | 1.1619093 | 11.04065 | 15.6013318 | 0.0000000 |
| Treatment_bisFull | Dark | -0.0336309 | 1.0163663 | 119.06383 | -0.0330893 | 0.9736588 |
| Treatment_bisSmart | Dark | 1.1933231 | 1.4962120 | 119.11142 | 0.7975628 | 0.4267114 |
| SexMale | Dark | -1.3171566 | 0.7549267 | 118.12777 | -1.7447477 | 0.0836295 |
| RegionLuxembourg | Dark | -1.1400370 | 1.6094219 | 10.17740 | -0.7083519 | 0.4946308 |
| Treatment_bisFull:SexMale | Dark | 0.2523698 | 1.1881265 | 119.34712 | 0.2124099 | 0.8321497 |
| Treatment_bisSmart:SexMale | Dark | 1.0276147 | 1.7549765 | 120.24537 | 0.5855433 | 0.5592798 |
| Treatment_bisFull:RegionLuxembourg | Dark | 1.0069124 | 1.1653922 | 118.42889 | 0.8640116 | 0.3893281 |
| Treatment_bisSmart:RegionLuxembourg | Dark | -1.3209253 | 1.7534389 | 119.29191 | -0.7533341 | 0.4527334 |
| (Intercept)1 | Smart | 19.3206564 | 1.7200318 | 45.56658 | 11.2327321 | 0.0000000 |
| Treatment_bisDark | Smart | -1.1933231 | 1.4962120 | 119.11142 | -0.7975628 | 0.4267114 |
| Treatment_bisFull1 | Smart | -1.2269539 | 1.6111442 | 119.34677 | -0.7615420 | 0.4478356 |
| SexMale1 | Smart | -0.2895419 | 1.5695339 | 119.96478 | -0.1844763 | 0.8539513 |
| RegionLuxembourg1 | Smart | -2.4609624 | 2.1240277 | 29.56550 | -1.1586301 | 0.2558803 |
| Treatment_bisDark:SexMale | Smart | -1.0276147 | 1.7549765 | 120.24537 | -0.5855433 | 0.5592798 |
| Treatment_bisFull:SexMale1 | Smart | -0.7752450 | 1.8126884 | 119.64544 | -0.4276769 | 0.6696551 |
| Treatment_bisDark:RegionLuxembourg | Smart | 1.3209253 | 1.7534389 | 119.29191 | 0.7533341 | 0.4527334 |
| Treatment_bisFull:RegionLuxembourg1 | Smart | 2.3278377 | 1.8189034 | 119.26195 | 1.2798028 | 0.2030985 |
| (Intercept)2 | Full | 18.0937024 | 1.2956818 | 17.24936 | 13.9646184 | 0.0000000 |
| Treatment_bisDark1 | Full | 0.0336309 | 1.0163663 | 119.06383 | 0.0330893 | 0.9736588 |
| Treatment_bisSmart1 | Full | 1.2269539 | 1.6111442 | 119.34677 | 0.7615420 | 0.4478356 |
| SexMale2 | Full | -1.0647868 | 0.9183491 | 120.30814 | -1.1594575 | 0.2485657 |
| RegionLuxembourg2 | Full | -0.1331246 | 1.6762151 | 12.09664 | -0.0794198 | 0.9379975 |
| Treatment_bisDark:SexMale1 | Full | -0.2523698 | 1.1881265 | 119.34712 | -0.2124099 | 0.8321497 |
| Treatment_bisSmart:SexMale1 | Full | 0.7752450 | 1.8126884 | 119.64544 | 0.4276769 | 0.6696551 |
| Treatment_bisDark:RegionLuxembourg1 | Full | -1.0069124 | 1.1653922 | 118.42889 | -0.8640116 | 0.3893281 |
| Treatment_bisSmart:RegionLuxembourg1 | Full | -2.3278377 | 1.8189034 | 119.26195 | -1.2798028 | 0.2030985 |
Info_Total_eaten_OP <- "
Mâles Dark mangent presque significativement moins
"
Info_Total_eaten_OP## [1] "\nMâles Dark mangent presque significativement moins\n"6.18 Total_eaten AE
6.18.1 Test
LM_Total_eaten_AE <- lmer(Total_eaten ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)## boundary (singular) fit: see help('isSingular')summary(LM_Total_eaten_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Total_eaten ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: 1396.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.3713 -0.6489 -0.1503 0.3957 4.4909
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 172.20 13.123
## Site (Intercept) 57.69 7.596
## Room (Intercept) 0.00 0.000
## Residual 348.77 18.675
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 66.1000 6.5508 16.0823 10.090
## Treatment_bisFull -1.5241 5.9526 136.1193 -0.256
## Treatment_bisSmart -3.4811 6.8808 135.6675 -0.506
## Treatment_bisMixt_smart -0.8384 7.0900 136.7241 -0.118
## SexMale -1.3826 5.5283 138.8362 -0.250
## RegionLuxembourg 7.2408 8.9250 16.1877 0.811
## Treatment_bisFull:SexMale 4.0984 7.6764 136.6759 0.534
## Treatment_bisSmart:SexMale -0.8524 9.4337 142.0837 -0.090
## Treatment_bisMixt_smart:SexMale -11.8032 9.2709 137.7702 -1.273
## Treatment_bisFull:RegionLuxembourg 6.6069 7.6410 136.6415 0.865
## Treatment_bisSmart:RegionLuxembourg -3.9513 8.6499 132.4259 -0.457
## Treatment_bisMixt_smart:RegionLuxembourg 22.4333 9.0685 136.6601 2.474
## Pr(>|t|)
## (Intercept) 2.31e-08 ***
## Treatment_bisFull 0.7983
## Treatment_bisSmart 0.6137
## Treatment_bisMixt_smart 0.9060
## SexMale 0.8029
## RegionLuxembourg 0.4290
## Treatment_bisFull:SexMale 0.5943
## Treatment_bisSmart:SexMale 0.9281
## Treatment_bisMixt_smart:SexMale 0.2051
## Treatment_bisFull:RegionLuxembourg 0.3887
## Treatment_bisSmart:RegionLuxembourg 0.6486
## Treatment_bisMixt_smart:RegionLuxembourg 0.0146 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM T_M_:S
## Trtmnt_bsFl -0.420
## Trtmnt_bsSm -0.364 0.426
## Trtmnt_bsM_ -0.354 0.418 0.365
## SexMale -0.325 0.376 0.328 0.326
## ReginLxmbrg -0.640 0.201 0.172 0.161 -0.050
## Trtmnt_F:SM 0.227 -0.566 -0.238 -0.241 -0.719 0.039
## Trtmnt_S:SM 0.198 -0.229 -0.491 -0.209 -0.595 0.028 0.428
## Trtmn_M_:SM 0.185 -0.223 -0.200 -0.552 -0.608 0.047 0.441 0.379
## Trtmnt_F:RL 0.230 -0.532 -0.228 -0.215 0.015 -0.422 0.006 -0.010 -0.028
## Trtmnt_S:RL 0.194 -0.227 -0.580 -0.186 0.029 -0.369 -0.021 -0.044 -0.031
## Trtmn_M_:RL 0.194 -0.223 -0.180 -0.515 0.019 -0.359 -0.015 -0.041 -0.049
## T_F:RL T_S:RL
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_F:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## Trtmnt_F:RL
## Trtmnt_S:RL 0.449
## Trtmn_M_:RL 0.452 0.379
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_Total_eaten_AE))
qqline(resid(LM_Total_eaten_AE))
il faudrait faire quelque chose
LM_Total_eaten_AE <- lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region, data = Data_AE)## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_Total_eaten_AE))
qqline(resid(LM_Total_eaten_AE))
C’est très bon.
Homogénité des variances
plot(LM_Total_eaten_AE)
c’est correcte
Distance de cook
plot(cooks.distance(LM_Total_eaten_AE))
6.18.2 Simplification du modèle
drop1(LM_Total_eaten_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.24192 0.080641 3 137.51 1.3159 0.27179
## Treatment_bis:Region 0.46110 0.153698 3 133.53 2.5080 0.06163 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Total_eaten1_AE <- update(LM_Total_eaten_AE, . ~ . - Treatment_bis:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_Total_eaten1_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Sex 0.04616 0.04616 1 140.63 0.7497 0.38805
## Treatment_bis:Region 0.44095 0.14699 3 136.55 2.3872 0.07172 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1On arrête la simplification de modèle.
Est-ce qu’elle a été utile ?
AIC(LM_Total_eaten1_AE)## [1] 96.1451AIC(LM_Total_eaten_AE)## [1] 106.0847Oui
LM_Total_eaten_AE <- LM_Total_eaten1_AE6.18.3 Treatment VS Treatment_bis
AIC(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE))## boundary (singular) fit: see help('isSingular')## [1] 96.1451AIC(lmer(log(Total_eaten) ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region, data = Data_AE))## [1] 96.10481summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df
## (Intercept) 4.10639404 0.08561276 15.51237
## Treatment_bisFull 0.05809835 0.06515423 135.88730
## Treatment_bisSmart -0.03344556 0.07961960 135.13695
## Treatment_bisMixt_smart -0.04254948 0.07853939 137.50970
## SexMale -0.03579516 0.04134108 140.62833
## RegionLuxembourg 0.15684714 0.12062512 17.56734
## Treatment_bisFull:RegionLuxembourg 0.01780827 0.10150200 139.32294
## Treatment_bisSmart:RegionLuxembourg -0.06198166 0.11482138 135.16171
## Treatment_bisMixt_smart:RegionLuxembourg 0.26337095 0.12034511 139.40396
## t value Pr(>|t|)
## (Intercept) 47.9647415 2.743436e-18
## Treatment_bisFull 0.8917049 3.741274e-01
## Treatment_bisSmart -0.4200670 6.751037e-01
## Treatment_bisMixt_smart -0.5417598 5.888607e-01
## SexMale -0.8658495 3.880475e-01
## RegionLuxembourg 1.3002859 2.103043e-01
## Treatment_bisFull:RegionLuxembourg 0.1754475 8.609828e-01
## Treatment_bisSmart:RegionLuxembourg -0.5398094 5.902167e-01
## Treatment_bisMixt_smart:RegionLuxembourg 2.1884640 3.030110e-02summary(lmer(log(Total_eaten) ~ Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region, data = Data_AE))$coeff## Estimate Std. Error df t value
## (Intercept) 4.104303823 0.08807482 12.85549 46.60019553
## TreatmentFull 0.055392422 0.06688990 137.13134 0.82811340
## TreatmentSmart -0.040372102 0.06672302 139.18905 -0.60507011
## SexMale -0.026152404 0.04223928 141.82338 -0.61914889
## RegionLuxembourg 0.160070875 0.11815017 18.17954 1.35480867
## TreatmentFull:RegionLuxembourg 0.009257067 0.10409183 140.52199 0.08893174
## TreatmentSmart:RegionLuxembourg 0.074816408 0.09983705 139.17388 0.74938523
## Pr(>|t|)
## (Intercept) 1.010615e-15
## TreatmentFull 4.090452e-01
## TreatmentSmart 5.461176e-01
## SexMale 5.368116e-01
## RegionLuxembourg 1.920769e-01
## TreatmentFull:RegionLuxembourg 9.292628e-01
## TreatmentSmart:RegionLuxembourg 4.548898e-01Aucun des 2 ne se justifie tellement par rapport à l’autre donc je vais continuer avec treatment_bis qui est plus fréquemment repris dans les autres modèles et plus rigoureux scientifiquement parlant.
6.18.4 Résultats
Analyse des P-val
summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE
##
## REML criterion at convergence: 70.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.1462 -0.6767 -0.0887 0.5050 3.7049
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.03117 0.1766
## Site (Intercept) 0.01131 0.1063
## Room (Intercept) 0.00000 0.0000
## Residual 0.06157 0.2481
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 4.10639 0.08561 15.51237 47.965
## Treatment_bisFull 0.05810 0.06515 135.88730 0.892
## Treatment_bisSmart -0.03345 0.07962 135.13695 -0.420
## Treatment_bisMixt_smart -0.04255 0.07854 137.50970 -0.542
## SexMale -0.03580 0.04134 140.62833 -0.866
## RegionLuxembourg 0.15685 0.12063 17.56734 1.300
## Treatment_bisFull:RegionLuxembourg 0.01781 0.10150 139.32294 0.175
## Treatment_bisSmart:RegionLuxembourg -0.06198 0.11482 135.16171 -0.540
## Treatment_bisMixt_smart:RegionLuxembourg 0.26337 0.12035 139.40396 2.188
## Pr(>|t|)
## (Intercept) <2e-16 ***
## Treatment_bisFull 0.3741
## Treatment_bisSmart 0.6751
## Treatment_bisMixt_smart 0.5889
## SexMale 0.3880
## RegionLuxembourg 0.2103
## Treatment_bisFull:RegionLuxembourg 0.8610
## Treatment_bisSmart:RegionLuxembourg 0.5902
## Treatment_bisMixt_smart:RegionLuxembourg 0.0303 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:RL T_S:RL
## Trtmnt_bsFl -0.364
## Trtmnt_bsSm -0.305 0.416
## Trtmnt_bsM_ -0.307 0.431 0.351
## SexMale -0.195 -0.043 0.038 -0.018
## ReginLxmbrg -0.679 0.265 0.211 0.221 -0.017
## Trtmnt_F:RL 0.237 -0.641 -0.267 -0.277 0.011 -0.415
## Trtmnt_S:RL 0.208 -0.289 -0.693 -0.243 -0.005 -0.362 0.449
## Trtmn_M_:RL 0.208 -0.280 -0.230 -0.652 -0.025 -0.351 0.451 0.378
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE_ref_smart
##
## REML criterion at convergence: 70.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.1462 -0.6767 -0.0887 0.5049 3.7049
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.03117 0.1766
## Site (Intercept) 0.01131 0.1063
## Room (Intercept) 0.00000 0.0000
## Residual 0.06157 0.2481
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 4.072948 0.097489 24.905906
## Treatment_bisDark 0.033446 0.079620 135.136945
## Treatment_bisFull 0.091544 0.079196 132.914782
## Treatment_bisMixt_smart -0.009104 0.090128 133.371378
## SexMale -0.035795 0.041341 140.628326
## RegionLuxembourg 0.094866 0.133095 25.549094
## Treatment_bisDark:RegionLuxembourg 0.061982 0.114821 135.161704
## Treatment_bisFull:RegionLuxembourg 0.079790 0.114085 134.470671
## Treatment_bisMixt_smart:RegionLuxembourg 0.325353 0.131227 135.418880
## t value Pr(>|t|)
## (Intercept) 41.779 <2e-16 ***
## Treatment_bisDark 0.420 0.6751
## Treatment_bisFull 1.156 0.2498
## Treatment_bisMixt_smart -0.101 0.9197
## SexMale -0.866 0.3880
## RegionLuxembourg 0.713 0.4825
## Treatment_bisDark:RegionLuxembourg 0.540 0.5902
## Treatment_bisFull:RegionLuxembourg 0.699 0.4855
## Treatment_bisMixt_smart:RegionLuxembourg 2.479 0.0144 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.548
## Trtmnt_bsFl -0.535 0.663
## Trtmnt_bsM_ -0.470 0.578 0.588
## SexMale -0.140 -0.038 -0.074 -0.050
## ReginLxmbrg -0.715 0.406 0.401 0.350 -0.020
## Trtmnt_D:RL 0.383 -0.693 -0.458 -0.400 0.005 -0.535
## Trtmnt_F:RL 0.376 -0.459 -0.691 -0.406 0.015 -0.528 0.607
## Trtmn_M_:RL 0.330 -0.395 -0.400 -0.684 -0.019 -0.461 0.528 0.550
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE_ref_full
##
## REML criterion at convergence: 70.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.1462 -0.6767 -0.0887 0.5050 3.7049
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.03117 0.1766
## Site (Intercept) 0.01131 0.1063
## Room (Intercept) 0.00000 0.0000
## Residual 0.06157 0.2481
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 4.16449 0.08669 16.64069 48.039
## Treatment_bisDark -0.05810 0.06515 135.88730 -0.892
## Treatment_bisSmart -0.09154 0.07920 132.91479 -1.156
## Treatment_bisMixt_smart -0.10065 0.07745 133.58249 -1.299
## SexMale -0.03580 0.04134 140.62833 -0.866
## RegionLuxembourg 0.17466 0.12125 18.54935 1.440
## Treatment_bisDark:RegionLuxembourg -0.01781 0.10150 139.32294 -0.175
## Treatment_bisSmart:RegionLuxembourg -0.07979 0.11408 134.47068 -0.699
## Treatment_bisMixt_smart:RegionLuxembourg 0.24556 0.11730 135.17563 2.094
## Pr(>|t|)
## (Intercept) <2e-16 ***
## Treatment_bisDark 0.3741
## Treatment_bisSmart 0.2498
## Treatment_bisMixt_smart 0.1960
## SexMale 0.3880
## RegionLuxembourg 0.1664
## Treatment_bisDark:RegionLuxembourg 0.8610
## Treatment_bisSmart:RegionLuxembourg 0.4855
## Treatment_bisMixt_smart:RegionLuxembourg 0.0382 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_D:RL T_S:RL
## Trtmnt_bsDr -0.392
## Trtmnt_bsSm -0.312 0.405
## Trtmnt_bsM_ -0.309 0.404 0.338
## SexMale -0.225 0.043 0.074 0.018
## ReginLxmbrg -0.677 0.273 0.211 0.218 -0.008
## Trtmnt_D:RL 0.248 -0.641 -0.259 -0.259 -0.011 -0.425
## Trtmnt_S:RL 0.208 -0.279 -0.691 -0.234 -0.015 -0.362 0.438
## Trtmn_M_:RL 0.209 -0.268 -0.225 -0.661 -0.036 -0.338 0.402 0.357
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_mixt_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Region
## Data: Data_AE_ref_mixt_smart
##
## REML criterion at convergence: 70.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.1462 -0.6767 -0.0887 0.5050 3.7049
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.03117 0.1766
## Site (Intercept) 0.01131 0.1063
## Room (Intercept) 0.00000 0.0000
## Residual 0.06157 0.2481
## Number of obs: 165, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 4.063845 0.096769 25.639744 41.995
## Treatment_bisDark 0.042549 0.078539 137.509700 0.542
## Treatment_bisFull 0.100648 0.077454 133.582489 1.299
## Treatment_bisSmart 0.009104 0.090128 133.371384 0.101
## SexMale -0.035795 0.041341 140.628331 -0.866
## RegionLuxembourg 0.420218 0.137267 28.731407 3.061
## Treatment_bisDark:RegionLuxembourg -0.263371 0.120345 139.403956 -2.188
## Treatment_bisFull:RegionLuxembourg -0.245563 0.117296 135.175629 -2.094
## Treatment_bisSmart:RegionLuxembourg -0.325353 0.131227 135.418884 -2.479
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Treatment_bisDark 0.58886
## Treatment_bisFull 0.19603
## Treatment_bisSmart 0.91969
## SexMale 0.38805
## RegionLuxembourg 0.00474 **
## Treatment_bisDark:RegionLuxembourg 0.03030 *
## Treatment_bisFull:RegionLuxembourg 0.03817 *
## Treatment_bisSmart:RegionLuxembourg 0.01439 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_D:RL T_F:RL
## Trtmnt_bsDr -0.540
## Trtmnt_bsFl -0.524 0.651
## Trtmnt_bsSm -0.458 0.562 0.562
## SexMale -0.188 0.018 -0.018 0.050
## ReginLxmbrg -0.673 0.377 0.372 0.314 -0.037
## Trtmnt_D:RL 0.345 -0.652 -0.426 -0.365 0.025 -0.568
## Trtmnt_F:RL 0.341 -0.430 -0.661 -0.370 0.036 -0.556 0.635
## Trtmnt_S:RL 0.304 -0.385 -0.387 -0.684 0.019 -0.509 0.586 0.584
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test4 <- data.frame(Reference = "Mixt_smart", as.data.frame(( summary(lmer(log(Total_eaten) ~ Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region, data = Data_AE_ref_mixt_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Total_eaten_AE <- rbind(test1,test2,test3,test4)
colnames(Results_Total_eaten_AE ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Total_eaten_AE , file = "output/Results_Total_eaten_AE.csv" )
kable(Results_Total_eaten_AE , caption = " Quantité mangée AE ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 4.1063940 | 0.0856128 | 15.51237 | 47.9647415 | 0.0000000 |
| Treatment_bisFull | Dark | 0.0580983 | 0.0651542 | 135.88730 | 0.8917049 | 0.3741274 |
| Treatment_bisSmart | Dark | -0.0334456 | 0.0796196 | 135.13695 | -0.4200670 | 0.6751037 |
| Treatment_bisMixt_smart | Dark | -0.0425495 | 0.0785394 | 137.50970 | -0.5417598 | 0.5888607 |
| SexMale | Dark | -0.0357952 | 0.0413411 | 140.62833 | -0.8658495 | 0.3880475 |
| RegionLuxembourg | Dark | 0.1568471 | 0.1206251 | 17.56734 | 1.3002859 | 0.2103043 |
| Treatment_bisFull:RegionLuxembourg | Dark | 0.0178083 | 0.1015020 | 139.32294 | 0.1754475 | 0.8609828 |
| Treatment_bisSmart:RegionLuxembourg | Dark | -0.0619817 | 0.1148214 | 135.16171 | -0.5398094 | 0.5902167 |
| Treatment_bisMixt_smart:RegionLuxembourg | Dark | 0.2633710 | 0.1203451 | 139.40396 | 2.1884640 | 0.0303011 |
| (Intercept)1 | Smart | 4.0729485 | 0.0974888 | 24.90591 | 41.7786403 | 0.0000000 |
| Treatment_bisDark | Smart | 0.0334455 | 0.0796196 | 135.13694 | 0.4200664 | 0.6751041 |
| Treatment_bisFull1 | Smart | 0.0915439 | 0.0791965 | 132.91478 | 1.1559092 | 0.2497918 |
| Treatment_bisMixt_smart1 | Smart | -0.0091039 | 0.0901281 | 133.37138 | -0.1010105 | 0.9196938 |
| SexMale1 | Smart | -0.0357952 | 0.0413411 | 140.62833 | -0.8658498 | 0.3880473 |
| RegionLuxembourg1 | Smart | 0.0948656 | 0.1330951 | 25.54909 | 0.7127659 | 0.4824502 |
| Treatment_bisDark:RegionLuxembourg | Smart | 0.0619817 | 0.1148214 | 135.16170 | 0.5398097 | 0.5902165 |
| Treatment_bisFull:RegionLuxembourg1 | Smart | 0.0797899 | 0.1140848 | 134.47067 | 0.6993913 | 0.4855155 |
| Treatment_bisMixt_smart:RegionLuxembourg1 | Smart | 0.3253526 | 0.1312269 | 135.41888 | 2.4793135 | 0.0143913 |
| (Intercept)2 | Full | 4.1644924 | 0.0866894 | 16.64069 | 48.0392100 | 0.0000000 |
| Treatment_bisDark1 | Full | -0.0580983 | 0.0651542 | 135.88730 | -0.8917049 | 0.3741274 |
| Treatment_bisSmart1 | Full | -0.0915439 | 0.0791965 | 132.91479 | -1.1559092 | 0.2497918 |
| Treatment_bisMixt_smart2 | Full | -0.1006478 | 0.0774540 | 133.58249 | -1.2994538 | 0.1960264 |
| SexMale2 | Full | -0.0357952 | 0.0413411 | 140.62833 | -0.8658495 | 0.3880475 |
| RegionLuxembourg2 | Full | 0.1746554 | 0.1212467 | 18.54935 | 1.4404961 | 0.1663937 |
| Treatment_bisDark:RegionLuxembourg1 | Full | -0.0178083 | 0.1015020 | 139.32294 | -0.1754475 | 0.8609828 |
| Treatment_bisSmart:RegionLuxembourg1 | Full | -0.0797899 | 0.1140848 | 134.47068 | -0.6993914 | 0.4855155 |
| Treatment_bisMixt_smart:RegionLuxembourg2 | Full | 0.2455627 | 0.1172965 | 135.17563 | 2.0935215 | 0.0381708 |
| (Intercept)3 | Mixt_smart | 4.0638446 | 0.0967694 | 25.63974 | 41.9951320 | 0.0000000 |
| Treatment_bisDark2 | Mixt_smart | 0.0425495 | 0.0785394 | 137.50970 | 0.5417598 | 0.5888607 |
| Treatment_bisFull2 | Mixt_smart | 0.1006478 | 0.0774540 | 133.58249 | 1.2994538 | 0.1960264 |
| Treatment_bisSmart2 | Mixt_smart | 0.0091039 | 0.0901281 | 133.37138 | 0.1010109 | 0.9196935 |
| SexMale3 | Mixt_smart | -0.0357952 | 0.0413411 | 140.62833 | -0.8658495 | 0.3880475 |
| RegionLuxembourg3 | Mixt_smart | 0.4202181 | 0.1372665 | 28.73141 | 3.0613301 | 0.0047442 |
| Treatment_bisDark:RegionLuxembourg2 | Mixt_smart | -0.2633710 | 0.1203451 | 139.40396 | -2.1884640 | 0.0303011 |
| Treatment_bisFull:RegionLuxembourg2 | Mixt_smart | -0.2455627 | 0.1172965 | 135.17563 | -2.0935215 | 0.0381708 |
| Treatment_bisSmart:RegionLuxembourg2 | Mixt_smart | -0.3253526 | 0.1312269 | 135.41888 | -2.4793134 | 0.0143913 |
Info_Total_eaten_AE <- "
Les individus dans le traitement mixt smart et qui étaient dans la région luxembourgeoise ont mangé significativement plus que l'effet de la région luxembourgeoise et de mixt smart additioné.
"
Info_Total_eaten_AE## [1] "\nLes individus dans le traitement mixt smart et qui étaient dans la région luxembourgeoise ont mangé significativement plus que l'effet de la région luxembourgeoise et de mixt smart additioné.\n"6.19 Pupa_mass * TT_pupation OP
6.19.1 Test
LM_Pupa_mass_by_TT_pupation_OP <- lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis, data = Data_OP)## boundary (singular) fit: see help('isSingular')summary(LM_Pupa_mass_by_TT_pupation_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region +
## TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis
## Data: Data_OP
##
## REML criterion at convergence: -564.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.77466 -0.58566 -0.02733 0.61730 2.10290
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.049e-04 0.014316
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 1.312e-05 0.003622
## Residual 2.110e-04 0.014527
## Number of obs: 127, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 1.444e-01 1.879e-02 1.022e+02 7.685
## TT_pupation 6.386e-04 1.159e-03 1.098e+02 0.551
## Treatment_bisFull -4.082e-03 2.145e-02 1.092e+02 -0.190
## Treatment_bisSmart 1.340e-02 2.771e-02 1.120e+02 0.484
## SexMale 2.404e-02 1.872e-02 1.103e+02 1.284
## RegionLuxembourg -4.539e-02 2.279e-02 9.121e+01 -1.991
## Treatment_bisFull:SexMale -4.050e-03 5.955e-03 1.052e+02 -0.680
## Treatment_bisSmart:SexMale 2.084e-02 8.924e-03 1.072e+02 2.335
## Treatment_bisFull:RegionLuxembourg -4.936e-04 5.846e-03 1.051e+02 -0.084
## Treatment_bisSmart:RegionLuxembourg -7.470e-03 8.943e-03 1.056e+02 -0.835
## TT_pupation:SexMale -1.690e-03 1.259e-03 1.104e+02 -1.343
## TT_pupation:RegionLuxembourg 2.667e-03 1.415e-03 1.115e+02 1.885
## TT_pupation:Treatment_bisFull 7.179e-04 1.406e-03 1.093e+02 0.511
## TT_pupation:Treatment_bisSmart -1.044e-03 1.802e-03 1.120e+02 -0.579
## Pr(>|t|)
## (Intercept) 9.68e-12 ***
## TT_pupation 0.5828
## Treatment_bisFull 0.8494
## Treatment_bisSmart 0.6295
## SexMale 0.2017
## RegionLuxembourg 0.0494 *
## Treatment_bisFull:SexMale 0.4979
## Treatment_bisSmart:SexMale 0.0214 *
## Treatment_bisFull:RegionLuxembourg 0.9329
## Treatment_bisSmart:RegionLuxembourg 0.4054
## TT_pupation:SexMale 0.1822
## TT_pupation:RegionLuxembourg 0.0621 .
## TT_pupation:Treatment_bisFull 0.6106
## TT_pupation:Treatment_bisSmart 0.5636
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 14 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Test des hypothèses
Normalité des réisuds
qqnorm(resid(LM_Pupa_mass_by_TT_pupation_OP))
qqline(resid(LM_Pupa_mass_by_TT_pupation_OP))
Homogénité des variances
plot(LM_Pupa_mass_by_TT_pupation_OP)
Distance de cook
plot(cooks.distance(LM_Pupa_mass_by_TT_pupation_OP))
6.19.2 Simplification du modèle
drop1(LM_Pupa_mass_by_TT_pupation_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.00157184 0.00078592 2 105.92 3.7239 0.02736 *
## Treatment_bis:Region 0.00015344 0.00007672 2 104.95 0.3635 0.69610
## TT_pupation:Sex 0.00038041 0.00038041 1 110.37 1.8025 0.18217
## TT_pupation:Region 0.00074974 0.00074974 1 111.53 3.5525 0.06206 .
## TT_pupation:Treatment_bis 0.00019789 0.00009895 2 108.48 0.4688 0.62699
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation1_OP <- update(LM_Pupa_mass_by_TT_pupation_OP, . ~ . - Treatment_bis:Region)
drop1(LM_Pupa_mass_by_TT_pupation1_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.00145250 0.00072625 2 107.75 3.4793 0.03433 *
## TT_pupation:Sex 0.00043311 0.00043311 1 111.97 2.0750 0.15252
## TT_pupation:Region 0.00072014 0.00072014 1 113.65 3.4501 0.06584 .
## TT_pupation:Treatment_bis 0.00027151 0.00013575 2 110.62 0.6504 0.52384
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation2_OP <- update(LM_Pupa_mass_by_TT_pupation1_OP, . ~ . - TT_pupation:Treatment_bis)## boundary (singular) fit: see help('isSingular')drop1(LM_Pupa_mass_by_TT_pupation2_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Sex + TT_pupation:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.00170623 0.00085311 2 110.14 4.1273 0.01869 *
## TT_pupation:Sex 0.00031541 0.00031541 1 114.08 1.5259 0.21927
## TT_pupation:Region 0.00061565 0.00061565 1 116.85 2.9784 0.08702 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation3_OP <- update(LM_Pupa_mass_by_TT_pupation2_OP, . ~ . - TT_pupation:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_Pupa_mass_by_TT_pupation3_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.00160162 0.00080081 2 111.52 3.8410 0.02437 *
## TT_pupation:Region 0.00067014 0.00067014 1 117.64 3.2143 0.07557 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation4_OP <- update(LM_Pupa_mass_by_TT_pupation3_OP, . ~ . - TT_pupation:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_Pupa_mass_by_TT_pupation4_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TT_pupation 0.00063657 0.00063657 1 117.318 2.9851 0.08667 .
## Region 0.00013388 0.00013388 1 9.975 0.6278 0.44660
## Treatment_bis:Sex 0.00159790 0.00079895 2 112.599 3.7465 0.02659 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Il n’y a plus d’interactions qui n’ont pas de P-val significative, nous décidons d’arrêter la simplification du modèle.
Est ce que cela a été utile
AIC(LM_Pupa_mass_by_TT_pupation4_OP)## [1] -595.0125AIC(LM_Pupa_mass_by_TT_pupation_OP)## [1] -528.1728Oui ca a été utile
LM_Pupa_mass_by_TT_pupation_OP <- LM_Pupa_mass_by_TT_pupation4_OP6.19.3 Treatment VS Teatment_bis
AIC(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] -595.0125AIC(lmer(Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP))## boundary (singular) fit: see help('isSingular')## [1] -597.3523summary(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 0.1369587775 0.0120791491 52.219598 11.3384459
## TT_pupation 0.0011490787 0.0006650799 117.317536 1.7277304
## Treatment_bisFull 0.0066872385 0.0041824362 110.862675 1.5988860
## Treatment_bisSmart -0.0041703437 0.0064524187 114.316969 -0.6463226
## SexMale -0.0003893792 0.0037745429 112.349677 -0.1031593
## RegionLuxembourg -0.0068409928 0.0086338757 9.974852 -0.7923432
## Treatment_bisFull:SexMale -0.0038756611 0.0058557396 110.680361 -0.6618568
## Treatment_bisSmart:SexMale 0.0203645384 0.0086953419 114.683612 2.3420055
## Pr(>|t|)
## (Intercept) 1.072302e-15
## TT_pupation 8.666801e-02
## Treatment_bisFull 1.126922e-01
## Treatment_bisSmart 5.193659e-01
## SexMale 9.180205e-01
## RegionLuxembourg 4.465952e-01
## Treatment_bisFull:SexMale 5.094386e-01
## Treatment_bisSmart:SexMale 2.090560e-02summary(lmer(Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 0.132962522 0.0118416789 61.59946 11.2283506
## TT_pupation 0.001297626 0.0006569609 117.95508 1.9751948
## TreatmentFull 0.008322570 0.0045223261 110.02814 1.8403295
## TreatmentSmart 0.003021375 0.0043861891 110.88681 0.6888383
## SexMale -0.001900135 0.0044575517 111.65676 -0.4262732
## RegionLuxembourg -0.006933699 0.0089587164 10.01680 -0.7739612
## TreatmentFull:SexMale -0.001997117 0.0063649682 111.09076 -0.3137670
## TreatmentSmart:SexMale 0.013208643 0.0066386542 110.20262 1.9896567
## Pr(>|t|)
## (Intercept) 1.536946e-16
## TT_pupation 5.058166e-02
## TreatmentFull 6.841489e-02
## TreatmentSmart 4.923638e-01
## SexMale 6.707294e-01
## RegionLuxembourg 4.568318e-01
## TreatmentFull:SexMale 7.542864e-01
## TreatmentSmart:SexMale 4.910575e-02Rien de très différent, on peut garder Treatment qui serait mieux selon l’AIC
6.19.4 Résultats
Analyse des pval
summary(lmer(Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment:Sex
## Data: Data_OP
##
## REML criterion at convergence: -621.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.60308 -0.61144 -0.07127 0.67163 2.31257
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.049e-04 1.432e-02
## Site (Intercept) 9.173e-14 3.029e-07
## Room (Intercept) 6.695e-06 2.588e-03
## Residual 2.065e-04 1.437e-02
## Number of obs: 127, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.132963 0.011842 61.599462 11.228 <2e-16 ***
## TT_pupation 0.001298 0.000657 117.955082 1.975 0.0506 .
## TreatmentFull 0.008323 0.004522 110.028139 1.840 0.0684 .
## TreatmentSmart 0.003021 0.004386 110.886805 0.689 0.4924
## SexMale -0.001900 0.004458 111.656764 -0.426 0.6707
## RegionLuxembourg -0.006934 0.008959 10.016796 -0.774 0.4568
## TreatmentFull:SexMale -0.001997 0.006365 111.090764 -0.314 0.7543
## TreatmentSmart:SexMale 0.013209 0.006639 110.202619 1.990 0.0491 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TT_ppt TrtmnF TrtmnS SexMal RgnLxm TrF:SM
## TT_pupation -0.809
## TreatmntFll -0.159 -0.016
## TretmntSmrt -0.088 -0.100 0.495
## SexMale -0.181 0.023 0.475 0.474
## ReginLxmbrg -0.304 -0.058 -0.032 -0.042 -0.059
## TrtmntFl:SM 0.062 0.074 -0.726 -0.366 -0.714 0.043
## TrtmntSm:SM 0.060 0.065 -0.343 -0.666 -0.671 0.052 0.502
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment:Sex
## Data: Data_OP_ref_full
##
## REML criterion at convergence: -621.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.60308 -0.61144 -0.07127 0.67163 2.31257
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.049e-04 1.432e-02
## Site (Intercept) 9.173e-14 3.029e-07
## Room (Intercept) 6.695e-06 2.588e-03
## Residual 2.065e-04 1.437e-02
## Number of obs: 127, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.141285 0.011987 63.691133 11.787 <2e-16 ***
## TT_pupation 0.001298 0.000657 117.955076 1.975 0.0506 .
## TreatmentDark -0.008323 0.004522 110.028139 -1.840 0.0684 .
## TreatmentSmart -0.005301 0.004476 110.140025 -1.184 0.2388
## SexMale -0.003897 0.004460 110.208746 -0.874 0.3841
## RegionLuxembourg -0.006934 0.008959 10.016796 -0.774 0.4568
## TreatmentDark:SexMale 0.001997 0.006365 111.090764 0.314 0.7543
## TreatmentSmart:SexMale 0.015206 0.006495 109.861452 2.341 0.0210 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TT_ppt TrtmnD TrtmnS SexMal RgnLxm TrD:SM
## TT_pupation -0.806
## TreatmntDrk -0.220 0.016
## TretmntSmrt -0.125 -0.081 0.525
## SexMale -0.304 0.129 0.561 0.519
## ReginLxmbrg -0.312 -0.058 0.032 -0.009 0.003
## TrtmntDr:SM 0.213 -0.074 -0.726 -0.374 -0.714 -0.043
## TrtmntSm:SM 0.137 -0.007 -0.360 -0.679 -0.653 0.011 0.467
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment:Sex
## Data: Data_OP_ref_smart
##
## REML criterion at convergence: -621.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.60308 -0.61144 -0.07127 0.67163 2.31257
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 2.049e-04 1.432e-02
## Site (Intercept) 9.173e-14 3.029e-07
## Room (Intercept) 6.695e-06 2.588e-03
## Residual 2.065e-04 1.437e-02
## Number of obs: 127, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.135984 0.012259 67.398714 11.093 <2e-16 ***
## TT_pupation 0.001298 0.000657 117.955081 1.975 0.0506 .
## TreatmentDark -0.003021 0.004386 110.886805 -0.689 0.4924
## TreatmentFull 0.005301 0.004476 110.140025 1.184 0.2388
## SexMale 0.011309 0.004922 110.740441 2.298 0.0235 *
## RegionLuxembourg -0.006934 0.008959 10.016796 -0.774 0.4568
## TreatmentDark:SexMale -0.013209 0.006639 110.202619 -1.990 0.0491 *
## TreatmentFull:SexMale -0.015206 0.006495 109.861452 -2.341 0.0210 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TT_ppt TrtmnD TrtmnF SexMal RgnLxm TrD:SM
## TT_pupation -0.817
## TreatmntDrk -0.272 0.100
## TreatmntFll -0.243 0.081 0.479
## SexMale -0.248 0.108 0.468 0.426
## ReginLxmbrg -0.308 -0.058 0.042 0.009 0.017
## TrtmntDr:SM 0.180 -0.065 -0.666 -0.306 -0.741 -0.052
## TrtmntFl:SM 0.114 0.007 -0.322 -0.679 -0.728 -0.011 0.530
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_OP_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Pupa_mass_by_TT_pupation_OP <- rbind(test1,test2,test3)
colnames(Results_Pupa_mass_by_TT_pupation_OP ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Pupa_mass_by_TT_pupation_OP , file = "output/Results_Pupa_mass_by_TT_pupation_OP.csv" )
kable(Results_Pupa_mass_by_TT_pupation_OP , caption = " Poids des chrysalides en fonction du temps pour rentrer en chrysalide OP", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 0.1329625 | 0.0118417 | 61.59946 | 11.2283506 | 0.0000000 |
| TT_pupation | Dark | 0.0012976 | 0.0006570 | 117.95508 | 1.9751948 | 0.0505817 |
| TreatmentFull | Dark | 0.0083226 | 0.0045223 | 110.02814 | 1.8403295 | 0.0684149 |
| TreatmentSmart | Dark | 0.0030214 | 0.0043862 | 110.88681 | 0.6888383 | 0.4923638 |
| SexMale | Dark | -0.0019001 | 0.0044576 | 111.65676 | -0.4262732 | 0.6707294 |
| RegionLuxembourg | Dark | -0.0069337 | 0.0089587 | 10.01680 | -0.7739612 | 0.4568318 |
| TreatmentFull:SexMale | Dark | -0.0019971 | 0.0063650 | 111.09076 | -0.3137670 | 0.7542864 |
| TreatmentSmart:SexMale | Dark | 0.0132086 | 0.0066387 | 110.20262 | 1.9896567 | 0.0491057 |
| (Intercept)1 | Smart | 0.1412851 | 0.0119866 | 63.69113 | 11.7868894 | 0.0000000 |
| TT_pupation1 | Smart | 0.0012976 | 0.0006570 | 117.95508 | 1.9751948 | 0.0505817 |
| TreatmentDark | Smart | -0.0083226 | 0.0045223 | 110.02814 | -1.8403295 | 0.0684149 |
| TreatmentSmart1 | Smart | -0.0053012 | 0.0044760 | 110.14002 | -1.1843581 | 0.2388209 |
| SexMale1 | Smart | -0.0038973 | 0.0044596 | 110.20875 | -0.8739025 | 0.3840717 |
| RegionLuxembourg1 | Smart | -0.0069337 | 0.0089587 | 10.01680 | -0.7739612 | 0.4568318 |
| TreatmentDark:SexMale | Smart | 0.0019971 | 0.0063650 | 111.09076 | 0.3137670 | 0.7542864 |
| TreatmentSmart:SexMale1 | Smart | 0.0152058 | 0.0064951 | 109.86145 | 2.3411298 | 0.0210293 |
| (Intercept)2 | Full | 0.1359839 | 0.0122589 | 67.39871 | 11.0926521 | 0.0000000 |
| TT_pupation2 | Full | 0.0012976 | 0.0006570 | 117.95508 | 1.9751948 | 0.0505817 |
| TreatmentDark1 | Full | -0.0030214 | 0.0043862 | 110.88680 | -0.6888383 | 0.4923638 |
| TreatmentFull1 | Full | 0.0053012 | 0.0044760 | 110.14002 | 1.1843581 | 0.2388209 |
| SexMale2 | Full | 0.0113085 | 0.0049221 | 110.74044 | 2.2975077 | 0.0234689 |
| RegionLuxembourg2 | Full | -0.0069337 | 0.0089587 | 10.01680 | -0.7739612 | 0.4568318 |
| TreatmentDark:SexMale1 | Full | -0.0132086 | 0.0066387 | 110.20262 | -1.9896567 | 0.0491057 |
| TreatmentFull:SexMale1 | Full | -0.0152058 | 0.0064951 | 109.86145 | -2.3411298 | 0.0210293 |
Info_Pupa_mass_by_TT_pupation_OP <- "
Au plus un individu met du temps pour entrer en chrysaldie, au plus sa chrysaldie est lourde (ce n'est pas parfaitement significatif p-val = 0.0506)
Les individus en traitement Full ont quasiment significativement (p-val = 0.0684) des chrysalides plus lourdes (0.0083 g) que les inbdividus en traitement dark.
Les chrysalides des individus mâles du traitement Smart sont significativements (p-val = 0.0235) plus lourdes (0.011 g) que celles des femelles.
"
Info_Pupa_mass_by_TT_pupation_OP## [1] "\nAu plus un individu met du temps pour entrer en chrysaldie, au plus sa chrysaldie est lourde (ce n'est pas parfaitement significatif p-val = 0.0506)\nLes individus en traitement Full ont quasiment significativement (p-val = 0.0684) des chrysalides plus lourdes (0.0083 g) que les inbdividus en traitement dark. \nLes chrysalides des individus mâles du traitement Smart sont significativements (p-val = 0.0235) plus lourdes (0.011 g) que celles des femelles.\n"6.20 Pupa_mass * TT_pupation AE
6.20.1 Test
LM_Pupa_mass_by_TT_pupation_AE <- lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis, data = Data_AE)## boundary (singular) fit: see help('isSingular')summary(LM_Pupa_mass_by_TT_pupation_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region +
## TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis
## Data: Data_AE
##
## REML criterion at convergence: -346.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.75030 -0.51678 0.01297 0.56880 2.29821
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.000340 0.01844
## Site (Intercept) 0.000177 0.01330
## Room (Intercept) 0.000000 0.00000
## Residual 0.002600 0.05099
## Number of obs: 161, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 1.742e-01 3.086e-02 1.237e+02
## TT_pupation 3.350e-03 6.219e-04 1.396e+02
## Treatment_bisFull 4.181e-03 3.807e-02 1.343e+02
## Treatment_bisSmart 2.572e-02 5.819e-02 1.390e+02
## Treatment_bisMixt_smart 8.286e-02 5.571e-02 1.405e+02
## SexMale 1.419e-02 3.583e-02 1.363e+02
## RegionLuxembourg 8.641e-02 4.316e-02 1.048e+02
## Treatment_bisFull:SexMale -1.078e-02 2.156e-02 1.324e+02
## Treatment_bisSmart:SexMale -4.973e-02 2.561e-02 1.400e+02
## Treatment_bisMixt_smart:SexMale -5.793e-02 2.593e-02 1.371e+02
## Treatment_bisFull:RegionLuxembourg 2.844e-04 2.191e-02 1.285e+02
## Treatment_bisSmart:RegionLuxembourg 1.419e-02 2.466e-02 1.304e+02
## Treatment_bisMixt_smart:RegionLuxembourg 2.414e-02 3.049e-02 1.366e+02
## TT_pupation:SexMale 2.963e-04 7.296e-04 1.376e+02
## TT_pupation:RegionLuxembourg -1.975e-03 8.467e-04 1.397e+02
## TT_pupation:Treatment_bisFull 5.285e-04 8.704e-04 1.324e+02
## TT_pupation:Treatment_bisSmart 1.301e-06 1.365e-03 1.401e+02
## TT_pupation:Treatment_bisMixt_smart -3.124e-04 1.240e-03 1.421e+02
## t value Pr(>|t|)
## (Intercept) 5.646 1.07e-07 ***
## TT_pupation 5.387 2.97e-07 ***
## Treatment_bisFull 0.110 0.9127
## Treatment_bisSmart 0.442 0.6592
## Treatment_bisMixt_smart 1.487 0.1392
## SexMale 0.396 0.6926
## RegionLuxembourg 2.002 0.0478 *
## Treatment_bisFull:SexMale -0.500 0.6180
## Treatment_bisSmart:SexMale -1.942 0.0541 .
## Treatment_bisMixt_smart:SexMale -2.234 0.0271 *
## Treatment_bisFull:RegionLuxembourg 0.013 0.9897
## Treatment_bisSmart:RegionLuxembourg 0.576 0.5659
## Treatment_bisMixt_smart:RegionLuxembourg 0.792 0.4298
## TT_pupation:SexMale 0.406 0.6852
## TT_pupation:RegionLuxembourg -2.332 0.0211 *
## TT_pupation:Treatment_bisFull 0.607 0.5448
## TT_pupation:Treatment_bisSmart 0.001 0.9992
## TT_pupation:Treatment_bisMixt_smart -0.252 0.8015
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 18 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Test des hypothèses
Normalité des réisuds
qqnorm(resid(LM_Pupa_mass_by_TT_pupation_AE))
qqline(resid(LM_Pupa_mass_by_TT_pupation_AE))
Homogénité des variances
plot(LM_Pupa_mass_by_TT_pupation_AE)
Distance de cook
plot(cooks.distance(LM_Pupa_mass_by_TT_pupation_AE))
1 gros outlier à retirer si possible
Data_Pupa_mass_AE <- (Data_AE %>% filter(Sex != "NA", Pupa_mass != "NA" ))[unname(cooks.distance(LM_Pupa_mass_by_TT_pupation_AE) != max(cooks.distance(LM_Pupa_mass_by_TT_pupation_AE))),]
Data_Pupa_mass_AE_ref_smart <- Data_Pupa_mass_AE
Data_Pupa_mass_AE_ref_smart$Treatment_bis <- relevel(Data_Pupa_mass_AE$Treatment_bis, ref = "Smart")
Data_Pupa_mass_AE_ref_full <- Data_Pupa_mass_AE
Data_Pupa_mass_AE_ref_full$Treatment_bis <- relevel(Data_Pupa_mass_AE$Treatment_bis, ref = "Full")
Data_Pupa_mass_AE_ref_mixt_smart <- Data_Pupa_mass_AE
Data_Pupa_mass_AE_ref_mixt_smart$Treatment_bis <- relevel(Data_Pupa_mass_AE$Treatment_bis, ref = "Mixt_smart")Et on refait les tests
LM_Pupa_mass_by_TT_pupation_AE <- lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis, data = Data_Pupa_mass_AE)## boundary (singular) fit: see help('isSingular')Test des hypothèses
Normalité des réisuds
qqnorm(resid(LM_Pupa_mass_by_TT_pupation_AE))
qqline(resid(LM_Pupa_mass_by_TT_pupation_AE))
Homogénité des variances
plot(LM_Pupa_mass_by_TT_pupation_AE)
Distance de cook
plot(cooks.distance(LM_Pupa_mass_by_TT_pupation_AE))
6.20.2 Simplification du modèle
drop1(LM_Pupa_mass_by_TT_pupation_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Sex + TT_pupation:Region + TT_pupation:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.0241345 0.0080448 3 135.07 3.3696 0.02049 *
## Treatment_bis:Region 0.0024038 0.0008013 3 131.10 0.3356 0.79961
## TT_pupation:Sex 0.0022687 0.0022687 1 137.08 0.9502 0.33137
## TT_pupation:Region 0.0050456 0.0050456 1 141.04 2.1133 0.14824
## TT_pupation:Treatment_bis 0.0020554 0.0006851 3 137.55 0.2870 0.83475
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation1_AE <- update(LM_Pupa_mass_by_TT_pupation_AE, . ~ . - TT_pupation:Treatment_bis)## boundary (singular) fit: see help('isSingular')drop1(LM_Pupa_mass_by_TT_pupation1_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + TT_pupation:Sex + TT_pupation:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.0226113 0.0075371 3 137.94 3.2021 0.02533 *
## Treatment_bis:Region 0.0012372 0.0004124 3 132.89 0.1752 0.91302
## TT_pupation:Sex 0.0035188 0.0035188 1 136.38 1.4949 0.22356
## TT_pupation:Region 0.0088535 0.0088535 1 144.58 3.7613 0.05440 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation2_AE <- update(LM_Pupa_mass_by_TT_pupation1_AE, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_Pupa_mass_by_TT_pupation2_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Sex + TT_pupation:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.0224964 0.0074988 3 141.24 3.2380 0.02412 *
## TT_pupation:Sex 0.0035112 0.0035112 1 140.12 1.5161 0.22027
## TT_pupation:Region 0.0110907 0.0110907 1 147.84 4.7890 0.03021 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_Pupa_mass_by_TT_pupation3_AE <- update(LM_Pupa_mass_by_TT_pupation2_AE, . ~ . - TT_pupation:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_Pupa_mass_by_TT_pupation3_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.0233515 0.0077838 3 142.66 3.3527 0.02079 *
## TT_pupation:Region 0.0092204 0.0092204 1 148.82 3.9714 0.04811 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Il n’y a plus d’interactions qui n’ont pas de P-val significative, nous décidons d’arrêter la simplification du modèle.
Est ce que cela a été utile
AIC(LM_Pupa_mass_by_TT_pupation3_AE)## [1] -388.1635AIC(LM_Pupa_mass_by_TT_pupation_AE)## [1] -311.0651Oui ca a été utile
LM_Pupa_mass_by_TT_pupation_AE <- LM_Pupa_mass_by_TT_pupation3_AE6.20.3 Treatment VS Teatment_bis
AIC(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE))## boundary (singular) fit: see help('isSingular')## [1] -388.1635AIC(lmer(Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE))## [1] -399.218summary(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 0.163661932 0.0248098577 85.55708 6.5966494
## TT_pupation 0.003535437 0.0004737540 146.72755 7.4626003
## Treatment_bisFull 0.027442317 0.0132922627 136.98381 2.0645331
## Treatment_bisSmart 0.035806593 0.0146653899 141.18930 2.4415711
## Treatment_bisMixt_smart 0.073485892 0.0161464105 141.72522 4.5512215
## SexMale 0.034197865 0.0145101790 142.99166 2.3568190
## RegionLuxembourg 0.069387917 0.0355604711 97.16244 1.9512654
## Treatment_bisFull:SexMale -0.016839485 0.0200227427 140.11365 -0.8410179
## Treatment_bisSmart:SexMale -0.061332541 0.0240548772 146.31100 -2.5496925
## Treatment_bisMixt_smart:SexMale -0.060484288 0.0239643576 143.10470 -2.5239270
## TT_pupation:RegionLuxembourg -0.001411724 0.0007083967 148.82178 -1.9928435
## Pr(>|t|)
## (Intercept) 3.326751e-09
## TT_pupation 6.904534e-12
## Treatment_bisFull 4.085362e-02
## Treatment_bisSmart 1.586039e-02
## Treatment_bisMixt_smart 1.137354e-05
## SexMale 1.978842e-02
## RegionLuxembourg 5.390552e-02
## Treatment_bisFull:SexMale 4.017709e-01
## Treatment_bisSmart:SexMale 1.181097e-02
## Treatment_bisMixt_smart:SexMale 1.269705e-02
## TT_pupation:RegionLuxembourg 4.810705e-02summary(lmer(Pupa_mass ~ TT_pupation + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE))$coeff## Estimate Std. Error df t value
## (Intercept) 0.169616792 0.0263330211 37.59508 6.441220
## TT_pupation 0.003468364 0.0004772750 148.09297 7.267014
## TreatmentFull 0.023456395 0.0134550218 138.45614 1.743319
## TreatmentSmart 0.050107876 0.0127178878 143.64853 3.939953
## SexMale 0.031144138 0.0146053194 144.05932 2.132383
## RegionLuxembourg 0.048197842 0.0343320695 94.97878 1.403872
## TreatmentFull:SexMale -0.011506877 0.0203328288 142.04022 -0.565926
## TreatmentSmart:SexMale -0.055389346 0.0199827751 147.16011 -2.771855
## TT_pupation:RegionLuxembourg -0.000957090 0.0006850904 149.92855 -1.397027
## Pr(>|t|)
## (Intercept) 1.483418e-07
## TT_pupation 1.953388e-11
## TreatmentFull 8.349774e-02
## TreatmentSmart 1.267428e-04
## SexMale 3.467107e-02
## RegionLuxembourg 1.636182e-01
## TreatmentFull:SexMale 5.723371e-01
## TreatmentSmart:SexMale 6.294382e-03
## TT_pupation:RegionLuxembourg 1.644697e-01Même si l’AIC trouve que c’est mieux de prendre treatment, comme Mixt smart a un effet significatif, je compte prendre Treatment_bis
6.20.4 Résultats
Analyse des pval
summary(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region
## Data: Data_Pupa_mass_AE
##
## REML criterion at convergence: -418.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.74936 -0.57066 -0.01126 0.52477 2.35322
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0002398 0.01549
## Site (Intercept) 0.0003281 0.01811
## Room (Intercept) 0.0000000 0.00000
## Residual 0.0023217 0.04818
## Number of obs: 160, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 1.637e-01 2.481e-02 8.556e+01 6.597
## TT_pupation 3.535e-03 4.738e-04 1.467e+02 7.463
## Treatment_bisFull 2.744e-02 1.329e-02 1.370e+02 2.065
## Treatment_bisSmart 3.581e-02 1.467e-02 1.412e+02 2.442
## Treatment_bisMixt_smart 7.349e-02 1.615e-02 1.417e+02 4.551
## SexMale 3.420e-02 1.451e-02 1.430e+02 2.357
## RegionLuxembourg 6.939e-02 3.556e-02 9.716e+01 1.951
## Treatment_bisFull:SexMale -1.684e-02 2.002e-02 1.401e+02 -0.841
## Treatment_bisSmart:SexMale -6.133e-02 2.405e-02 1.463e+02 -2.550
## Treatment_bisMixt_smart:SexMale -6.048e-02 2.396e-02 1.431e+02 -2.524
## TT_pupation:RegionLuxembourg -1.412e-03 7.084e-04 1.488e+02 -1.993
## Pr(>|t|)
## (Intercept) 3.33e-09 ***
## TT_pupation 6.90e-12 ***
## Treatment_bisFull 0.0409 *
## Treatment_bisSmart 0.0159 *
## Treatment_bisMixt_smart 1.14e-05 ***
## SexMale 0.0198 *
## RegionLuxembourg 0.0539 .
## Treatment_bisFull:SexMale 0.4018
## Treatment_bisSmart:SexMale 0.0118 *
## Treatment_bisMixt_smart:SexMale 0.0127 *
## TT_pupation:RegionLuxembourg 0.0481 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TT_ppt Trtm_F Trtm_S Trt_M_ SexMal RgnLxm T_F:SM T_S:SM
## TT_pupation -0.836
## Trtmnt_bsFl -0.335 0.089
## Trtmnt_bsSm -0.300 0.084 0.449
## Trtmnt_bsM_ -0.295 0.083 0.428 0.360
## SexMale -0.291 0.053 0.461 0.419 0.412
## ReginLxmbrg -0.617 0.556 0.073 -0.068 0.213 0.076
## Trtmnt_F:SM 0.219 -0.058 -0.672 -0.316 -0.278 -0.714 0.005
## Trtmnt_S:SM 0.164 -0.007 -0.283 -0.620 -0.268 -0.609 -0.021 0.437
## Trtmn_M_:SM 0.169 -0.025 -0.285 -0.248 -0.680 -0.618 -0.098 0.436 0.388
## TT_pptn:RgL 0.586 -0.669 -0.084 0.049 -0.232 -0.093 -0.905 0.005 0.017
## T_M_:S
## TT_pupation
## Trtmnt_bsFl
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_F:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## TT_pptn:RgL 0.109
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region
## Data: Data_Pupa_mass_AE_ref_smart
##
## REML criterion at convergence: -418.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.74936 -0.57066 -0.01126 0.52477 2.35322
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0002398 0.01549
## Site (Intercept) 0.0003281 0.01811
## Room (Intercept) 0.0000000 0.00000
## Residual 0.0023217 0.04818
## Number of obs: 160, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 1.995e-01 2.474e-02 9.190e+01 8.061
## TT_pupation 3.535e-03 4.738e-04 1.467e+02 7.463
## Treatment_bisDark -3.581e-02 1.467e-02 1.412e+02 -2.442
## Treatment_bisFull -8.364e-03 1.473e-02 1.391e+02 -0.568
## Treatment_bisMixt_smart 3.768e-02 1.747e-02 1.377e+02 2.157
## SexMale -2.713e-02 1.907e-02 1.462e+02 -1.423
## RegionLuxembourg 6.939e-02 3.556e-02 9.716e+01 1.951
## Treatment_bisDark:SexMale 6.133e-02 2.405e-02 1.463e+02 2.550
## Treatment_bisFull:SexMale 4.449e-02 2.363e-02 1.440e+02 1.883
## Treatment_bisMixt_smart:SexMale 8.483e-04 2.656e-02 1.424e+02 0.032
## TT_pupation:RegionLuxembourg -1.412e-03 7.084e-04 1.488e+02 -1.993
## Pr(>|t|)
## (Intercept) 2.7e-12 ***
## TT_pupation 6.9e-12 ***
## Treatment_bisDark 0.0159 *
## Treatment_bisFull 0.5709
## Treatment_bisMixt_smart 0.0328 *
## SexMale 0.1570
## RegionLuxembourg 0.0539 .
## Treatment_bisDark:SexMale 0.0118 *
## Treatment_bisFull:SexMale 0.0618 .
## Treatment_bisMixt_smart:SexMale 0.9746
## TT_pupation:RegionLuxembourg 0.0481 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TT_ppt Trtm_D Trtm_F Trt_M_ SexMal RgnLxm T_D:SM T_F:SM
## TT_pupation -0.788
## Trtmnt_bsDr -0.292 -0.084
## Trtmnt_bsFl -0.354 -0.004 0.591
## Trtmnt_bsM_ -0.321 0.006 0.507 0.521
## SexMale -0.288 0.031 0.463 0.456 0.366
## ReginLxmbrg -0.659 0.556 0.068 0.134 0.254 0.032
## Trtmnt_D:SM 0.203 0.007 -0.620 -0.362 -0.272 -0.798 0.021
## Trtmnt_F:SM 0.233 -0.041 -0.363 -0.616 -0.270 -0.805 0.025 0.648
## Trtmn_M_:SM 0.204 -0.015 -0.337 -0.337 -0.625 -0.705 -0.070 0.555 0.563
## TT_pptn:RgL 0.617 -0.669 -0.049 -0.125 -0.256 -0.049 -0.905 -0.017 -0.013
## T_M_:S
## TT_pupation
## Trtmnt_bsDr
## Trtmnt_bsFl
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_D:SM
## Trtmnt_F:SM
## Trtmn_M_:SM
## TT_pptn:RgL 0.083
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region
## Data: Data_Pupa_mass_AE_ref_full
##
## REML criterion at convergence: -418.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.74936 -0.57066 -0.01126 0.52477 2.35322
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0002398 0.01549
## Site (Intercept) 0.0003281 0.01811
## Room (Intercept) 0.0000000 0.00000
## Residual 0.0023217 0.04818
## Number of obs: 160, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 1.911e-01 2.390e-02 7.990e+01 7.996
## TT_pupation 3.535e-03 4.738e-04 1.467e+02 7.463
## Treatment_bisDark -2.744e-02 1.329e-02 1.370e+02 -2.065
## Treatment_bisSmart 8.364e-03 1.473e-02 1.391e+02 0.568
## Treatment_bisMixt_smart 4.604e-02 1.593e-02 1.386e+02 2.890
## SexMale 1.736e-02 1.401e-02 1.379e+02 1.239
## RegionLuxembourg 6.939e-02 3.556e-02 9.716e+01 1.951
## Treatment_bisDark:SexMale 1.684e-02 2.002e-02 1.401e+02 0.841
## Treatment_bisSmart:SexMale -4.449e-02 2.363e-02 1.440e+02 -1.883
## Treatment_bisMixt_smart:SexMale -4.364e-02 2.359e-02 1.393e+02 -1.850
## TT_pupation:RegionLuxembourg -1.412e-03 7.084e-04 1.488e+02 -1.993
## Pr(>|t|)
## (Intercept) 8.28e-12 ***
## TT_pupation 6.90e-12 ***
## Treatment_bisDark 0.04085 *
## Treatment_bisSmart 0.57093
## Treatment_bisMixt_smart 0.00447 **
## SexMale 0.21759
## RegionLuxembourg 0.05391 .
## Treatment_bisDark:SexMale 0.40177
## Treatment_bisSmart:SexMale 0.06176 .
## Treatment_bisMixt_smart:SexMale 0.06643 .
## TT_pupation:RegionLuxembourg 0.04811 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TT_ppt Trtm_D Trtm_S Trt_M_ SexMal RgnLxm T_D:SM T_S:SM
## TT_pupation -0.819
## Trtmnt_bsDr -0.208 -0.089
## Trtmnt_bsSm -0.250 0.004 0.456
## Trtmnt_bsM_ -0.243 0.010 0.401 0.352
## SexMale -0.257 -0.027 0.483 0.418 0.434
## ReginLxmbrg -0.599 0.556 -0.073 -0.134 0.155 0.086
## Trtmnt_D:SM 0.147 0.058 -0.672 -0.292 -0.279 -0.689 -0.005
## Trtmnt_S:SM 0.138 0.041 -0.282 -0.616 -0.274 -0.590 -0.025 0.402
## Trtmn_M_:SM 0.142 0.024 -0.281 -0.237 -0.695 -0.602 -0.104 0.406 0.367
## TT_pptn:RgL 0.562 -0.669 0.084 0.125 -0.165 -0.089 -0.905 -0.005 0.013
## T_M_:S
## TT_pupation
## Trtmnt_bsDr
## Trtmnt_bsSm
## Trtmnt_bsM_
## SexMale
## ReginLxmbrg
## Trtmnt_D:SM
## Trtmnt_S:SM
## Trtmn_M_:SM
## TT_pptn:RgL 0.106
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE_ref_mixt_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region
## Data: Data_Pupa_mass_AE_ref_mixt_smart
##
## REML criterion at convergence: -418.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.74936 -0.57066 -0.01126 0.52477 2.35322
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0002398 0.01549
## Site (Intercept) 0.0003281 0.01811
## Room (Intercept) 0.0000000 0.00000
## Residual 0.0023217 0.04818
## Number of obs: 160, groups: Mother, 23; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 2.371e-01 2.530e-02 9.773e+01 9.375 2.82e-15
## TT_pupation 3.535e-03 4.738e-04 1.467e+02 7.463 6.90e-12
## Treatment_bisDark -7.349e-02 1.615e-02 1.417e+02 -4.551 1.14e-05
## Treatment_bisFull -4.604e-02 1.593e-02 1.386e+02 -2.890 0.00447
## Treatment_bisSmart -3.768e-02 1.747e-02 1.377e+02 -2.157 0.03277
## SexMale -2.629e-02 1.884e-02 1.421e+02 -1.396 0.16503
## RegionLuxembourg 6.939e-02 3.556e-02 9.716e+01 1.951 0.05391
## Treatment_bisDark:SexMale 6.048e-02 2.396e-02 1.431e+02 2.524 0.01270
## Treatment_bisFull:SexMale 4.364e-02 2.359e-02 1.393e+02 1.850 0.06643
## Treatment_bisSmart:SexMale -8.483e-04 2.656e-02 1.424e+02 -0.032 0.97457
## TT_pupation:RegionLuxembourg -1.412e-03 7.084e-04 1.488e+02 -1.993 0.04811
##
## (Intercept) ***
## TT_pupation ***
## Treatment_bisDark ***
## Treatment_bisFull **
## Treatment_bisSmart *
## SexMale
## RegionLuxembourg .
## Treatment_bisDark:SexMale *
## Treatment_bisFull:SexMale .
## Treatment_bisSmart:SexMale
## TT_pupation:RegionLuxembourg *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) TT_ppt Trtm_D Trtm_F Trtm_S SexMal RgnLxm T_D:SM T_F:SM
## TT_pupation -0.767
## Trtmnt_bsDr -0.349 -0.083
## Trtmnt_bsFl -0.400 -0.010 0.657
## Trtmnt_bsSm -0.377 -0.006 0.622 0.615
## SexMale -0.357 0.010 0.547 0.548 0.511
## ReginLxmbrg -0.469 0.556 -0.213 -0.155 -0.254 -0.066
## Trtmnt_D:SM 0.268 0.025 -0.680 -0.451 -0.420 -0.796 0.098
## Trtmnt_F:SM 0.304 -0.024 -0.455 -0.695 -0.434 -0.804 0.104 0.646
## Trtmnt_S:SM 0.232 0.015 -0.370 -0.374 -0.625 -0.696 0.070 0.551 0.561
## TT_pptn:RgL 0.427 -0.669 0.232 0.165 0.256 0.067 -0.905 -0.109 -0.106
## T_S:SM
## TT_pupation
## Trtmnt_bsDr
## Trtmnt_bsFl
## Trtmnt_bsSm
## SexMale
## ReginLxmbrg
## Trtmnt_D:SM
## Trtmnt_F:SM
## Trtmnt_S:SM
## TT_pptn:RgL -0.083
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test4 <- data.frame(Reference = "Mixt_smart", as.data.frame(( summary(lmer(Pupa_mass ~ TT_pupation + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + TT_pupation:Region, data = Data_Pupa_mass_AE_ref_mixt_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Pupa_mass_by_TT_pupation_AE <- rbind(test1,test2,test3,test4)
colnames(Results_Pupa_mass_by_TT_pupation_AE ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Pupa_mass_by_TT_pupation_AE , file = "output/Results_Pupa_mass_by_TT_pupation_AE.csv" )
kable(Results_Pupa_mass_by_TT_pupation_AE , caption = " Poids des chrysalides en fonction du temps pour rentrer en chrysalide AE", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 0.1636619 | 0.0248099 | 85.55708 | 6.5966494 | 0.0000000 |
| TT_pupation | Dark | 0.0035354 | 0.0004738 | 146.72755 | 7.4626003 | 0.0000000 |
| Treatment_bisFull | Dark | 0.0274423 | 0.0132923 | 136.98381 | 2.0645331 | 0.0408536 |
| Treatment_bisSmart | Dark | 0.0358066 | 0.0146654 | 141.18930 | 2.4415711 | 0.0158604 |
| Treatment_bisMixt_smart | Dark | 0.0734859 | 0.0161464 | 141.72522 | 4.5512215 | 0.0000114 |
| SexMale | Dark | 0.0341979 | 0.0145102 | 142.99166 | 2.3568190 | 0.0197884 |
| RegionLuxembourg | Dark | 0.0693879 | 0.0355605 | 97.16244 | 1.9512654 | 0.0539055 |
| Treatment_bisFull:SexMale | Dark | -0.0168395 | 0.0200227 | 140.11365 | -0.8410179 | 0.4017709 |
| Treatment_bisSmart:SexMale | Dark | -0.0613325 | 0.0240549 | 146.31100 | -2.5496925 | 0.0118110 |
| Treatment_bisMixt_smart:SexMale | Dark | -0.0604843 | 0.0239644 | 143.10470 | -2.5239270 | 0.0126971 |
| TT_pupation:RegionLuxembourg | Dark | -0.0014117 | 0.0007084 | 148.82178 | -1.9928435 | 0.0481070 |
| (Intercept)1 | Smart | 0.1994685 | 0.0247435 | 91.89547 | 8.0614386 | 0.0000000 |
| TT_pupation1 | Smart | 0.0035354 | 0.0004738 | 146.72755 | 7.4626003 | 0.0000000 |
| Treatment_bisDark | Smart | -0.0358066 | 0.0146654 | 141.18930 | -2.4415711 | 0.0158604 |
| Treatment_bisFull1 | Smart | -0.0083643 | 0.0147251 | 139.09801 | -0.5680266 | 0.5709327 |
| Treatment_bisMixt_smart1 | Smart | 0.0376793 | 0.0174712 | 137.65842 | 2.1566499 | 0.0327701 |
| SexMale1 | Smart | -0.0271347 | 0.0190728 | 146.15536 | -1.4226888 | 0.1569572 |
| RegionLuxembourg1 | Smart | 0.0693879 | 0.0355605 | 97.16244 | 1.9512654 | 0.0539055 |
| Treatment_bisDark:SexMale | Smart | 0.0613325 | 0.0240549 | 146.31100 | 2.5496925 | 0.0118110 |
| Treatment_bisFull:SexMale1 | Smart | 0.0444931 | 0.0236328 | 144.04251 | 1.8826854 | 0.0617597 |
| Treatment_bisMixt_smart:SexMale1 | Smart | 0.0008483 | 0.0265589 | 142.43076 | 0.0319386 | 0.9745658 |
| TT_pupation:RegionLuxembourg1 | Smart | -0.0014117 | 0.0007084 | 148.82178 | -1.9928435 | 0.0481070 |
| (Intercept)2 | Full | 0.1911042 | 0.0238991 | 79.90131 | 7.9963051 | 0.0000000 |
| TT_pupation2 | Full | 0.0035354 | 0.0004738 | 146.72755 | 7.4626003 | 0.0000000 |
| Treatment_bisDark1 | Full | -0.0274423 | 0.0132923 | 136.98381 | -2.0645331 | 0.0408536 |
| Treatment_bisSmart1 | Full | 0.0083643 | 0.0147251 | 139.09801 | 0.5680266 | 0.5709327 |
| Treatment_bisMixt_smart2 | Full | 0.0460436 | 0.0159308 | 138.61207 | 2.8902268 | 0.0044699 |
| SexMale2 | Full | 0.0173584 | 0.0140144 | 137.87065 | 1.2386096 | 0.2175948 |
| RegionLuxembourg2 | Full | 0.0693879 | 0.0355605 | 97.16243 | 1.9512654 | 0.0539055 |
| Treatment_bisDark:SexMale1 | Full | 0.0168395 | 0.0200227 | 140.11365 | 0.8410179 | 0.4017709 |
| Treatment_bisSmart:SexMale1 | Full | -0.0444931 | 0.0236328 | 144.04251 | -1.8826854 | 0.0617597 |
| Treatment_bisMixt_smart:SexMale2 | Full | -0.0436448 | 0.0235911 | 139.26385 | -1.8500523 | 0.0664253 |
| TT_pupation:RegionLuxembourg2 | Full | -0.0014117 | 0.0007084 | 148.82178 | -1.9928435 | 0.0481070 |
| (Intercept)3 | Mixt_smart | 0.2371478 | 0.0252965 | 97.73242 | 9.3747209 | 0.0000000 |
| TT_pupation3 | Mixt_smart | 0.0035354 | 0.0004738 | 146.72755 | 7.4626003 | 0.0000000 |
| Treatment_bisDark2 | Mixt_smart | -0.0734859 | 0.0161464 | 141.72522 | -4.5512215 | 0.0000114 |
| Treatment_bisFull2 | Mixt_smart | -0.0460436 | 0.0159308 | 138.61207 | -2.8902268 | 0.0044699 |
| Treatment_bisSmart2 | Mixt_smart | -0.0376793 | 0.0174712 | 137.65842 | -2.1566499 | 0.0327701 |
| SexMale3 | Mixt_smart | -0.0262864 | 0.0188360 | 142.12225 | -1.3955433 | 0.1650287 |
| RegionLuxembourg3 | Mixt_smart | 0.0693879 | 0.0355605 | 97.16244 | 1.9512654 | 0.0539055 |
| Treatment_bisDark:SexMale2 | Mixt_smart | 0.0604843 | 0.0239644 | 143.10470 | 2.5239270 | 0.0126971 |
| Treatment_bisFull:SexMale2 | Mixt_smart | 0.0436448 | 0.0235911 | 139.26385 | 1.8500523 | 0.0664253 |
| Treatment_bisSmart:SexMale2 | Mixt_smart | -0.0008483 | 0.0265589 | 142.43076 | -0.0319386 | 0.9745658 |
| TT_pupation:RegionLuxembourg3 | Mixt_smart | -0.0014117 | 0.0007084 | 148.82178 | -1.9928435 | 0.0481070 |
Info_Pupa_mass_by_TT_pupation_AE <- "
Au plus un individu met du temps pour entrer en chrysalide, au plus sa chrysalide sera lourde (p-val = 6.90e-12).
Les chrysalides des individus des traitements Full et Smart sont significatiment (p-val = 0.0409 et 0.0159 respectivement) plus lourdes (0.027 g et 0.036 g respectivement) que celles du traitement Dark.
Celles de Mixt-smart sont significativement (p-val = 1.14e-05 et 0.00447 et 0.0328 respectivement) plus lourdes (0.073 g, 0.046 g et 0.038 g respectivement) que celles des traitements Dark, Full et Smart.
Les chrysalides venant d'individus mâles dans le traitement Dark sont significativement (p-val = 0.0198) plus lourdes (0.034 g) que celles des femelles.
Les chrysalides des individus déscendant d'une mère provenant de la région luxembourgeoise sont quasiement significativement (p-val = 0.0539) plus lourdes (0.069 g) que celles du brabant mais les individus ont significativement (p-val = 0.0481) moins bien optimisé le temps avant l'entrée en chrysaldie pour augmenter la masse finale de la chrysalide (0.0014 g en moins par semaine passée).
"
Info_Pupa_mass_by_TT_pupation_AE## [1] "\nAu plus un individu met du temps pour entrer en chrysalide, au plus sa chrysalide sera lourde (p-val = 6.90e-12).\nLes chrysalides des individus des traitements Full et Smart sont significatiment (p-val = 0.0409 et 0.0159 respectivement) plus lourdes (0.027 g et 0.036 g respectivement) que celles du traitement Dark.\nCelles de Mixt-smart sont significativement (p-val = 1.14e-05 et 0.00447 et 0.0328 respectivement) plus lourdes (0.073 g, 0.046 g et 0.038 g respectivement) que celles des traitements Dark, Full et Smart.\nLes chrysalides venant d'individus mâles dans le traitement Dark sont significativement (p-val = 0.0198) plus lourdes (0.034 g) que celles des femelles.\nLes chrysalides des individus déscendant d'une mère provenant de la région luxembourgeoise sont quasiement significativement (p-val = 0.0539) plus lourdes (0.069 g) que celles du brabant mais les individus ont significativement (p-val = 0.0481) moins bien optimisé le temps avant l'entrée en chrysaldie pour augmenter la masse finale de la chrysalide (0.0014 g en moins par semaine passée).\n"6.21 Mass_by_Time OP
Dévelloppement du jeux de données
Data_mass <- Data[,1:31] %>% pivot_longer(cols = M0:M20, names_to = "Numéro_de_masse", values_to = "Mass")
Data_mass$Time <- rep(0:20, length.out = nrow(Data_mass))Data_mass_OP <- Data_mass %>% filter(Species == "OP")
Data_mass_AE <- Data_mass %>% filter(Species == "AE")Data_mass_OP_ref_smart <- Data_mass_OP
Data_mass_OP_ref_smart$Treatment <- relevel(Data_mass_OP$Treatment, ref = "Smart")
Data_mass_OP_ref_smart$Treatment_bis <- relevel(Data_mass_OP$Treatment_bis, ref = "Smart")
Data_mass_OP_ref_full <- Data_mass_OP
Data_mass_OP_ref_full$Treatment <- relevel(Data_mass_OP$Treatment, ref = "Full")
Data_mass_OP_ref_full$Treatment_bis <- relevel(Data_mass_OP$Treatment_bis, ref = "Full")
Data_mass_AE_ref_smart <- Data_mass_AE
Data_mass_AE_ref_smart$Treatment <- relevel(Data_mass_AE$Treatment, ref = "Smart")
Data_mass_AE_ref_smart$Treatment_bis <- relevel(Data_mass_AE$Treatment_bis, ref = "Smart")
Data_mass_AE_ref_full <- Data_mass_AE
Data_mass_AE_ref_full$Treatment <- relevel(Data_mass_AE$Treatment, ref = "Full")
Data_mass_AE_ref_full$Treatment_bis <- relevel(Data_mass_AE$Treatment_bis, ref = "Full")
Data_mass_AE_ref_mixt_smart <- Data_mass_AE
Data_mass_AE_ref_mixt_smart$Treatment_bis <- relevel(Data_mass_AE$Treatment_bis, ref = "Mixt_smart")6.21.1 Test
LM_mass_by_time_OP <- lmer(Mass ~ Time + Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Time:Sex + Time:Region + Time:Treatment_bis, data = Data_mass_OP)## boundary (singular) fit: see help('isSingular')summary(LM_mass_by_time_OP)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Mass ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region +
## Time:Sex + Time:Region + Time:Treatment_bis
## Data: Data_mass_OP
##
## REML criterion at convergence: -697.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.2967 -0.5231 -0.1635 0.4271 3.2827
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 5.959e-04 0.024411
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 7.933e-05 0.008907
## Residual 5.622e-03 0.074983
## Number of obs: 340, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 0.057193 0.017070 13.323503 3.351
## Time 0.134394 0.010227 318.674967 13.141
## Treatment_bisFull -0.009552 0.018769 321.112729 -0.509
## Treatment_bisSmart -0.028187 0.026872 300.016428 -1.049
## SexMale -0.014241 0.014671 318.731994 -0.971
## RegionLuxembourg -0.003663 0.020565 18.437854 -0.178
## Treatment_bisFull:SexMale 0.029530 0.018609 323.259347 1.587
## Treatment_bisSmart:SexMale 0.037074 0.026209 325.188218 1.415
## Treatment_bisFull:RegionLuxembourg 0.001946 0.018165 318.269645 0.107
## Treatment_bisSmart:RegionLuxembourg 0.013948 0.026286 324.513027 0.531
## Time:SexMale -0.001798 0.011257 316.082921 -0.160
## Time:RegionLuxembourg -0.009891 0.011245 318.772953 -0.880
## Time:Treatment_bisFull 0.003894 0.012472 315.991611 0.312
## Time:Treatment_bisSmart -0.019730 0.016540 314.725178 -1.193
## Pr(>|t|)
## (Intercept) 0.00506 **
## Time < 2e-16 ***
## Treatment_bisFull 0.61115
## Treatment_bisSmart 0.29505
## SexMale 0.33246
## RegionLuxembourg 0.86056
## Treatment_bisFull:SexMale 0.11352
## Treatment_bisSmart:SexMale 0.15816
## Treatment_bisFull:RegionLuxembourg 0.91475
## Treatment_bisSmart:RegionLuxembourg 0.59604
## Time:SexMale 0.87317
## Time:RegionLuxembourg 0.37974
## Time:Treatment_bisFull 0.75507
## Time:Treatment_bisSmart 0.23384
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 14 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_mass_by_time_OP))
qqline(resid(LM_mass_by_time_OP))
Il faudrait modifier les données
LM_mass_by_time_OP <- lmer(sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Time:Sex + Time:Region + Time:Treatment_bis, data = Data_mass_OP)## boundary (singular) fit: see help('isSingular')qqnorm(resid(LM_mass_by_time_OP))
qqline(resid(LM_mass_by_time_OP))
Homogénité des variances
plot(LM_mass_by_time_OP)
Distance de cook
plot(cooks.distance(LM_mass_by_time_OP))
6.21.2 Simplification du modèle
drop1(LM_mass_by_time_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Time:Sex + Time:Region + Time:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.0239834 0.0119917 2 322.99 1.4888 0.2272
## Treatment_bis:Region 0.0023772 0.0011886 2 320.14 0.1476 0.8629
## Time:Sex 0.0000081 0.0000081 1 315.05 0.0010 0.9747
## Time:Region 0.0034646 0.0034646 1 317.28 0.4301 0.5124
## Time:Treatment_bis 0.0083163 0.0041581 2 314.57 0.5162 0.5973LM_mass_by_time1_OP <- update(LM_mass_by_time_OP, . ~ . - Time:Sex)## boundary (singular) fit: see help('isSingular')drop1(LM_mass_by_time1_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Time:Region + Time:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.0239586 0.0119793 2 324.01 1.4920 0.2265
## Treatment_bis:Region 0.0023854 0.0011927 2 321.13 0.1485 0.8620
## Time:Region 0.0034846 0.0034846 1 318.25 0.4340 0.5105
## Time:Treatment_bis 0.0083517 0.0041759 2 315.53 0.5201 0.5950LM_mass_by_time2_OP <- update(LM_mass_by_time1_OP, . ~ . - Treatment_bis:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_mass_by_time2_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Time:Region + Time:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.0261048 0.0130524 2 325.75 1.6342 0.1967
## Time:Region 0.0033492 0.0033492 1 320.40 0.4193 0.5177
## Time:Treatment_bis 0.0083862 0.0041931 2 317.49 0.5250 0.5921LM_mass_by_time3_OP <- update(LM_mass_by_time2_OP, . ~ . - Time:Treatment_bis)## boundary (singular) fit: see help('isSingular')drop1(LM_mass_by_time3_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Time:Region
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Treatment_bis:Sex 0.0265620 0.0132810 2 327.8 1.6677 0.1903
## Time:Region 0.0038125 0.0038125 1 322.6 0.4787 0.4895LM_mass_by_time4_OP <- update(LM_mass_by_time3_OP, . ~ . - Time:Region)## boundary (singular) fit: see help('isSingular')drop1(LM_mass_by_time4_OP)## Single term deletions using Satterthwaite's method:
##
## Model:
## sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## Time 6.1829 6.1829 1 322.80 777.6929 <2e-16 ***
## Region 0.0026 0.0026 1 8.29 0.3265 0.5829
## Treatment_bis:Sex 0.0257 0.0128 2 328.82 1.6132 0.2008
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Plus aucune interaction ne peut être retirée, on arrête la simplification ici.
A-t-elle été utile ?
AIC(LM_mass_by_time4_OP)## [1] -588.0614AIC(LM_mass_by_time_OP)## [1] -540.6358Oui
LM_mass_by_time_OP <- LM_mass_by_time4_OP6.21.3 Treatment VS Teatment_bis
AIC(lmer(sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_mass_OP))## boundary (singular) fit: see help('isSingular')## [1] -588.0614AIC(lmer(sqrt(Mass) ~ Time + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_mass_OP))## boundary (singular) fit: see help('isSingular')## [1] -586.3493summary(lmer(sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_mass_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 0.220724276 0.020750234 10.67268 10.6371943
## Time 0.184932177 0.006631449 322.79757 27.8871449
## Treatment_bisFull -0.004852993 0.015235595 318.10720 -0.3185299
## Treatment_bisSmart -0.044586795 0.022074852 202.78652 -2.0198004
## SexMale -0.013763824 0.013787010 322.49172 -0.9983182
## RegionLuxembourg -0.014130903 0.024730564 8.29156 -0.5713943
## Treatment_bisFull:SexMale 0.030282903 0.022100770 326.19562 1.3702193
## Treatment_bisSmart:SexMale 0.047042537 0.030940365 330.56177 1.5204260
## Pr(>|t|)
## (Intercept) 5.168431e-07
## Time 5.648613e-88
## Treatment_bisFull 7.502920e-01
## Treatment_bisSmart 4.471995e-02
## SexMale 3.188736e-01
## RegionLuxembourg 5.828857e-01
## Treatment_bisFull:SexMale 1.715607e-01
## Treatment_bisSmart:SexMale 1.293598e-01summary(lmer(sqrt(Mass) ~ Time + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Sex, data = Data_mass_OP))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) 0.22659730 0.021554322 15.986170 10.5128476
## Time 0.18491748 0.006639799 323.829950 27.8498622
## TreatmentFull -0.01024599 0.016940827 326.795431 -0.6048106
## TreatmentSmart -0.02683642 0.015908217 325.105880 -1.6869536
## SexMale -0.01501092 0.016925973 324.243868 -0.8868572
## RegionLuxembourg -0.01513882 0.026020536 8.577493 -0.5818028
## TreatmentFull:SexMale 0.03071164 0.024323967 327.849850 1.2626082
## TreatmentSmart:SexMale 0.02110689 0.024611818 324.645621 0.8575917
## Pr(>|t|)
## (Intercept) 1.375492e-08
## Time 5.862102e-88
## TreatmentFull 5.457246e-01
## TreatmentSmart 9.257148e-02
## SexMale 3.758131e-01
## RegionLuxembourg 5.756683e-01
## TreatmentFull:SexMale 2.076273e-01
## TreatmentSmart:SexMale 3.917506e-01Si je me base sur les AIC je continue avec treatment_bis
6.21.4 Résultats
Analyse des P-val
summary(lmer(sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_mass_OP))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Data: Data_mass_OP
##
## REML criterion at convergence: -612.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4446 -0.6284 -0.1251 0.6382 2.5225
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.470e-03 0.038347
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 9.135e-05 0.009558
## Residual 7.950e-03 0.089165
## Number of obs: 340, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.220724 0.020750 10.672683 10.637 5.17e-07
## Time 0.184932 0.006631 322.797568 27.887 < 2e-16
## Treatment_bisFull -0.004853 0.015236 318.107205 -0.319 0.7503
## Treatment_bisSmart -0.044587 0.022075 202.786518 -2.020 0.0447
## SexMale -0.013764 0.013787 322.491722 -0.998 0.3189
## RegionLuxembourg -0.014131 0.024731 8.291560 -0.571 0.5829
## Treatment_bisFull:SexMale 0.030283 0.022101 326.195624 1.370 0.1716
## Treatment_bisSmart:SexMale 0.047043 0.030940 330.561768 1.520 0.1294
##
## (Intercept) ***
## Time ***
## Treatment_bisFull
## Treatment_bisSmart *
## SexMale
## RegionLuxembourg
## Treatment_bisFull:SexMale
## Treatment_bisSmart:SexMale
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Time Trtm_F Trtm_S SexMal RgnLxm T_F:SM
## Time -0.245
## Trtmnt_bsFl -0.247 -0.002
## Trtmnt_bsSm -0.166 -0.017 0.284
## SexMale -0.260 0.003 0.368 0.290
## ReginLxmbrg -0.591 -0.005 -0.030 -0.057 -0.012
## Trtmnt_F:SM 0.166 0.030 -0.697 -0.215 -0.630 0.023
## Trtmnt_S:SM 0.118 0.008 -0.170 -0.679 -0.463 0.018 0.301
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_mass_OP_ref_full))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Data: Data_mass_OP_ref_full
##
## REML criterion at convergence: -612.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4446 -0.6284 -0.1251 0.6382 2.5225
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.470e-03 0.038347
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 9.135e-05 0.009558
## Residual 7.950e-03 0.089165
## Number of obs: 340, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.215871 0.022501 14.965224 9.594 8.77e-08
## Time 0.184932 0.006631 322.797581 27.887 < 2e-16
## Treatment_bisDark 0.004853 0.015236 318.107213 0.319 0.7503
## Treatment_bisSmart -0.039734 0.022988 306.923596 -1.728 0.0849
## SexMale 0.016519 0.017162 328.492168 0.963 0.3365
## RegionLuxembourg -0.014131 0.024731 8.291531 -0.571 0.5829
## Treatment_bisDark:SexMale -0.030283 0.022101 326.195630 -1.370 0.1716
## Treatment_bisSmart:SexMale 0.016760 0.032149 328.800638 0.521 0.6025
##
## (Intercept) ***
## Time ***
## Treatment_bisDark
## Treatment_bisSmart .
## SexMale
## RegionLuxembourg
## Treatment_bisDark:SexMale
## Treatment_bisSmart:SexMale
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Time Trtm_D Trtm_S SexMal RgnLxm T_D:SM
## Time -0.227
## Trtmnt_bsDr -0.449 0.002
## Trtmnt_bsSm -0.260 -0.016 0.390
## SexMale -0.404 0.040 0.602 0.357
## ReginLxmbrg -0.566 -0.005 0.030 -0.034 0.021
## Trtmnt_D:SM 0.319 -0.030 -0.697 -0.256 -0.782 -0.023
## Trtmnt_S:SM 0.214 -0.013 -0.316 -0.695 -0.522 0.001 0.397
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')summary(lmer(sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_mass_OP_ref_smart))## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) +
## (1 | Site) + (1 | Room) + Treatment_bis:Sex
## Data: Data_mass_OP_ref_smart
##
## REML criterion at convergence: -612.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4446 -0.6284 -0.1251 0.6382 2.5225
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.470e-03 0.038347
## Site (Intercept) 0.000e+00 0.000000
## Room (Intercept) 9.135e-05 0.009558
## Residual 7.950e-03 0.089165
## Number of obs: 340, groups: Mother, 12; Site, 8; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.176137 0.027675 28.422980 6.364 6.45e-07 ***
## Time 0.184932 0.006631 322.797573 27.887 < 2e-16 ***
## Treatment_bisDark 0.044587 0.022075 202.786524 2.020 0.0447 *
## Treatment_bisFull 0.039734 0.022988 306.923592 1.728 0.0849 .
## SexMale 0.033279 0.027433 330.000961 1.213 0.2260
## RegionLuxembourg -0.014131 0.024731 8.291547 -0.571 0.5829
## Treatment_bisDark:SexMale -0.047043 0.030940 330.561768 -1.520 0.1294
## Treatment_bisFull:SexMale -0.016760 0.032149 328.800636 -0.521 0.6025
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) Time Trtm_D Trtm_F SexMal RgnLxm T_D:SM
## Time -0.198
## Trtmnt_bsDr -0.673 0.017
## Trtmnt_bsFl -0.619 0.016 0.772
## SexMale -0.492 0.010 0.620 0.591
## ReginLxmbrg -0.489 -0.005 0.057 0.034 0.014
## Trtmnt_D:SM 0.453 -0.008 -0.679 -0.539 -0.895 -0.018
## Trtmnt_F:SM 0.403 0.013 -0.506 -0.695 -0.846 -0.001 0.755
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')test1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_mass_OP))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_mass_OP_ref_full))$coeff)[,]))## boundary (singular) fit: see help('isSingular')test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(sqrt(Mass) ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex, data = Data_mass_OP_ref_smart))$coeff)[,]))## boundary (singular) fit: see help('isSingular')Results_Mass_by_time_OP <- rbind(test1,test2,test3)
colnames(Results_Mass_by_time_OP ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Mass_by_time_OP , file = "output/Results_Mass_by_time_OP.csv" )
kable(Results_Mass_by_time_OP , caption = " Poids en fonction du temps OP ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | 0.2207243 | 0.0207502 | 10.672683 | 10.6371943 | 0.0000005 |
| Time | Dark | 0.1849322 | 0.0066314 | 322.797568 | 27.8871449 | 0.0000000 |
| Treatment_bisFull | Dark | -0.0048530 | 0.0152356 | 318.107205 | -0.3185299 | 0.7502920 |
| Treatment_bisSmart | Dark | -0.0445868 | 0.0220749 | 202.786518 | -2.0198004 | 0.0447199 |
| SexMale | Dark | -0.0137638 | 0.0137870 | 322.491722 | -0.9983182 | 0.3188736 |
| RegionLuxembourg | Dark | -0.0141309 | 0.0247306 | 8.291559 | -0.5713943 | 0.5828857 |
| Treatment_bisFull:SexMale | Dark | 0.0302829 | 0.0221008 | 326.195624 | 1.3702193 | 0.1715607 |
| Treatment_bisSmart:SexMale | Dark | 0.0470425 | 0.0309404 | 330.561769 | 1.5204260 | 0.1293598 |
| (Intercept)1 | Smart | 0.2158713 | 0.0225005 | 14.965224 | 9.5940617 | 0.0000001 |
| Time1 | Smart | 0.1849322 | 0.0066314 | 322.797581 | 27.8871466 | 0.0000000 |
| Treatment_bisDark | Smart | 0.0048530 | 0.0152356 | 318.107213 | 0.3185302 | 0.7502918 |
| Treatment_bisSmart1 | Smart | -0.0397338 | 0.0229875 | 306.923596 | -1.7284922 | 0.0849057 |
| SexMale1 | Smart | 0.0165191 | 0.0171621 | 328.492168 | 0.9625306 | 0.3364912 |
| RegionLuxembourg1 | Smart | -0.0141309 | 0.0247306 | 8.291531 | -0.5713942 | 0.5828858 |
| Treatment_bisDark:SexMale | Smart | -0.0302829 | 0.0221008 | 326.195630 | -1.3702194 | 0.1715607 |
| Treatment_bisSmart:SexMale1 | Smart | 0.0167596 | 0.0321488 | 328.800638 | 0.5213135 | 0.6024993 |
| (Intercept)2 | Full | 0.1761375 | 0.0276751 | 28.422980 | 6.3644741 | 0.0000006 |
| Time2 | Full | 0.1849322 | 0.0066314 | 322.797573 | 27.8871457 | 0.0000000 |
| Treatment_bisDark1 | Full | 0.0445868 | 0.0220749 | 202.786524 | 2.0198000 | 0.0447200 |
| Treatment_bisFull1 | Full | 0.0397338 | 0.0229875 | 306.923592 | 1.7284928 | 0.0849056 |
| SexMale2 | Full | 0.0332787 | 0.0274326 | 330.000961 | 1.2131097 | 0.2259555 |
| RegionLuxembourg2 | Full | -0.0141309 | 0.0247306 | 8.291547 | -0.5713942 | 0.5828858 |
| Treatment_bisDark:SexMale1 | Full | -0.0470425 | 0.0309404 | 330.561769 | -1.5204256 | 0.1293599 |
| Treatment_bisFull:SexMale1 | Full | -0.0167596 | 0.0321488 | 328.800636 | -0.5213140 | 0.6024990 |
Info_Mass_by_Time_OP <- "
Augmentation de la masse avec le temps.
Smart est plus léger que Dark.
Full est presque plus lourd que smart (p val 0.0849)
"
Info_Mass_by_Time_OP## [1] "\nAugmentation de la masse avec le temps.\nSmart est plus léger que Dark.\nFull est presque plus lourd que smart (p val 0.0849)\n"6.22 Mass_by_Time AE
6.22.1 Test
LM_mass_by_time_AE <- lmer(Mass ~ Time + Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Time:Sex + Time:Region + Time:Treatment_bis, data = Data_mass_AE)## boundary (singular) fit: see help('isSingular')summary(LM_mass_by_time_AE)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Mass ~ Time + Treatment_bis + Sex + Region + (1 | Mother) + (1 |
## Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region +
## Time:Sex + Time:Region + Time:Treatment_bis
## Data: Data_mass_AE
##
## REML criterion at convergence: -1326.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.7359 -0.5761 -0.1620 0.3832 4.1216
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 1.367e-03 0.036972
## Site (Intercept) 8.966e-05 0.009469
## Room (Intercept) 0.000e+00 0.000000
## Residual 2.207e-02 0.148548
## Number of obs: 1523, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 2.257e-02 1.919e-02 2.933e+01
## Time 5.465e-02 2.313e-03 1.503e+03
## Treatment_bisFull -1.368e-02 1.972e-02 1.500e+03
## Treatment_bisSmart -8.441e-02 2.489e-02 1.505e+03
## Treatment_bisMixt_smart -2.763e-02 2.363e-02 1.498e+03
## SexMale -2.054e-02 1.823e-02 1.491e+03
## RegionLuxembourg -6.609e-03 2.434e-02 2.232e+01
## Treatment_bisFull:SexMale -1.356e-02 2.001e-02 1.480e+03
## Treatment_bisSmart:SexMale -2.137e-02 2.585e-02 1.388e+03
## Treatment_bisMixt_smart:SexMale 4.613e-03 2.407e-02 1.426e+03
## Treatment_bisFull:RegionLuxembourg -3.866e-02 2.006e-02 1.467e+03
## Treatment_bisSmart:RegionLuxembourg 8.279e-02 2.382e-02 1.504e+03
## Treatment_bisMixt_smart:RegionLuxembourg -4.795e-02 2.363e-02 1.455e+03
## Time:SexMale 4.988e-03 2.363e-03 1.493e+03
## Time:RegionLuxembourg -6.482e-03 2.434e-03 1.503e+03
## Time:Treatment_bisFull 1.277e-02 2.812e-03 1.498e+03
## Time:Treatment_bisSmart 2.871e-02 4.034e-03 1.494e+03
## Time:Treatment_bisMixt_smart 1.752e-02 3.398e-03 1.493e+03
## t value Pr(>|t|)
## (Intercept) 1.176 0.249038
## Time 23.625 < 2e-16 ***
## Treatment_bisFull -0.694 0.487870
## Treatment_bisSmart -3.392 0.000712 ***
## Treatment_bisMixt_smart -1.169 0.242428
## SexMale -1.127 0.259979
## RegionLuxembourg -0.272 0.788446
## Treatment_bisFull:SexMale -0.678 0.498003
## Treatment_bisSmart:SexMale -0.826 0.408704
## Treatment_bisMixt_smart:SexMale 0.192 0.848071
## Treatment_bisFull:RegionLuxembourg -1.927 0.054117 .
## Treatment_bisSmart:RegionLuxembourg 3.476 0.000523 ***
## Treatment_bisMixt_smart:RegionLuxembourg -2.029 0.042605 *
## Time:SexMale 2.110 0.034987 *
## Time:RegionLuxembourg -2.663 0.007824 **
## Time:Treatment_bisFull 4.539 6.10e-06 ***
## Time:Treatment_bisSmart 7.117 1.70e-12 ***
## Time:Treatment_bisMixt_smart 5.156 2.85e-07 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 18 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')Vérification des hypothèses
qqnorm(resid(LM_mass_by_time_AE))
qqline(resid(LM_mass_by_time_AE))
Il faudrait modifier les données
LM_mass_by_time_AE <- lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1|Mother) + (1|Site) + (1|Room) + Treatment_bis:Sex + Treatment_bis:Region + Time:Sex + Time:Region + Time:Treatment_bis, data = Data_mass_AE)qqnorm(resid(LM_mass_by_time_AE))
qqline(resid(LM_mass_by_time_AE))
Homogénité des variances
plot(LM_mass_by_time_AE)
Distance de cook
plot(cooks.distance(LM_mass_by_time_AE))
6.22.2 Simplification du modèle
drop1(LM_mass_by_time_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Time:Sex + Time:Region + Time:Treatment_bis
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## log(Time + 1) 393.47 393.47 1 1486.0 1543.0572 < 2.2e-16 ***
## Treatment_bis:Sex 1.66 0.55 3 1202.4 2.1682 0.09007 .
## Treatment_bis:Region 14.23 4.74 3 1496.5 18.6006 7.558e-12 ***
## Sex:Time 6.70 3.35 2 1491.2 13.1445 2.193e-06 ***
## Region:Time 0.02 0.02 1 1495.9 0.0944 0.75876
## Treatment_bis:Time 9.33 3.11 3 1488.3 12.1935 6.960e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_mass_by_time1_AE <- update(LM_mass_by_time_AE, . ~ . - Region:Time)
drop1(LM_mass_by_time1_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Sex + Treatment_bis:Region + Sex:Time + Treatment_bis:Time
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## log(Time + 1) 398.38 398.38 1 1486.8 1563.2356 < 2.2e-16 ***
## Treatment_bis:Sex 1.64 0.55 3 1197.4 2.1469 0.09263 .
## Treatment_bis:Region 14.24 4.75 3 1496.9 18.6227 7.323e-12 ***
## Sex:Time 7.39 3.70 2 1492.1 14.4993 5.800e-07 ***
## Treatment_bis:Time 9.47 3.16 3 1489.4 12.3925 5.240e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1LM_mass_by_time2_AE <- update(LM_mass_by_time1_AE, . ~ . - Treatment_bis:Sex)
drop1(LM_mass_by_time2_AE)## Single term deletions using Satterthwaite's method:
##
## Model:
## log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## log(Time + 1) 399.05 399.05 1 1490.1 1561.105 < 2.2e-16 ***
## Treatment_bis:Region 13.80 4.60 3 1498.1 18.000 1.773e-11 ***
## Sex:Time 7.61 3.80 2 1495.7 14.882 3.982e-07 ***
## Treatment_bis:Time 9.43 3.14 3 1492.7 12.295 6.021e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Plus aucune interaction ne peut être retirée, on arrête la simplification ici.
A-t-elle été utile ?
AIC(LM_mass_by_time2_AE)## [1] 2401.794AIC(LM_mass_by_time_AE)## [1] 2421.181Oui
LM_mass_by_time_AE <- LM_mass_by_time2_AE6.22.3 Treatment VS Teatment_bis
AIC(lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time, data = Data_mass_AE))## [1] 2401.794AIC(lmer(log(Mass) ~ log(Time + 1) + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region + Sex:Time + Treatment:Time, data = Data_mass_AE))## boundary (singular) fit: see help('isSingular')## [1] 2446.118summary(lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time, data = Data_mass_AE))$coeff## Estimate Std. Error df
## (Intercept) -4.44361062 0.089768114 21.49434
## log(Time + 1) 1.91333827 0.048425669 1490.12099
## Treatment_bisFull -0.08259230 0.060264609 1500.63377
## Treatment_bisSmart -0.30684313 0.080215588 1023.06236
## Treatment_bisMixt_smart -0.03446372 0.073320391 613.46518
## SexMale -0.06647218 0.045287925 1501.49311
## RegionLuxembourg -0.23506408 0.106400734 13.97362
## Treatment_bisFull:RegionLuxembourg -0.07319669 0.068774496 1502.57903
## Treatment_bisSmart:RegionLuxembourg 0.44695597 0.080586138 1503.01309
## Treatment_bisMixt_smart:RegionLuxembourg -0.15058163 0.080883405 1502.89824
## SexFemale:Time -0.06326390 0.011596056 1497.79215
## SexMale:Time -0.05270663 0.012351026 1499.65244
## Treatment_bisFull:Time 0.03069469 0.009462657 1495.29475
## Treatment_bisSmart:Time 0.08002726 0.013980137 1492.62092
## Treatment_bisMixt_smart:Time 0.03637843 0.011410995 1492.23637
## t value Pr(>|t|)
## (Intercept) -49.5009913 1.218434e-23
## log(Time + 1) 39.5108277 3.616177e-234
## Treatment_bisFull -1.3704943 1.707376e-01
## Treatment_bisSmart -3.8252307 1.385582e-04
## Treatment_bisMixt_smart -0.4700428 6.384915e-01
## SexMale -1.4677682 1.423766e-01
## RegionLuxembourg -2.2092337 4.436000e-02
## Treatment_bisFull:RegionLuxembourg -1.0642999 2.873639e-01
## Treatment_bisSmart:RegionLuxembourg 5.5463134 3.441909e-08
## Treatment_bisMixt_smart:RegionLuxembourg -1.8617123 6.283873e-02
## SexFemale:Time -5.4556395 5.701479e-08
## SexMale:Time -4.2673888 2.101638e-05
## Treatment_bisFull:Time 3.2437707 1.205630e-03
## Treatment_bisSmart:Time 5.7243548 1.252999e-08
## Treatment_bisMixt_smart:Time 3.1880152 1.462244e-03summary(lmer(log(Mass) ~ log(Time + 1) + Treatment + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment:Region + Sex:Time + Treatment:Time, data = Data_mass_AE))$coeff## boundary (singular) fit: see help('isSingular')## Estimate Std. Error df t value
## (Intercept) -4.46431856 0.086085787 25.09907 -51.8589504
## log(Time + 1) 1.95669407 0.049010482 1494.33051 39.9239916
## TreatmentFull -0.07952621 0.061506258 1503.89313 -1.2929776
## TreatmentSmart -0.09926120 0.062187684 1506.00280 -1.5961552
## SexMale -0.07870978 0.046117013 1505.05502 -1.7067406
## RegionLuxembourg -0.24038054 0.102776140 14.45272 -2.3388749
## TreatmentFull:RegionLuxembourg -0.06219461 0.070159896 1506.51870 -0.8864695
## TreatmentSmart:RegionLuxembourg 0.13865660 0.067594576 1508.16205 2.0512977
## SexFemale:Time -0.07240102 0.011770060 1502.03735 -6.1512875
## SexMale:Time -0.06146513 0.012535319 1503.37316 -4.9033561
## TreatmentFull:Time 0.03034798 0.009652753 1499.36338 3.1439713
## TreatmentSmart:Time 0.04009804 0.009987649 1499.69933 4.0147628
## Pr(>|t|)
## (Intercept) 4.716225e-27
## log(Time + 1) 7.975599e-238
## TreatmentFull 1.962174e-01
## TreatmentSmart 1.106639e-01
## SexMale 8.807655e-02
## RegionLuxembourg 3.417564e-02
## TreatmentFull:RegionLuxembourg 3.755061e-01
## TreatmentSmart:RegionLuxembourg 4.041037e-02
## SexFemale:Time 9.835797e-10
## SexMale:Time 1.044262e-06
## TreatmentFull:Time 1.699395e-03
## TreatmentSmart:Time 6.244627e-05Je continue avec treatment_bis
6.22.4 Résultats
Analyse des P-val
summary(lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time, data = Data_mass_AE))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Sex:Time + Treatment_bis:Time
## Data: Data_mass_AE
##
## REML criterion at convergence: 2363.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.7886 -0.6332 0.0249 0.6948 2.3466
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0260547 0.16141
## Site (Intercept) 0.0130938 0.11443
## Room (Intercept) 0.0006075 0.02465
## Residual 0.2556202 0.50559
## Number of obs: 1523, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -4.444e+00 8.977e-02 2.149e+01
## log(Time + 1) 1.913e+00 4.843e-02 1.490e+03
## Treatment_bisFull -8.259e-02 6.026e-02 1.501e+03
## Treatment_bisSmart -3.068e-01 8.022e-02 1.023e+03
## Treatment_bisMixt_smart -3.446e-02 7.332e-02 6.135e+02
## SexMale -6.647e-02 4.529e-02 1.501e+03
## RegionLuxembourg -2.351e-01 1.064e-01 1.397e+01
## Treatment_bisFull:RegionLuxembourg -7.320e-02 6.877e-02 1.503e+03
## Treatment_bisSmart:RegionLuxembourg 4.470e-01 8.059e-02 1.503e+03
## Treatment_bisMixt_smart:RegionLuxembourg -1.506e-01 8.088e-02 1.503e+03
## SexFemale:Time -6.326e-02 1.160e-02 1.498e+03
## SexMale:Time -5.271e-02 1.235e-02 1.500e+03
## Treatment_bisFull:Time 3.070e-02 9.463e-03 1.495e+03
## Treatment_bisSmart:Time 8.003e-02 1.398e-02 1.493e+03
## Treatment_bisMixt_smart:Time 3.638e-02 1.141e-02 1.492e+03
## t value Pr(>|t|)
## (Intercept) -49.501 < 2e-16 ***
## log(Time + 1) 39.511 < 2e-16 ***
## Treatment_bisFull -1.370 0.170738
## Treatment_bisSmart -3.825 0.000139 ***
## Treatment_bisMixt_smart -0.470 0.638491
## SexMale -1.468 0.142377
## RegionLuxembourg -2.209 0.044360 *
## Treatment_bisFull:RegionLuxembourg -1.064 0.287364
## Treatment_bisSmart:RegionLuxembourg 5.546 3.44e-08 ***
## Treatment_bisMixt_smart:RegionLuxembourg -1.862 0.062839 .
## SexFemale:Time -5.456 5.70e-08 ***
## SexMale:Time -4.267 2.10e-05 ***
## Treatment_bisFull:Time 3.244 0.001206 **
## Treatment_bisSmart:Time 5.724 1.25e-08 ***
## Treatment_bisMixt_smart:Time 3.188 0.001462 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 15 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need itsummary(lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time, data = Data_mass_AE_ref_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Sex:Time + Treatment_bis:Time
## Data: Data_mass_AE_ref_smart
##
## REML criterion at convergence: 2363.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.7886 -0.6332 0.0249 0.6948 2.3466
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0260547 0.16141
## Site (Intercept) 0.0130938 0.11443
## Room (Intercept) 0.0006075 0.02465
## Residual 0.2556202 0.50559
## Number of obs: 1523, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -4.75045 0.10164 33.33352
## log(Time + 1) 1.91334 0.04843 1490.12098
## Treatment_bisDark 0.30684 0.08022 1023.06235
## Treatment_bisFull 0.22425 0.08002 850.97112
## Treatment_bisMixt_smart 0.27238 0.09141 189.99750
## SexMale -0.06647 0.04529 1501.49311
## RegionLuxembourg 0.21189 0.11563 19.70058
## Treatment_bisDark:RegionLuxembourg -0.44696 0.08059 1503.01309
## Treatment_bisFull:RegionLuxembourg -0.52015 0.08065 1489.13361
## Treatment_bisMixt_smart:RegionLuxembourg -0.59754 0.09143 1501.35834
## SexFemale:Time 0.01676 0.01711 1493.63679
## SexMale:Time 0.02732 0.01801 1495.10793
## Treatment_bisDark:Time -0.08003 0.01398 1492.62092
## Treatment_bisFull:Time -0.04933 0.01429 1491.86546
## Treatment_bisMixt_smart:Time -0.04365 0.01548 1488.91049
## t value Pr(>|t|)
## (Intercept) -46.736 < 2e-16 ***
## log(Time + 1) 39.511 < 2e-16 ***
## Treatment_bisDark 3.825 0.000139 ***
## Treatment_bisFull 2.803 0.005184 **
## Treatment_bisMixt_smart 2.980 0.003261 **
## SexMale -1.468 0.142377
## RegionLuxembourg 1.833 0.082033 .
## Treatment_bisDark:RegionLuxembourg -5.546 3.44e-08 ***
## Treatment_bisFull:RegionLuxembourg -6.450 1.51e-10 ***
## Treatment_bisMixt_smart:RegionLuxembourg -6.535 8.67e-11 ***
## SexFemale:Time 0.980 0.327247
## SexMale:Time 1.517 0.129446
## Treatment_bisDark:Time -5.724 1.25e-08 ***
## Treatment_bisFull:Time -3.452 0.000572 ***
## Treatment_bisMixt_smart:Time -2.820 0.004864 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 15 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need itsummary(lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time, data = Data_mass_AE_ref_full))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Sex:Time + Treatment_bis:Time
## Data: Data_mass_AE_ref_full
##
## REML criterion at convergence: 2363.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.7886 -0.6332 0.0249 0.6948 2.3466
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0260547 0.16141
## Site (Intercept) 0.0130938 0.11443
## Room (Intercept) 0.0006075 0.02465
## Residual 0.2556202 0.50559
## Number of obs: 1523, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) -4.526e+00 9.046e-02 2.240e+01
## log(Time + 1) 1.913e+00 4.843e-02 1.490e+03
## Treatment_bisDark 8.259e-02 6.026e-02 1.501e+03
## Treatment_bisSmart -2.243e-01 8.002e-02 8.510e+02
## Treatment_bisMixt_smart 4.813e-02 7.220e-02 7.538e+02
## SexMale -6.647e-02 4.529e-02 1.501e+03
## RegionLuxembourg -3.083e-01 1.071e-01 1.469e+01
## Treatment_bisDark:RegionLuxembourg 7.320e-02 6.877e-02 1.503e+03
## Treatment_bisSmart:RegionLuxembourg 5.202e-01 8.065e-02 1.489e+03
## Treatment_bisMixt_smart:RegionLuxembourg -7.738e-02 7.914e-02 1.502e+03
## SexFemale:Time -3.257e-02 1.263e-02 1.494e+03
## SexMale:Time -2.201e-02 1.269e-02 1.496e+03
## Treatment_bisDark:Time -3.070e-02 9.463e-03 1.495e+03
## Treatment_bisSmart:Time 4.933e-02 1.429e-02 1.492e+03
## Treatment_bisMixt_smart:Time 5.684e-03 1.186e-02 1.491e+03
## t value Pr(>|t|)
## (Intercept) -50.037 < 2e-16 ***
## log(Time + 1) 39.511 < 2e-16 ***
## Treatment_bisDark 1.370 0.170738
## Treatment_bisSmart -2.803 0.005184 **
## Treatment_bisMixt_smart 0.667 0.505233
## SexMale -1.468 0.142377
## RegionLuxembourg -2.878 0.011685 *
## Treatment_bisDark:RegionLuxembourg 1.064 0.287364
## Treatment_bisSmart:RegionLuxembourg 6.450 1.51e-10 ***
## Treatment_bisMixt_smart:RegionLuxembourg -0.978 0.328333
## SexFemale:Time -2.580 0.009984 **
## SexMale:Time -1.735 0.082912 .
## Treatment_bisDark:Time -3.244 0.001206 **
## Treatment_bisSmart:Time 3.452 0.000572 ***
## Treatment_bisMixt_smart:Time 0.479 0.631777
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 15 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need itsummary(lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time, data = Data_mass_AE_ref_mixt_smart))## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 |
## Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region +
## Sex:Time + Treatment_bis:Time
## Data: Data_mass_AE_ref_mixt_smart
##
## REML criterion at convergence: 2363.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.7886 -0.6332 0.0249 0.6948 2.3466
##
## Random effects:
## Groups Name Variance Std.Dev.
## Mother (Intercept) 0.0260547 0.16141
## Site (Intercept) 0.0130938 0.11443
## Room (Intercept) 0.0006075 0.02465
## Residual 0.2556202 0.50559
## Number of obs: 1523, groups: Mother, 24; Site, 13; Room, 2
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) -4.478e+00 9.875e-02 2.933e+01 -45.345
## log(Time + 1) 1.913e+00 4.843e-02 1.490e+03 39.511
## Treatment_bisDark 3.446e-02 7.332e-02 6.135e+02 0.470
## Treatment_bisFull -4.813e-02 7.220e-02 7.538e+02 -0.667
## Treatment_bisSmart -2.724e-01 9.141e-02 1.900e+02 -2.980
## SexMale -6.647e-02 4.529e-02 1.501e+03 -1.468
## RegionLuxembourg -3.856e-01 1.154e-01 1.945e+01 -3.341
## Treatment_bisDark:RegionLuxembourg 1.506e-01 8.088e-02 1.503e+03 1.862
## Treatment_bisFull:RegionLuxembourg 7.738e-02 7.914e-02 1.502e+03 0.978
## Treatment_bisSmart:RegionLuxembourg 5.975e-01 9.143e-02 1.501e+03 6.535
## SexFemale:Time -2.688e-02 1.412e-02 1.493e+03 -1.904
## SexMale:Time -1.633e-02 1.497e-02 1.493e+03 -1.091
## Treatment_bisDark:Time -3.638e-02 1.141e-02 1.492e+03 -3.188
## Treatment_bisFull:Time -5.684e-03 1.186e-02 1.491e+03 -0.479
## Treatment_bisSmart:Time 4.365e-02 1.548e-02 1.489e+03 2.820
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## log(Time + 1) < 2e-16 ***
## Treatment_bisDark 0.63849
## Treatment_bisFull 0.50523
## Treatment_bisSmart 0.00326 **
## SexMale 0.14238
## RegionLuxembourg 0.00335 **
## Treatment_bisDark:RegionLuxembourg 0.06284 .
## Treatment_bisFull:RegionLuxembourg 0.32833
## Treatment_bisSmart:RegionLuxembourg 8.67e-11 ***
## SexFemale:Time 0.05706 .
## SexMale:Time 0.27566
## Treatment_bisDark:Time 0.00146 **
## Treatment_bisFull:Time 0.63178
## Treatment_bisSmart:Time 0.00486 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 15 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need ittest1 <- data.frame(Reference = "Dark", as.data.frame(( summary(lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time, data = Data_mass_AE))$coeff)[,]))
test2 <- data.frame(Reference = "Smart", as.data.frame(( summary(lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time, data = Data_mass_AE_ref_smart))$coeff)[,]))
test3 <- data.frame(Reference = "Full", as.data.frame(( summary(lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time, data = Data_mass_AE_ref_full))$coeff)[,]))
test4 <- data.frame(Reference = "Mixt_smart", as.data.frame(( summary(lmer(log(Mass) ~ log(Time + 1) + Treatment_bis + Sex + Region + (1 | Mother) + (1 | Site) + (1 | Room) + Treatment_bis:Region + Sex:Time + Treatment_bis:Time, data = Data_mass_AE_ref_mixt_smart))$coeff)[,]))
Results_Mass_by_time_AE <- rbind(test1,test2,test3,test4)
colnames(Results_Mass_by_time_AE ) <- c("Reference","Estimate", "Std. Error", "df", "t.value", "Pr(>|z|)")
write.csv2( Results_Mass_by_time_AE , file = "output/Results_Mass_by_time_AE.csv" )
kable(Results_Mass_by_time_AE , caption = " Poids en fonction du temps OP ", padding = 1 )| Reference | Estimate | Std. Error | df | t.value | Pr(>|z|) | |
|---|---|---|---|---|---|---|
| (Intercept) | Dark | -4.4436106 | 0.0897681 | 21.49434 | -49.5009913 | 0.0000000 |
| log(Time + 1) | Dark | 1.9133383 | 0.0484257 | 1490.12099 | 39.5108277 | 0.0000000 |
| Treatment_bisFull | Dark | -0.0825923 | 0.0602646 | 1500.63377 | -1.3704943 | 0.1707376 |
| Treatment_bisSmart | Dark | -0.3068431 | 0.0802156 | 1023.06236 | -3.8252307 | 0.0001386 |
| Treatment_bisMixt_smart | Dark | -0.0344637 | 0.0733204 | 613.46518 | -0.4700428 | 0.6384915 |
| SexMale | Dark | -0.0664722 | 0.0452879 | 1501.49311 | -1.4677682 | 0.1423766 |
| RegionLuxembourg | Dark | -0.2350641 | 0.1064007 | 13.97362 | -2.2092337 | 0.0443600 |
| Treatment_bisFull:RegionLuxembourg | Dark | -0.0731967 | 0.0687745 | 1502.57903 | -1.0642999 | 0.2873639 |
| Treatment_bisSmart:RegionLuxembourg | Dark | 0.4469560 | 0.0805861 | 1503.01309 | 5.5463134 | 0.0000000 |
| Treatment_bisMixt_smart:RegionLuxembourg | Dark | -0.1505816 | 0.0808834 | 1502.89824 | -1.8617123 | 0.0628387 |
| SexFemale:Time | Dark | -0.0632639 | 0.0115961 | 1497.79215 | -5.4556395 | 0.0000001 |
| SexMale:Time | Dark | -0.0527066 | 0.0123510 | 1499.65244 | -4.2673888 | 0.0000210 |
| Treatment_bisFull:Time | Dark | 0.0306947 | 0.0094627 | 1495.29475 | 3.2437707 | 0.0012056 |
| Treatment_bisSmart:Time | Dark | 0.0800273 | 0.0139801 | 1492.62092 | 5.7243548 | 0.0000000 |
| Treatment_bisMixt_smart:Time | Dark | 0.0363784 | 0.0114110 | 1492.23637 | 3.1880152 | 0.0014622 |
| (Intercept)1 | Smart | -4.7504537 | 0.1016436 | 33.33352 | -46.7363764 | 0.0000000 |
| log(Time + 1)1 | Smart | 1.9133383 | 0.0484257 | 1490.12098 | 39.5108277 | 0.0000000 |
| Treatment_bisDark | Smart | 0.3068431 | 0.0802156 | 1023.06235 | 3.8252307 | 0.0001386 |
| Treatment_bisFull1 | Smart | 0.2242508 | 0.0800151 | 850.97112 | 2.8026063 | 0.0051843 |
| Treatment_bisMixt_smart1 | Smart | 0.2723794 | 0.0914083 | 189.99750 | 2.9798107 | 0.0032611 |
| SexMale1 | Smart | -0.0664722 | 0.0452879 | 1501.49311 | -1.4677682 | 0.1423766 |
| RegionLuxembourg1 | Smart | 0.2118919 | 0.1156285 | 19.70058 | 1.8325234 | 0.0820334 |
| Treatment_bisDark:RegionLuxembourg | Smart | -0.4469560 | 0.0805861 | 1503.01309 | -5.5463134 | 0.0000000 |
| Treatment_bisFull:RegionLuxembourg1 | Smart | -0.5201527 | 0.0806479 | 1489.13361 | -6.4496726 | 0.0000000 |
| Treatment_bisMixt_smart:RegionLuxembourg1 | Smart | -0.5975376 | 0.0914316 | 1501.35834 | -6.5353503 | 0.0000000 |
| SexFemale:Time1 | Smart | 0.0167634 | 0.0171056 | 1493.63679 | 0.9799951 | 0.3272472 |
| SexMale:Time1 | Smart | 0.0273206 | 0.0180082 | 1495.10793 | 1.5171261 | 0.1294462 |
| Treatment_bisDark:Time | Smart | -0.0800273 | 0.0139801 | 1492.62092 | -5.7243548 | 0.0000000 |
| Treatment_bisFull:Time1 | Smart | -0.0493326 | 0.0142913 | 1491.86546 | -3.4519409 | 0.0005721 |
| Treatment_bisMixt_smart:Time1 | Smart | -0.0436488 | 0.0154777 | 1488.91049 | -2.8201069 | 0.0048644 |
| (Intercept)2 | Full | -4.5262029 | 0.0904563 | 22.39562 | -50.0374423 | 0.0000000 |
| log(Time + 1)2 | Full | 1.9133383 | 0.0484257 | 1490.12098 | 39.5108277 | 0.0000000 |
| Treatment_bisDark1 | Full | 0.0825923 | 0.0602646 | 1500.63377 | 1.3704943 | 0.1707376 |
| Treatment_bisSmart1 | Full | -0.2242508 | 0.0800151 | 850.97114 | -2.8026062 | 0.0051843 |
| Treatment_bisMixt_smart2 | Full | 0.0481286 | 0.0722003 | 753.82942 | 0.6665977 | 0.5052331 |
| SexMale2 | Full | -0.0664722 | 0.0452879 | 1501.49311 | -1.4677682 | 0.1423766 |
| RegionLuxembourg2 | Full | -0.3082608 | 0.1070983 | 14.68677 | -2.8782974 | 0.0116854 |
| Treatment_bisDark:RegionLuxembourg1 | Full | 0.0731967 | 0.0687745 | 1502.57903 | 1.0642999 | 0.2873639 |
| Treatment_bisSmart:RegionLuxembourg1 | Full | 0.5201527 | 0.0806479 | 1489.13361 | 6.4496726 | 0.0000000 |
| Treatment_bisMixt_smart:RegionLuxembourg2 | Full | -0.0773849 | 0.0791422 | 1501.52959 | -0.9777963 | 0.3283326 |
| SexFemale:Time2 | Full | -0.0325692 | 0.0126252 | 1493.70720 | -2.5796945 | 0.0099836 |
| SexMale:Time2 | Full | -0.0220119 | 0.0126856 | 1495.58449 | -1.7351963 | 0.0829120 |
| Treatment_bisDark:Time1 | Full | -0.0306947 | 0.0094627 | 1495.29475 | -3.2437707 | 0.0012056 |
| Treatment_bisSmart:Time1 | Full | 0.0493326 | 0.0142913 | 1491.86546 | 3.4519409 | 0.0005721 |
| Treatment_bisMixt_smart:Time2 | Full | 0.0056837 | 0.0118578 | 1491.37488 | 0.4793259 | 0.6317770 |
| (Intercept)3 | Mixt_smart | -4.4780743 | 0.0987552 | 29.32734 | -45.3452161 | 0.0000000 |
| log(Time + 1)3 | Mixt_smart | 1.9133383 | 0.0484257 | 1490.12099 | 39.5108277 | 0.0000000 |
| Treatment_bisDark2 | Mixt_smart | 0.0344637 | 0.0733204 | 613.46517 | 0.4700428 | 0.6384915 |
| Treatment_bisFull2 | Mixt_smart | -0.0481286 | 0.0722003 | 753.82940 | -0.6665977 | 0.5052331 |
| Treatment_bisSmart2 | Mixt_smart | -0.2723794 | 0.0914083 | 189.99750 | -2.9798107 | 0.0032611 |
| SexMale3 | Mixt_smart | -0.0664722 | 0.0452879 | 1501.49311 | -1.4677682 | 0.1423766 |
| RegionLuxembourg3 | Mixt_smart | -0.3856457 | 0.1154138 | 19.45421 | -3.3414188 | 0.0033459 |
| Treatment_bisDark:RegionLuxembourg2 | Mixt_smart | 0.1505816 | 0.0808834 | 1502.89824 | 1.8617123 | 0.0628387 |
| Treatment_bisFull:RegionLuxembourg2 | Mixt_smart | 0.0773849 | 0.0791422 | 1501.52959 | 0.9777963 | 0.3283326 |
| Treatment_bisSmart:RegionLuxembourg2 | Mixt_smart | 0.5975376 | 0.0914316 | 1501.35834 | 6.5353503 | 0.0000000 |
| SexFemale:Time3 | Mixt_smart | -0.0268855 | 0.0141181 | 1492.69888 | -1.9043201 | 0.0570606 |
| SexMale:Time3 | Mixt_smart | -0.0163282 | 0.0149730 | 1493.40299 | -1.0905120 | 0.2756636 |
| Treatment_bisDark:Time2 | Mixt_smart | -0.0363784 | 0.0114110 | 1492.23637 | -3.1880152 | 0.0014622 |
| Treatment_bisFull:Time2 | Mixt_smart | -0.0056837 | 0.0118578 | 1491.37488 | -0.4793259 | 0.6317770 |
| Treatment_bisSmart:Time2 | Mixt_smart | 0.0436488 | 0.0154777 | 1488.91049 | 2.8201069 | 0.0048644 |
Info_Mass_by_Time_AE <- "
Augmentation de la masse en fonction du temps
Smart est plus légere que n'importe quel autre traitement
Luxembourg est plus léger que Brabant pour les individus dans Dark
Luxembourg est plus léger que Brabant pour les individus dans Full
Par ordre d'optimisation du temps pour prendre de la masse croissant : Dark < Full & Mixt Smart < Smart
"
Info_Mass_by_Time_AE## [1] "\nAugmentation de la masse en fonction du temps\nSmart est plus légere que n'importe quel autre traitement\nLuxembourg est plus léger que Brabant pour les individus dans Dark\nLuxembourg est plus léger que Brabant pour les individus dans Full\nPar ordre d'optimisation du temps pour prendre de la masse croissant : Dark < Full & Mixt Smart < Smart\n"