R Markdown
library(knitr)
library(rmarkdown)
library(lattice)
library(permute)
library(ggplot2)
library(lme4)
## Loading required package: Matrix
library(MuMIn)
library(vegan)
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library(emmeans)
library(lmerTest)
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## lmer
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library(tibble)
library(plyr)
library(dplyr)
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## summarize
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library(readr)
library(janitor)
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library(pbkrtest)
library(tidyr)
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library(ggpubr)
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library(ggthemes)
library(stringr)
library(ggfortify)
library(tidyverse)
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library(car)
## Loading required package: carData
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Input and sort data
library(readr)
Behaviour_and_resp <- read_csv("C:/Users/jc819096/OneDrive - James Cook University/DATA/Lab 3/Behaviour data/Behaviour_and_resp_JMD2.csv")
## Rows: 544 Columns: 37
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (17): Maternal, Maternal_GF, Maternal_GM, Paternal, Paternal_GF, Paterna...
## dbl (20): Tank, Density, Female, Male, Age, Wet_weight, Weight, RMR, Mo2_res...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
View(Behaviour_and_resp)
Behaviour_and_resp <- Behaviour_and_resp %>%
unite(Temp:Control_CO2, col="Juv_treat", sep="_", remove=FALSE)
head(Behaviour_and_resp)
## # A tibble: 6 × 38
## Tank Density Female Male Maternal Maternal_GF Maternal_GM Paternal
## <dbl> <dbl> <dbl> <dbl> <chr> <chr> <chr> <chr>
## 1 100 18 132 9 DC D C CA
## 2 30 17 132 9 DC D C CA
## 3 113 14 75 9 AE A E CA
## 4 107 15 190 139 AE A E FA
## 5 32 17 190 139 AE A E FA
## 6 117 19 42 138 DA D A CA
## # ℹ 30 more variables: Paternal_GF <chr>, Paternal_GM <chr>,
## # Parental_treatment <chr>, DOM <chr>, DOT <chr>, DOD <chr>, Age <dbl>,
## # am_pm <chr>, Wet_weight <dbl>, Weight <dbl>, Juv_treat <chr>,
## # Control_CO2 <chr>, Temp <chr>, Chamber_ID <chr>, Parental_number <chr>,
## # RMR <dbl>, Mo2_rest <dbl>, MMR <dbl>, AS <dbl>, FS <dbl>, Mo2_max <dbl>,
## # Mo2_AS <dbl>, `Behaviour day` <chr>, Cam <dbl>, `Video ID` <chr>,
## # Time_emerge_s <dbl>, Time_emerge_min <dbl>, Bold <dbl>, Sum_score <dbl>, …
str(Behaviour_and_resp)
## tibble [544 × 38] (S3: tbl_df/tbl/data.frame)
## $ Tank : num [1:544] 100 30 113 107 32 117 39 167 113 75 ...
## $ Density : num [1:544] 18 17 14 15 17 19 16 3 14 17 ...
## $ Female : num [1:544] 132 132 75 190 190 42 190 185 75 190 ...
## $ Male : num [1:544] 9 9 9 139 139 138 197 190 9 139 ...
## $ Maternal : chr [1:544] "DC" "DC" "AE" "AE" ...
## $ Maternal_GF : chr [1:544] "D" "D" "A" "A" ...
## $ Maternal_GM : chr [1:544] "C" "C" "E" "E" ...
## $ Paternal : chr [1:544] "CA" "CA" "CA" "FA" ...
## $ Paternal_GF : chr [1:544] "C" "C" "C" "F" ...
## $ Paternal_GM : chr [1:544] "A" "A" "A" "A" ...
## $ Parental_treatment: chr [1:544] "HHHC" "HHHC" "HHHC" "CCCC" ...
## $ DOM : chr [1:544] "8/01/2022" "8/01/2022" "6/03/2022" "16/02/2022" ...
## $ DOT : chr [1:544] "6/05/2022" "6/05/2022" "2/07/2022" "27/06/2022" ...
## $ DOD : chr [1:544] "7/05/2022" "7/05/2022" "3/07/2022" "28/06/2022" ...
## $ Age : num [1:544] 119 119 119 132 121 130 104 129 119 131 ...
## $ am_pm : chr [1:544] "pm" "am" "pm" "pm" ...
## $ Wet_weight : num [1:544] 1.55 1.45 2.04 1.59 1.42 1.26 1.24 2.61 1.9 1.86 ...
## $ Weight : num [1:544] 0.00155 0.00145 0.00204 0.00159 0.00142 0.00126 0.00124 0.00261 0.0019 0.00186 ...
## $ Juv_treat : chr [1:544] "zero_control" "elevated_control" "zero_control" "zero_control" ...
## $ Control_CO2 : chr [1:544] "control" "control" "control" "control" ...
## $ Temp : chr [1:544] "zero" "elevated" "zero" "zero" ...
## $ Chamber_ID : chr [1:544] "A" "D" "D" "C" ...
## $ Parental_number : chr [1:544] "65" "65" "9b" "92b" ...
## $ RMR : num [1:544] 216 205 219 244 205 ...
## $ Mo2_rest : num [1:544] 0.34 0.3 0.45 0.39 0.29 0.21 0.31 0.44 0.32 0.33 ...
## $ MMR : num [1:544] 592 512 528 719 585 ...
## $ AS : num [1:544] 376 307 309 475 380 ...
## $ FS : num [1:544] 2.74 2.5 2.41 2.95 2.85 ...
## $ Mo2_max : num [1:544] 0.918 0.742 1.078 1.144 0.831 ...
## $ Mo2_AS : num [1:544] 0.58 0.45 0.63 0.76 0.54 0.82 0.54 2.12 0.84 0.68 ...
## $ Behaviour day : chr [1:544] "7/05/2022" "7/05/2022" "3/07/2022" "28/06/2022" ...
## $ Cam : num [1:544] 3 4 4 4 4 3 4 4 4 2 ...
## $ Video ID : chr [1:544] "4349" "4352" "4734" "4674" ...
## $ Time_emerge_s : num [1:544] 3 23 0 0 0 0 0 0 0 0 ...
## $ Time_emerge_min : num [1:544] 0.05 0.383 0 0 0 ...
## $ Bold : num [1:544] 4 4 1 1 1 1 1 2 2 2 ...
## $ Sum_score : num [1:544] 8 8 2 2 2 2 2 4 4 4 ...
## $ Sum_score_v2 : num [1:544] 5 5 2 2 2 2 2 3 3 3 ...
Behaviour_and_resp$Tank= factor (Behaviour_and_resp$Tank)
Behaviour_and_resp$Parental_number = factor (Behaviour_and_resp$Parental_number)
Behaviour_and_resp$Parental_treatment = factor (Behaviour_and_resp$Parental_treatment, levels=c("CCCC", "CCCH", "HHCC", "CCHC","HHHC"))
Behaviour_and_resp$Temp = factor (Behaviour_and_resp$Temp)
Behaviour_and_resp$Control_CO2 = factor (Behaviour_and_resp$Control_CO2)
Behaviour_and_resp$am_pm = factor (Behaviour_and_resp$am_pm)
str(Behaviour_and_resp)
## tibble [544 × 38] (S3: tbl_df/tbl/data.frame)
## $ Tank : Factor w/ 162 levels "1","2","3","4",..: 89 23 102 96 25 106 31 147 102 64 ...
## $ Density : num [1:544] 18 17 14 15 17 19 16 3 14 17 ...
## $ Female : num [1:544] 132 132 75 190 190 42 190 185 75 190 ...
## $ Male : num [1:544] 9 9 9 139 139 138 197 190 9 139 ...
## $ Maternal : chr [1:544] "DC" "DC" "AE" "AE" ...
## $ Maternal_GF : chr [1:544] "D" "D" "A" "A" ...
## $ Maternal_GM : chr [1:544] "C" "C" "E" "E" ...
## $ Paternal : chr [1:544] "CA" "CA" "CA" "FA" ...
## $ Paternal_GF : chr [1:544] "C" "C" "C" "F" ...
## $ Paternal_GM : chr [1:544] "A" "A" "A" "A" ...
## $ Parental_treatment: Factor w/ 5 levels "CCCC","CCCH",..: 5 5 5 1 2 3 1 2 5 1 ...
## $ DOM : chr [1:544] "8/01/2022" "8/01/2022" "6/03/2022" "16/02/2022" ...
## $ DOT : chr [1:544] "6/05/2022" "6/05/2022" "2/07/2022" "27/06/2022" ...
## $ DOD : chr [1:544] "7/05/2022" "7/05/2022" "3/07/2022" "28/06/2022" ...
## $ Age : num [1:544] 119 119 119 132 121 130 104 129 119 131 ...
## $ am_pm : Factor w/ 2 levels "am","pm": 2 1 2 2 1 2 2 2 2 1 ...
## $ Wet_weight : num [1:544] 1.55 1.45 2.04 1.59 1.42 1.26 1.24 2.61 1.9 1.86 ...
## $ Weight : num [1:544] 0.00155 0.00145 0.00204 0.00159 0.00142 0.00126 0.00124 0.00261 0.0019 0.00186 ...
## $ Juv_treat : chr [1:544] "zero_control" "elevated_control" "zero_control" "zero_control" ...
## $ Control_CO2 : Factor w/ 2 levels "CO","control": 2 2 2 2 2 1 2 2 2 1 ...
## $ Temp : Factor w/ 2 levels "elevated","zero": 2 1 2 2 1 1 2 1 2 2 ...
## $ Chamber_ID : chr [1:544] "A" "D" "D" "C" ...
## $ Parental_number : Factor w/ 24 levels "13","15","4",..: 8 8 24 20 6 14 19 21 24 20 ...
## $ RMR : num [1:544] 216 205 219 244 205 ...
## $ Mo2_rest : num [1:544] 0.34 0.3 0.45 0.39 0.29 0.21 0.31 0.44 0.32 0.33 ...
## $ MMR : num [1:544] 592 512 528 719 585 ...
## $ AS : num [1:544] 376 307 309 475 380 ...
## $ FS : num [1:544] 2.74 2.5 2.41 2.95 2.85 ...
## $ Mo2_max : num [1:544] 0.918 0.742 1.078 1.144 0.831 ...
## $ Mo2_AS : num [1:544] 0.58 0.45 0.63 0.76 0.54 0.82 0.54 2.12 0.84 0.68 ...
## $ Behaviour day : chr [1:544] "7/05/2022" "7/05/2022" "3/07/2022" "28/06/2022" ...
## $ Cam : num [1:544] 3 4 4 4 4 3 4 4 4 2 ...
## $ Video ID : chr [1:544] "4349" "4352" "4734" "4674" ...
## $ Time_emerge_s : num [1:544] 3 23 0 0 0 0 0 0 0 0 ...
## $ Time_emerge_min : num [1:544] 0.05 0.383 0 0 0 ...
## $ Bold : num [1:544] 4 4 1 1 1 1 1 2 2 2 ...
## $ Sum_score : num [1:544] 8 8 2 2 2 2 2 4 4 4 ...
## $ Sum_score_v2 : num [1:544] 5 5 2 2 2 2 2 3 3 3 ...
Behaviour_and_resp$Juv_treat = factor (Behaviour_and_resp$Juv_treat, levels=c("zero_control", "elevated_control", "zero_CO", "elevated_CO"))
head(Behaviour_and_resp)
## # A tibble: 6 × 38
## Tank Density Female Male Maternal Maternal_GF Maternal_GM Paternal
## <fct> <dbl> <dbl> <dbl> <chr> <chr> <chr> <chr>
## 1 100 18 132 9 DC D C CA
## 2 30 17 132 9 DC D C CA
## 3 113 14 75 9 AE A E CA
## 4 107 15 190 139 AE A E FA
## 5 32 17 190 139 AE A E FA
## 6 117 19 42 138 DA D A CA
## # ℹ 30 more variables: Paternal_GF <chr>, Paternal_GM <chr>,
## # Parental_treatment <fct>, DOM <chr>, DOT <chr>, DOD <chr>, Age <dbl>,
## # am_pm <fct>, Wet_weight <dbl>, Weight <dbl>, Juv_treat <fct>,
## # Control_CO2 <fct>, Temp <fct>, Chamber_ID <chr>, Parental_number <fct>,
## # RMR <dbl>, Mo2_rest <dbl>, MMR <dbl>, AS <dbl>, FS <dbl>, Mo2_max <dbl>,
## # Mo2_AS <dbl>, `Behaviour day` <chr>, Cam <dbl>, `Video ID` <chr>,
## # Time_emerge_s <dbl>, Time_emerge_min <dbl>, Bold <dbl>, Sum_score <dbl>, …
Exploring raw data
ggplot(data=Behaviour_and_resp, aes(x=Bold, color=Parental_treatment, fill= Parental_treatment)) +
geom_density(aes(y=..density..), position="identity", alpha=0.5) + theme_classic() + facet_wrap(~Juv_treat)
## Warning: The dot-dot notation (`..density..`) was deprecated in ggplot2 3.4.0.
## ℹ Please use `after_stat(density)` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
ggplot(Behaviour_and_resp, aes(x=Bold, y=AS, colour=Parental_treatment)) + geom_point() + theme_classic() + geom_smooth(method = lm, se=FALSE) + facet_wrap(~Juv_treat)
## `geom_smooth()` using formula = 'y ~ x'
ggplot(Behaviour_and_resp, aes(x=Bold, y=RMR, colour=Parental_treatment)) + geom_point() + theme_classic() + geom_smooth(method = lm, se=FALSE)+ facet_wrap(~Juv_treat)
## `geom_smooth()` using formula = 'y ~ x'
Raw data checks
qqPlot(Behaviour_and_resp$Bold)
## [1] 3 4
qqPlot(Behaviour_and_resp$RMR)
## [1] 288 345
qqPlot(Behaviour_and_resp$AS)
## [1] 73 189
RMR model
ggplot(Behaviour_and_resp, aes(x=Bold, y=RMR, colour=Parental_treatment)) + theme_classic() + geom_smooth(method = lm) + facet_grid(~Juv_treat)
## `geom_smooth()` using formula = 'y ~ x'
lmer.bold.RMR= lmer(RMR ~ Parental_treatment * Temp * Control_CO2 * Bold + (1 | Parental_number) + (1 | Chamber_ID), data = Behaviour_and_resp)
model analysis
summary(lmer.bold.RMR)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## RMR ~ Parental_treatment * Temp * Control_CO2 * Bold + (1 | Parental_number) +
## (1 | Chamber_ID)
## Data: Behaviour_and_resp
##
## REML criterion at convergence: 5262.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.54804 -0.65217 0.04187 0.63304 2.52837
##
## Random effects:
## Groups Name Variance Std.Dev.
## Parental_number (Intercept) 54.57 7.387
## Chamber_ID (Intercept) 137.53 11.727
## Residual 1479.91 38.470
## Number of obs: 544, groups: Parental_number, 24; Chamber_ID, 4
##
## Fixed effects:
## Estimate Std. Error
## (Intercept) 142.081 30.617
## Parental_treatmentCCCH 107.809 38.996
## Parental_treatmentHHCC 72.567 36.899
## Parental_treatmentCCHC 67.899 37.840
## Parental_treatmentHHHC 66.338 40.799
## Tempzero 60.797 40.129
## Control_CO2control 134.417 37.646
## Bold 24.609 8.524
## Parental_treatmentCCCH:Tempzero -67.120 52.163
## Parental_treatmentHHCC:Tempzero -45.192 55.006
## Parental_treatmentCCHC:Tempzero -56.797 51.283
## Parental_treatmentHHHC:Tempzero -81.870 53.866
## Parental_treatmentCCCH:Control_CO2control -170.907 49.886
## Parental_treatmentHHCC:Control_CO2control -107.978 51.786
## Parental_treatmentCCHC:Control_CO2control -104.169 47.598
## Parental_treatmentHHHC:Control_CO2control -115.172 54.386
## Tempzero:Control_CO2control -69.479 51.168
## Parental_treatmentCCCH:Bold -32.974 10.855
## Parental_treatmentHHCC:Bold -19.223 10.375
## Parental_treatmentCCHC:Bold -26.142 10.636
## Parental_treatmentHHHC:Bold -16.307 11.616
## Tempzero:Bold -17.287 11.741
## Control_CO2control:Bold -37.477 10.911
## Parental_treatmentCCCH:Tempzero:Control_CO2control 112.552 67.100
## Parental_treatmentHHCC:Tempzero:Control_CO2control 63.157 73.070
## Parental_treatmentCCHC:Tempzero:Control_CO2control 58.871 66.640
## Parental_treatmentHHHC:Tempzero:Control_CO2control 92.268 71.515
## Parental_treatmentCCCH:Tempzero:Bold 19.428 15.270
## Parental_treatmentHHCC:Tempzero:Bold 10.007 15.901
## Parental_treatmentCCHC:Tempzero:Bold 22.528 14.943
## Parental_treatmentHHHC:Tempzero:Bold 24.906 16.167
## Parental_treatmentCCCH:Control_CO2control:Bold 47.456 14.242
## Parental_treatmentHHCC:Control_CO2control:Bold 30.993 14.516
## Parental_treatmentCCHC:Control_CO2control:Bold 33.714 13.719
## Parental_treatmentHHHC:Control_CO2control:Bold 34.452 15.922
## Tempzero:Control_CO2control:Bold 19.970 15.407
## Parental_treatmentCCCH:Tempzero:Control_CO2control:Bold -28.702 20.200
## Parental_treatmentHHCC:Tempzero:Control_CO2control:Bold -15.886 21.350
## Parental_treatmentCCHC:Tempzero:Control_CO2control:Bold -20.911 19.876
## Parental_treatmentHHHC:Tempzero:Control_CO2control:Bold -34.449 21.703
## df t value
## (Intercept) 388.018 4.641
## Parental_treatmentCCCH 452.129 2.765
## Parental_treatmentHHCC 463.359 1.967
## Parental_treatmentCCHC 471.124 1.794
## Parental_treatmentHHHC 458.386 1.626
## Tempzero 488.733 1.515
## Control_CO2control 499.923 3.571
## Bold 485.507 2.887
## Parental_treatmentCCCH:Tempzero 492.715 -1.287
## Parental_treatmentHHCC:Tempzero 501.289 -0.822
## Parental_treatmentCCHC:Tempzero 500.007 -1.108
## Parental_treatmentHHHC:Tempzero 501.055 -1.520
## Parental_treatmentCCCH:Control_CO2control 499.909 -3.426
## Parental_treatmentHHCC:Control_CO2control 500.904 -2.085
## Parental_treatmentCCHC:Control_CO2control 500.597 -2.189
## Parental_treatmentHHHC:Control_CO2control 489.309 -2.118
## Tempzero:Control_CO2control 500.809 -1.358
## Parental_treatmentCCCH:Bold 483.988 -3.038
## Parental_treatmentHHCC:Bold 496.412 -1.853
## Parental_treatmentCCHC:Bold 496.137 -2.458
## Parental_treatmentHHHC:Bold 493.583 -1.404
## Tempzero:Bold 495.024 -1.472
## Control_CO2control:Bold 494.698 -3.435
## Parental_treatmentCCCH:Tempzero:Control_CO2control 500.979 1.677
## Parental_treatmentHHCC:Tempzero:Control_CO2control 500.876 0.864
## Parental_treatmentCCHC:Tempzero:Control_CO2control 500.993 0.883
## Parental_treatmentHHHC:Tempzero:Control_CO2control 500.681 1.290
## Parental_treatmentCCCH:Tempzero:Bold 499.343 1.272
## Parental_treatmentHHCC:Tempzero:Bold 501.301 0.629
## Parental_treatmentCCHC:Tempzero:Bold 500.859 1.508
## Parental_treatmentHHHC:Tempzero:Bold 500.378 1.541
## Parental_treatmentCCCH:Control_CO2control:Bold 495.855 3.332
## Parental_treatmentHHCC:Control_CO2control:Bold 499.404 2.135
## Parental_treatmentCCHC:Control_CO2control:Bold 501.342 2.457
## Parental_treatmentHHHC:Control_CO2control:Bold 478.402 2.164
## Tempzero:Control_CO2control:Bold 500.968 1.296
## Parental_treatmentCCCH:Tempzero:Control_CO2control:Bold 501.158 -1.421
## Parental_treatmentHHCC:Tempzero:Control_CO2control:Bold 500.987 -0.744
## Parental_treatmentCCHC:Tempzero:Control_CO2control:Bold 500.730 -1.052
## Parental_treatmentHHHC:Tempzero:Control_CO2control:Bold 500.095 -1.587
## Pr(>|t|)
## (Intercept) 4.76e-06 ***
## Parental_treatmentCCCH 0.005932 **
## Parental_treatmentHHCC 0.049823 *
## Parental_treatmentCCHC 0.073392 .
## Parental_treatmentHHHC 0.104642
## Tempzero 0.130410
## Control_CO2control 0.000391 ***
## Bold 0.004064 **
## Parental_treatmentCCCH:Tempzero 0.198787
## Parental_treatmentHHCC:Tempzero 0.411713
## Parental_treatmentCCHC:Tempzero 0.268605
## Parental_treatmentHHHC:Tempzero 0.129173
## Parental_treatmentCCCH:Control_CO2control 0.000663 ***
## Parental_treatmentHHCC:Control_CO2control 0.037569 *
## Parental_treatmentCCHC:Control_CO2control 0.029094 *
## Parental_treatmentHHHC:Control_CO2control 0.034708 *
## Tempzero:Control_CO2control 0.175118
## Parental_treatmentCCCH:Bold 0.002513 **
## Parental_treatmentHHCC:Bold 0.064496 .
## Parental_treatmentCCHC:Bold 0.014315 *
## Parental_treatmentHHHC:Bold 0.160989
## Tempzero:Bold 0.141557
## Control_CO2control:Bold 0.000643 ***
## Parental_treatmentCCCH:Tempzero:Control_CO2control 0.094092 .
## Parental_treatmentHHCC:Tempzero:Control_CO2control 0.387822
## Parental_treatmentCCHC:Tempzero:Control_CO2control 0.377435
## Parental_treatmentHHHC:Tempzero:Control_CO2control 0.197580
## Parental_treatmentCCCH:Tempzero:Bold 0.203874
## Parental_treatmentHHCC:Tempzero:Bold 0.529425
## Parental_treatmentCCHC:Tempzero:Bold 0.132299
## Parental_treatmentHHHC:Tempzero:Bold 0.124059
## Parental_treatmentCCCH:Control_CO2control:Bold 0.000926 ***
## Parental_treatmentHHCC:Control_CO2control:Bold 0.033240 *
## Parental_treatmentCCHC:Control_CO2control:Bold 0.014334 *
## Parental_treatmentHHHC:Control_CO2control:Bold 0.030972 *
## Tempzero:Control_CO2control:Bold 0.195510
## Parental_treatmentCCCH:Tempzero:Control_CO2control:Bold 0.155970
## Parental_treatmentHHCC:Tempzero:Control_CO2control:Bold 0.457186
## Parental_treatmentCCHC:Tempzero:Control_CO2control:Bold 0.293275
## Parental_treatmentHHHC:Tempzero:Control_CO2control:Bold 0.113082
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation matrix not shown by default, as p = 40 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it
Anova(lmer.bold.RMR)
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: RMR
## Chisq Df Pr(>Chisq)
## Parental_treatment 4.3914 4 0.35562
## Temp 0.4341 1 0.51000
## Control_CO2 4.7936 1 0.02857 *
## Bold 0.0239 1 0.87725
## Parental_treatment:Temp 5.7365 4 0.21971
## Parental_treatment:Control_CO2 1.9469 4 0.74552
## Temp:Control_CO2 0.1826 1 0.66916
## Parental_treatment:Bold 4.4520 4 0.34828
## Temp:Bold 0.1969 1 0.65725
## Control_CO2:Bold 4.8343 1 0.02790 *
## Parental_treatment:Temp:Control_CO2 3.8510 4 0.42654
## Parental_treatment:Temp:Bold 1.5869 4 0.81114
## Parental_treatment:Control_CO2:Bold 11.3979 4 0.02244 *
## Temp:Control_CO2:Bold 0.0114 1 0.91509
## Parental_treatment:Temp:Control_CO2:Bold 3.0958 4 0.54192
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
post model checks
performance::check_model(lmer.bold.RMR, check="homogeneity")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
performance::check_model(lmer.bold.RMR, check="outliers")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
performance::check_model(lmer.bold.RMR, check="qq")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
performance::check_model(lmer.bold.RMR, check="normality")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
performance::check_model(lmer.bold.RMR, check="linearity")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
performance::check_model(lmer.bold.RMR, check="pp_check")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
plot(lmer.bold.RMR)
hist(residuals(lmer.bold.RMR), col="darkgray")
shapiro.test(residuals(lmer.bold.RMR))
##
## Shapiro-Wilk normality test
##
## data: residuals(lmer.bold.RMR)
## W = 0.99531, p-value = 0.09984
qqnorm(resid(lmer.bold.RMR))
qqline(resid(lmer.bold.RMR))
library(sjPlot)
## Install package "strengejacke" from GitHub (`devtools::install_github("strengejacke/strengejacke")`) to load all sj-packages at once!
plot_model(lmer.bold.RMR, type = "diag")
## Warning in checkMatrixPackageVersion(): Package version inconsistency detected.
## TMB was built with Matrix version 1.5.3
## Current Matrix version is 1.5.4
## Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
## [[1]]
## `geom_smooth()` using formula = 'y ~ x'
##
## [[2]]
## [[2]]$Parental_number
## `geom_smooth()` using formula = 'y ~ x'
##
## [[2]]$Chamber_ID
## `geom_smooth()` using formula = 'y ~ x'
##
##
## [[3]]
##
## [[4]]
## `geom_smooth()` using formula = 'y ~ x'
outlierTest(lmer.bold.RMR)
## No Studentized residuals with Bonferroni p < 0.05
## Largest |rstudent|:
## rstudent unadjusted p-value Bonferroni p
## 506 2.706483 0.0070325 NA
library(DHARMa)
## This is DHARMa 0.4.6. For overview type '?DHARMa'. For recent changes, type news(package = 'DHARMa')
plot(simulateResiduals(lmer.bold.RMR))
emmeans(lmer.bold.RMR, pairwise ~ Control_CO2, adjust="tukey")
## NOTE: Results may be misleading due to involvement in interactions
## $emmeans
## Control_CO2 emmean SE df lower.CL upper.CL
## CO 225 6.55 3.96 207 244
## control 232 6.51 3.86 214 250
##
## Results are averaged over the levels of: Parental_treatment, Temp
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## CO - control -6.86 3.45 491 -1.988 0.0473
##
## Results are averaged over the levels of: Parental_treatment, Temp
## Degrees-of-freedom method: kenward-roger
plot(emmeans(lmer.bold.RMR, pairwise ~ Control_CO2, adjust="tukey"))
## NOTE: Results may be misleading due to involvement in interactions
emmeans(lmer.bold.RMR, pairwise ~ Parental_treatment * Control_CO2, adjust="tukey")
## NOTE: Results may be misleading due to involvement in interactions
## $emmeans
## Parental_treatment Control_CO2 emmean SE df lower.CL upper.CL
## CCCC CO 223 8.73 11.6 204 242
## CCCH CO 224 8.76 11.8 204 243
## HHCC CO 228 8.49 10.4 209 247
## CCHC CO 215 8.73 11.7 196 235
## HHHC CO 236 9.13 13.4 217 256
## CCCC control 236 8.41 10.0 217 254
## CCCH control 226 8.64 11.2 207 245
## HHCC control 237 8.49 10.4 218 256
## CCHC control 227 8.34 9.7 208 246
## HHHC control 234 9.20 13.6 215 254
##
## Results are averaged over the levels of: Temp
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## CCCC CO - CCCH CO -0.577 9.17 49.8 -0.063 1.0000
## CCCC CO - HHCC CO -4.934 8.92 44.6 -0.553 0.9999
## CCCC CO - CCHC CO 7.621 9.15 49.4 0.833 0.9976
## CCCC CO - HHHC CO -13.197 9.53 46.6 -1.385 0.9259
## CCCC CO - CCCC control -12.604 7.47 486.8 -1.686 0.8029
## CCCC CO - CCCH control -3.402 9.07 47.3 -0.375 1.0000
## CCCC CO - HHCC control -14.144 8.92 44.5 -1.586 0.8478
## CCCC CO - CCHC control -3.915 8.77 42.3 -0.446 1.0000
## CCCC CO - HHHC control -11.327 9.60 45.5 -1.180 0.9718
## CCCH CO - HHCC CO -4.357 8.94 45.4 -0.487 1.0000
## CCCH CO - CCHC CO 8.197 9.17 50.4 0.894 0.9960
## CCCH CO - HHHC CO -12.621 9.55 47.3 -1.322 0.9435
## CCCH CO - CCCC control -12.027 8.87 44.1 -1.356 0.9340
## CCCH CO - CCCH control -2.825 7.80 492.3 -0.362 1.0000
## CCCH CO - HHCC control -13.568 8.94 45.4 -1.517 0.8783
## CCCH CO - CCHC control -3.339 8.79 43.1 -0.380 1.0000
## CCCH CO - HHHC control -10.751 9.61 46.1 -1.118 0.9802
## HHCC CO - CCHC CO 12.554 8.92 45.1 1.408 0.9185
## HHCC CO - HHHC CO -8.264 9.31 42.7 -0.888 0.9961
## HHCC CO - CCCC control -7.670 8.61 39.2 -0.891 0.9959
## HHCC CO - CCCH control 1.532 8.84 43.1 0.173 1.0000
## HHCC CO - HHCC control -9.211 7.29 490.1 -1.263 0.9612
## HHCC CO - CCHC control 1.018 8.53 38.2 0.119 1.0000
## HHCC CO - HHHC control -6.394 9.37 41.7 -0.682 0.9995
## CCHC CO - HHHC CO -20.818 9.53 47.1 -2.184 0.4812
## CCHC CO - CCCC control -20.225 8.85 43.8 -2.286 0.4176
## CCHC CO - CCCH control -11.022 9.07 48.0 -1.216 0.9662
## CCHC CO - HHCC control -21.765 8.92 45.1 -2.441 0.3274
## CCHC CO - CCHC control -11.536 7.41 485.3 -1.557 0.8677
## CCHC CO - HHHC control -18.948 9.59 45.9 -1.975 0.6198
## HHHC CO - CCCC control 0.594 9.25 41.8 0.064 1.0000
## HHHC CO - CCCH control 9.796 9.46 45.4 1.036 0.9883
## HHHC CO - HHCC control -0.947 9.31 42.8 -0.102 1.0000
## HHHC CO - CCHC control 9.282 9.18 40.9 1.011 0.9899
## HHHC CO - HHHC control 1.870 8.46 495.2 0.221 1.0000
## CCCC control - CCCH control 9.202 8.76 41.8 1.051 0.9868
## CCCC control - HHCC control -1.540 8.60 39.1 -0.179 1.0000
## CCCC control - CCHC control 8.689 8.45 36.8 1.029 0.9884
## CCCC control - HHHC control 1.277 9.30 40.6 0.137 1.0000
## CCCH control - HHCC control -10.743 8.83 43.0 -1.216 0.9656
## CCCH control - CCHC control -0.514 8.68 40.8 -0.059 1.0000
## CCCH control - HHHC control -7.926 9.52 44.2 -0.833 0.9976
## HHCC control - CCHC control 10.229 8.53 38.1 1.200 0.9679
## HHCC control - HHHC control 2.817 9.37 41.7 0.301 1.0000
## CCHC control - HHHC control -7.412 9.23 39.6 -0.803 0.9981
##
## Results are averaged over the levels of: Temp
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 10 estimates
plot(emmeans(lmer.bold.RMR, pairwise ~ Parental_treatment * Control_CO2, adjust="tukey"))
## NOTE: Results may be misleading due to involvement in interactions
emmeans(lmer.bold.RMR, pairwise ~ Parental_treatment * Temp * Control_CO2, adjust="tukey")
## NOTE: Results may be misleading due to involvement in interactions
## $emmeans
## Parental_treatment Temp Control_CO2 emmean SE df lower.CL upper.CL
## CCCC elevated CO 220 10.58 24.5 198 242
## CCCH elevated CO 223 10.37 22.9 202 245
## HHCC elevated CO 232 9.82 18.6 211 252
## CCHC elevated CO 205 10.46 23.7 184 227
## HHHC elevated CO 235 10.69 24.9 213 257
## CCCC zero CO 226 10.14 21.0 205 247
## CCCH zero CO 224 10.49 23.6 202 246
## HHCC zero CO 224 10.03 20.1 203 245
## CCHC zero CO 226 10.27 22.0 204 247
## HHHC zero CO 238 11.12 29.2 215 261
## CCCC elevated control 236 9.76 18.1 215 256
## CCCH elevated control 219 10.53 24.3 197 240
## HHCC elevated control 238 10.43 23.3 216 259
## CCHC elevated control 223 9.67 17.5 203 244
## HHHC elevated control 244 11.37 30.9 221 268
## CCCC zero control 236 9.84 18.7 215 256
## CCCH zero control 234 9.86 18.8 214 255
## HHCC zero control 237 9.41 15.7 217 257
## CCHC zero control 230 9.67 17.5 210 251
## HHHC zero control 224 10.56 23.7 203 246
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio
## CCCC elevated CO - CCCH elevated CO -3.3702 12.26 134.9 -0.275
## CCCC elevated CO - HHCC elevated CO -11.6818 11.82 119.0 -0.989
## CCCC elevated CO - CCHC elevated CO 14.8986 12.34 136.4 1.207
## CCCC elevated CO - HHHC elevated CO -14.6901 12.53 119.3 -1.172
## CCCC elevated CO - CCCC zero CO -6.0444 11.15 498.2 -0.542
## CCCC elevated CO - CCCH zero CO -3.8273 12.37 128.6 -0.309
## CCCC elevated CO - HHCC zero CO -4.2299 11.99 123.3 -0.353
## CCCC elevated CO - CCHC zero CO -5.7012 12.19 129.6 -0.468
## CCCC elevated CO - HHHC zero CO -17.7491 12.92 132.4 -1.374
## CCCC elevated CO - CCCC elevated control -15.7180 10.73 489.9 -1.465
## CCCC elevated CO - CCCH elevated control 1.5128 12.41 136.3 0.122
## CCCC elevated CO - HHCC elevated control -17.5856 12.32 132.9 -1.427
## CCCC elevated CO - CCHC elevated control -3.4313 11.68 114.7 -0.294
## CCCC elevated CO - HHHC elevated control -24.3551 13.12 128.2 -1.856
## CCCC elevated CO - CCCC zero control -15.5341 10.80 489.9 -1.439
## CCCC elevated CO - CCCH zero control -14.3604 11.85 118.4 -1.212
## CCCC elevated CO - HHCC zero control -16.7473 11.48 108.5 -1.459
## CCCC elevated CO - CCHC zero control -10.4436 11.68 115.4 -0.894
## CCCC elevated CO - HHHC zero control -4.3439 12.43 115.7 -0.349
## CCCH elevated CO - HHCC elevated CO -8.3116 11.62 119.8 -0.715
## CCCH elevated CO - CCHC elevated CO 18.2687 12.15 137.8 1.504
## CCCH elevated CO - HHHC elevated CO -11.3200 12.36 120.3 -0.916
## CCCH elevated CO - CCCC zero CO -2.6742 11.90 128.5 -0.225
## CCCH elevated CO - CCCH zero CO -0.4571 11.31 500.8 -0.040
## CCCH elevated CO - HHCC zero CO -0.8598 11.79 124.2 -0.073
## CCCH elevated CO - CCHC zero CO -2.3311 12.01 131.2 -0.194
## CCCH elevated CO - HHHC zero CO -14.3790 12.74 133.3 -1.129
## CCCH elevated CO - CCCC elevated control -12.3478 11.56 117.6 -1.068
## CCCH elevated CO - CCCH elevated control 4.8829 11.32 493.8 0.431
## CCCH elevated CO - HHCC elevated control -14.2155 12.12 134.2 -1.172
## CCCH elevated CO - CCHC elevated control -0.0612 11.48 115.3 -0.005
## CCCH elevated CO - HHHC elevated control -20.9849 12.93 128.9 -1.622
## CCCH elevated CO - CCCC zero control -12.1639 11.63 118.7 -1.046
## CCCH elevated CO - CCCH zero control -10.9902 10.69 490.3 -1.028
## CCCH elevated CO - HHCC zero control -13.3772 11.29 109.2 -1.185
## CCCH elevated CO - CCHC zero control -7.0734 11.49 116.1 -0.616
## CCCH elevated CO - HHHC zero control -0.9738 12.25 116.2 -0.080
## HHCC elevated CO - CCHC elevated CO 26.5803 11.71 121.4 2.270
## HHCC elevated CO - HHHC elevated CO -3.0083 11.90 105.5 -0.253
## HHCC elevated CO - CCCC zero CO 5.6374 11.42 111.5 0.494
## HHCC elevated CO - CCCH zero CO 7.8545 11.73 113.6 0.670
## HHCC elevated CO - HHCC zero CO 7.4519 10.29 485.9 0.724
## HHCC elevated CO - CCHC zero CO 5.9805 11.54 114.2 0.518
## HHCC elevated CO - HHHC zero CO -6.0674 12.29 118.0 -0.494
## HHCC elevated CO - CCCC elevated control -4.0362 11.09 101.5 -0.364
## HHCC elevated CO - CCCH elevated control 13.1945 11.78 121.5 1.120
## HHCC elevated CO - HHCC elevated control -5.9039 10.70 491.1 -0.552
## HHCC elevated CO - CCHC elevated control 8.2505 11.01 99.4 0.749
## HHCC elevated CO - HHHC elevated control -12.6733 12.52 115.3 -1.012
## HHCC elevated CO - CCCC zero control -3.8523 11.17 102.8 -0.345
## HHCC elevated CO - CCCH zero control -2.6786 11.18 102.8 -0.240
## HHCC elevated CO - HHCC zero control -5.0655 9.71 485.6 -0.522
## HHCC elevated CO - CCHC zero control 1.2382 11.01 100.0 0.112
## HHCC elevated CO - HHHC zero control 7.3378 11.79 101.8 0.622
## CCHC elevated CO - HHHC elevated CO -29.5887 12.43 121.6 -2.380
## CCHC elevated CO - CCCC zero CO -20.9429 11.98 130.1 -1.748
## CCHC elevated CO - CCCH zero CO -18.7258 12.26 131.2 -1.527
## CCHC elevated CO - HHCC zero CO -19.1285 11.88 125.9 -1.610
## CCHC elevated CO - CCHC zero CO -20.5998 11.17 493.8 -1.845
## CCHC elevated CO - HHHC zero CO -32.6477 12.82 134.7 -2.547
## CCHC elevated CO - CCCC elevated control -30.6165 11.65 119.4 -2.628
## CCHC elevated CO - CCCH elevated control -13.3858 12.31 139.6 -1.087
## CCHC elevated CO - HHCC elevated control -32.4842 12.21 135.8 -2.661
## CCHC elevated CO - CCHC elevated control -18.3299 10.57 486.5 -1.734
## CCHC elevated CO - HHHC elevated control -39.2536 13.01 130.4 -3.017
## CCHC elevated CO - CCCC zero control -30.4326 11.72 120.5 -2.596
## CCHC elevated CO - CCCH zero control -29.2589 11.75 121.2 -2.490
## CCHC elevated CO - HHCC zero control -31.6458 11.38 111.0 -2.780
## CCHC elevated CO - CCHC zero control -25.3421 10.59 486.9 -2.393
## CCHC elevated CO - HHHC zero control -19.2425 12.33 117.8 -1.560
## HHHC elevated CO - CCCC zero CO 8.6457 12.17 113.1 0.710
## HHHC elevated CO - CCCH zero CO 10.8628 12.45 114.8 0.872
## HHHC elevated CO - HHCC zero CO 10.4602 12.09 109.8 0.865
## HHHC elevated CO - CCHC zero CO 8.9889 12.28 115.4 0.732
## HHHC elevated CO - HHHC zero CO -3.0590 11.92 490.9 -0.257
## HHHC elevated CO - CCCC elevated control -1.0279 11.86 104.1 -0.087
## HHHC elevated CO - CCCH elevated control 16.2029 12.51 121.8 1.296
## HHHC elevated CO - HHCC elevated control -2.8955 12.42 118.8 -0.233
## HHHC elevated CO - CCHC elevated control 11.2588 11.78 102.1 0.956
## HHHC elevated CO - HHHC elevated control -9.6650 12.08 494.8 -0.800
## HHHC elevated CO - CCCC zero control -0.8440 11.93 105.2 -0.071
## HHHC elevated CO - CCCH zero control 0.3297 11.94 105.3 0.028
## HHHC elevated CO - HHCC zero control -2.0572 11.58 96.3 -0.178
## HHHC elevated CO - CCHC zero control 4.2466 11.79 102.8 0.360
## HHHC elevated CO - HHHC zero control 10.3462 11.37 487.2 0.910
## CCCC zero CO - CCCH zero CO 2.2171 12.00 122.1 0.185
## CCCC zero CO - HHCC zero CO 1.8145 11.61 116.3 0.156
## CCCC zero CO - CCHC zero CO 0.3431 11.81 122.5 0.029
## CCCC zero CO - HHHC zero CO -11.7048 12.56 126.0 -0.932
## CCCC zero CO - CCCC elevated control -9.6736 10.37 490.4 -0.933
## CCCC zero CO - CCCH elevated control 7.5571 12.04 129.9 0.628
## CCCC zero CO - HHCC elevated control -11.5413 11.96 126.7 -0.965
## CCCC zero CO - CCHC elevated control 2.6131 11.30 107.9 0.231
## CCCC zero CO - HHHC elevated control -18.3107 12.78 122.7 -1.433
## CCCC zero CO - CCCC zero control -9.4897 10.46 492.9 -0.908
## CCCC zero CO - CCCH zero control -8.3160 11.45 111.0 -0.726
## CCCC zero CO - HHCC zero control -10.7029 11.07 100.8 -0.967
## CCCC zero CO - CCHC zero control -4.3992 11.29 108.3 -0.389
## CCCC zero CO - HHHC zero control 1.7004 12.06 109.3 0.141
## CCCH zero CO - HHCC zero CO -0.4026 11.91 118.3 -0.034
## CCCH zero CO - CCHC zero CO -1.8740 12.11 124.6 -0.155
## CCCH zero CO - HHHC zero CO -13.9219 12.83 127.2 -1.085
## CCCH zero CO - CCCC elevated control -11.8907 11.68 112.2 -1.018
## CCCH zero CO - CCCH elevated control 5.3400 11.40 499.1 0.468
## CCCH zero CO - HHCC elevated control -13.7584 12.24 128.0 -1.124
## CCCH zero CO - CCHC elevated control 0.3960 11.60 110.0 0.034
## CCCH zero CO - HHHC elevated control -20.5278 13.04 123.9 -1.574
## CCCH zero CO - CCCC zero control -11.7068 11.75 113.3 -0.996
## CCCH zero CO - CCCH zero control -10.5331 10.78 498.4 -0.977
## CCCH zero CO - HHCC zero control -12.9200 11.40 103.8 -1.133
## CCCH zero CO - CCHC zero control -6.6163 11.61 110.8 -0.570
## CCCH zero CO - HHHC zero control -0.5167 12.36 111.4 -0.042
## HHCC zero CO - CCHC zero CO -1.4713 11.72 118.9 -0.126
## HHCC zero CO - HHHC zero CO -13.5192 12.47 122.5 -1.084
## HHCC zero CO - CCCC elevated control -11.4881 11.27 105.9 -1.019
## HHCC zero CO - CCCH elevated control 5.7427 11.95 125.9 0.481
## HHCC zero CO - HHCC elevated control -13.3557 10.85 488.2 -1.231
## HHCC zero CO - CCHC elevated control 0.7986 11.19 103.8 0.071
## HHCC zero CO - HHHC elevated control -20.1252 12.68 118.9 -1.587
## HHCC zero CO - CCCC zero control -11.3042 11.34 107.0 -0.997
## HHCC zero CO - CCCH zero control -10.1305 11.37 107.4 -0.891
## HHCC zero CO - HHCC zero control -12.5174 9.94 490.1 -1.259
## HHCC zero CO - CCHC zero control -6.2137 11.19 104.3 -0.555
## HHCC zero CO - HHHC zero control -0.1140 11.97 105.8 -0.010
## CCHC zero CO - HHHC zero CO -12.0479 12.67 128.4 -0.951
## CCHC zero CO - CCCC elevated control -10.0167 11.49 112.4 -0.872
## CCHC zero CO - CCCH elevated control 7.2140 12.15 132.4 0.594
## CCHC zero CO - HHCC elevated control -11.8844 12.07 129.3 -0.985
## CCHC zero CO - CCHC elevated control 2.2699 10.40 488.1 0.218
## CCHC zero CO - HHHC elevated control -18.6538 12.88 125.0 -1.448
## CCHC zero CO - CCCC zero control -9.8329 11.56 113.6 -0.851
## CCHC zero CO - CCCH zero control -8.6592 11.57 113.5 -0.748
## CCHC zero CO - HHCC zero control -11.0461 11.19 103.4 -0.987
## CCHC zero CO - CCHC zero control -4.7423 10.40 488.5 -0.456
## CCHC zero CO - HHHC zero control 1.3573 12.17 111.6 0.112
## HHHC zero CO - CCCC elevated control 2.0312 12.26 116.8 0.166
## HHHC zero CO - CCCH elevated control 19.2619 12.89 134.9 1.495
## HHHC zero CO - HHCC elevated control 0.1635 12.80 131.7 0.013
## HHHC zero CO - CCHC elevated control 14.3178 12.18 114.9 1.175
## HHHC zero CO - HHHC elevated control -6.6059 12.50 497.9 -0.529
## HHHC zero CO - CCCC zero control 2.2150 12.33 118.0 0.180
## HHHC zero CO - CCCH zero control 3.3888 12.34 118.1 0.275
## HHHC zero CO - HHCC zero control 1.0018 11.99 108.8 0.084
## HHHC zero CO - CCHC zero control 7.3056 12.19 115.6 0.599
## HHHC zero CO - HHHC zero control 13.4052 11.81 491.5 1.135
## CCCC elevated control - CCCH elevated control 17.2307 11.71 119.4 1.471
## CCCC elevated control - HHCC elevated control -1.8677 11.62 116.0 -0.161
## CCCC elevated control - CCHC elevated control 12.2867 10.94 97.3 1.123
## CCCC elevated control - HHHC elevated control -8.6371 12.47 113.4 -0.693
## CCCC elevated control - CCCC zero control 0.1839 10.05 487.1 0.018
## CCCC elevated control - CCCH zero control 1.3576 11.12 101.0 0.122
## CCCC elevated control - HHCC zero control -1.0293 10.73 90.9 -0.096
## CCCC elevated control - CCHC zero control 5.2744 10.94 97.7 0.482
## CCCC elevated control - HHHC zero control 11.3740 11.74 100.1 0.969
## CCCH elevated control - HHCC elevated control -19.0984 12.28 136.0 -1.555
## CCCH elevated control - CCHC elevated control -4.9441 11.64 117.3 -0.425
## CCCH elevated control - HHHC elevated control -25.8678 13.09 130.6 -1.977
## CCCH elevated control - CCCC zero control -17.0469 11.78 120.4 -1.447
## CCCH elevated control - CCCH zero control -15.8731 10.84 493.9 -1.465
## CCCH elevated control - HHCC zero control -18.2601 11.43 110.7 -1.597
## CCCH elevated control - CCHC zero control -11.9563 11.64 117.8 -1.028
## CCCH elevated control - HHHC zero control -5.8567 12.39 117.8 -0.473
## HHCC elevated control - CCHC elevated control 14.1543 11.54 113.7 1.227
## HHCC elevated control - HHHC elevated control -6.7694 12.99 127.3 -0.521
## HHCC elevated control - CCCC zero control 2.0515 11.69 117.0 0.176
## HHCC elevated control - CCCH zero control 3.2253 11.72 117.7 0.275
## HHCC elevated control - HHCC zero control 0.8384 10.32 489.5 0.081
## HHCC elevated control - CCHC zero control 7.1421 11.54 114.5 0.619
## HHCC elevated control - HHHC zero control 13.2417 12.30 114.8 1.076
## CCHC elevated control - HHHC elevated control -20.9238 12.39 111.4 -1.689
## CCHC elevated control - CCCC zero control -12.1028 11.02 98.4 -1.099
## CCHC elevated control - CCCH zero control -10.9291 11.05 99.2 -0.989
## CCHC elevated control - HHCC zero control -13.3160 10.66 89.1 -1.250
## CCHC elevated control - CCHC zero control -7.0122 9.79 482.8 -0.716
## CCHC elevated control - HHHC zero control -0.9126 11.66 98.2 -0.078
## HHHC elevated control - CCCC zero control 8.8210 12.53 114.3 0.704
## HHHC elevated control - CCCH zero control 9.9947 12.57 115.1 0.795
## HHHC elevated control - HHCC zero control 7.6078 12.22 106.4 0.623
## HHHC elevated control - CCHC zero control 13.9115 12.40 112.1 1.122
## HHHC elevated control - HHHC zero control 20.0111 11.94 492.6 1.675
## CCCC zero control - CCCH zero control 1.1737 11.19 102.2 0.105
## CCCC zero control - HHCC zero control -1.2132 10.80 92.2 -0.112
## CCCC zero control - CCHC zero control 5.0906 11.01 98.8 0.462
## CCCC zero control - HHHC zero control 11.1902 11.81 101.1 0.948
## CCCH zero control - HHCC zero control -2.3869 10.82 92.1 -0.221
## CCCH zero control - CCHC zero control 3.9168 11.04 99.3 0.355
## CCCH zero control - HHHC zero control 10.0165 11.83 101.5 0.847
## HHCC zero control - CCHC zero control 6.3037 10.64 89.2 0.592
## HHCC zero control - HHHC zero control 12.4034 11.46 92.5 1.083
## CCHC zero control - HHHC zero control 6.0996 11.66 98.6 0.523
## p.value
## 1.0000
## 1.0000
## 0.9996
## 0.9998
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9980
## 0.9961
## 1.0000
## 0.9967
## 1.0000
## 0.9449
## 0.9969
## 0.9996
## 0.9955
## 1.0000
## 1.0000
## 1.0000
## 0.9939
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9999
## 0.9999
## 1.0000
## 0.9998
## 1.0000
## 0.9855
## 1.0000
## 1.0000
## 0.9997
## 1.0000
## 1.0000
## 0.7504
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9999
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.6747
## 0.9687
## 0.9926
## 0.9866
## 0.9516
## 0.5502
## 0.4910
## 0.9999
## 0.4657
## 0.9736
## 0.2392
## 0.5140
## 0.5937
## 0.3835
## 0.6665
## 0.9904
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9990
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9965
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9999
## 1.0000
## 1.0000
## 0.9999
## 1.0000
## 0.9895
## 1.0000
## 1.0000
## 0.9998
## 1.0000
## 1.0000
## 1.0000
## 0.9999
## 1.0000
## 1.0000
## 0.9996
## 1.0000
## 0.9884
## 1.0000
## 1.0000
## 0.9995
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9960
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9943
## 1.0000
## 0.9997
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9999
## 0.9952
## 1.0000
## 0.9999
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9910
## 1.0000
## 0.9059
## 0.9960
## 0.9961
## 0.9874
## 1.0000
## 1.0000
## 0.9995
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9999
## 0.9773
## 0.9999
## 1.0000
## 0.9993
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9999
## 0.9817
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9999
## 1.0000
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 20 estimates
plot(emmeans(lmer.bold.RMR, pairwise ~ Parental_treatment * Temp * Control_CO2, adjust="tukey"))
## NOTE: Results may be misleading due to involvement in interactions
BoldRMR = (emmeans(lmer.bold.RMR, ~ Parental_treatment * Temp * Control_CO2) %>% as.data.frame)
## NOTE: Results may be misleading due to involvement in interactions
BoldRMR
## Parental_treatment Temp Control_CO2 emmean SE df lower.CL
## CCCC elevated CO 220.0250 10.577903 24.49 198.2163
## CCCH elevated CO 223.3951 10.365983 22.95 201.9488
## HHCC elevated CO 231.7067 9.820583 18.55 211.1183
## CCHC elevated CO 205.1264 10.464084 23.74 183.5171
## HHHC elevated CO 234.7151 10.685283 24.91 212.7042
## CCCC zero CO 226.0693 10.137488 21.00 204.9872
## CCCH zero CO 223.8522 10.490055 23.57 202.1811
## HHCC zero CO 224.2549 10.033039 20.12 203.3341
## CCHC zero CO 225.7262 10.267284 22.01 204.4340
## HHHC zero CO 237.7741 11.124755 29.16 215.0270
## CCCC elevated control 235.7429 9.758533 18.10 215.2488
## CCCH elevated control 218.5122 10.530972 24.26 196.7895
## HHCC elevated control 237.6106 10.433221 23.34 216.0454
## CCHC elevated control 223.4563 9.672716 17.47 203.0905
## HHHC elevated control 244.3800 11.368758 30.91 221.1905
## CCCC zero control 235.5591 9.841118 18.66 214.9356
## CCCH zero control 234.3853 9.859564 18.78 213.7330
## HHCC zero control 236.7723 9.411743 15.72 216.7908
## CCHC zero control 230.4685 9.667406 17.47 210.1141
## HHHC zero control 224.3689 10.555604 23.74 202.5708
## upper.CL
## 241.8337
## 244.8414
## 252.2951
## 226.7358
## 256.7260
## 247.1515
## 245.5233
## 245.1756
## 247.0184
## 260.5212
## 256.2371
## 240.2349
## 259.1759
## 243.8220
## 267.5696
## 256.1825
## 255.0377
## 256.7537
## 250.8229
## 246.1670
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
plot data
BoldRMR = (emmeans(lmer.bold.RMR, ~ Parental_treatment * Temp * Control_CO2) %>% as.data.frame)
## NOTE: Results may be misleading due to involvement in interactions
BoldRMR
## Parental_treatment Temp Control_CO2 emmean SE df lower.CL
## CCCC elevated CO 220.0250 10.577903 24.49 198.2163
## CCCH elevated CO 223.3951 10.365983 22.95 201.9488
## HHCC elevated CO 231.7067 9.820583 18.55 211.1183
## CCHC elevated CO 205.1264 10.464084 23.74 183.5171
## HHHC elevated CO 234.7151 10.685283 24.91 212.7042
## CCCC zero CO 226.0693 10.137488 21.00 204.9872
## CCCH zero CO 223.8522 10.490055 23.57 202.1811
## HHCC zero CO 224.2549 10.033039 20.12 203.3341
## CCHC zero CO 225.7262 10.267284 22.01 204.4340
## HHHC zero CO 237.7741 11.124755 29.16 215.0270
## CCCC elevated control 235.7429 9.758533 18.10 215.2488
## CCCH elevated control 218.5122 10.530972 24.26 196.7895
## HHCC elevated control 237.6106 10.433221 23.34 216.0454
## CCHC elevated control 223.4563 9.672716 17.47 203.0905
## HHHC elevated control 244.3800 11.368758 30.91 221.1905
## CCCC zero control 235.5591 9.841118 18.66 214.9356
## CCCH zero control 234.3853 9.859564 18.78 213.7330
## HHCC zero control 236.7723 9.411743 15.72 216.7908
## CCHC zero control 230.4685 9.667406 17.47 210.1141
## HHHC zero control 224.3689 10.555604 23.74 202.5708
## upper.CL
## 241.8337
## 244.8414
## 252.2951
## 226.7358
## 256.7260
## 247.1515
## 245.5233
## 245.1756
## 247.0184
## 260.5212
## 256.2371
## 240.2349
## 259.1759
## 243.8220
## 267.5696
## 256.1825
## 255.0377
## 256.7537
## 250.8229
## 246.1670
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
library(broom.mixed)
ab <- augment(lmer.bold.RMR)
ab
## # A tibble: 544 × 18
## RMR Parental_treatment Temp Control_CO2 Bold Parental_number Chamber_ID
## <dbl> <fct> <fct> <fct> <dbl> <fct> <fct>
## 1 216. HHHC zero control 4 65 A
## 2 205. HHHC elevat… control 4 65 D
## 3 219. HHHC zero control 1 9b D
## 4 244. CCCC zero control 1 92b C
## 5 205. CCCH elevat… control 1 5 B
## 6 170. HHCC elevat… CO 1 81 A
## 7 251. CCCC zero control 1 92 C
## 8 168. CCCH elevat… control 2 94 A
## 9 168. HHHC zero control 2 9b B
## 10 175. CCCC zero CO 2 92b C
## # ℹ 534 more rows
## # ℹ 11 more variables: .fitted <dbl>, .resid <dbl>, .hat <dbl>, .cooksd <dbl>,
## # .fixed <dbl>, .mu <dbl>, .offset <dbl>, .sqrtXwt <dbl>, .sqrtrwt <dbl>,
## # .weights <dbl>, .wtres <dbl>
ggplot(ab, aes(x=Bold, y=.fitted)) + geom_jitter(aes (x=Bold, y=.fitted),height = .2, width = .2, alpha=0.3) + theme_classic() + geom_smooth(method = lm, se=TRUE) + theme(text = element_text(size=20))
## `geom_smooth()` using formula = 'y ~ x'
graph.1 <- ggplot(ab, aes(x=Bold, y=.fitted, colour=Control_CO2, fill= Control_CO2)) + geom_jitter(aes (x=Bold, y=.fitted, colour = Control_CO2),height = .2, width = .2, alpha=0.3) + theme_classic() + geom_smooth(method = lm, se=TRUE) + stat_regline_equation(label.y= c(300, 280), label.x= (c(1))) + stat_cor(aes(label = paste(..rr.label.., ..p.label.., sep = "~`,`~")), label.y= c(300, 280), label.x= (c(2.5))) + scale_color_manual(values=c("control" = "black", "CO" = "tan")) + scale_fill_manual(values=c("control" = "black", "CO" = "tan")) + theme(text = element_text(size=20))
graph.2 <- ggplot(ab, aes(x=Bold, y=RMR, colour= Control_CO2, fill= Control_CO2)) + geom_jitter(aes (, colour= Control_CO2),height = .2, width = .2, alpha=0.3) + theme_classic() + geom_smooth(method = lm, se=TRUE) + facet_grid(~Parental_treatment) + scale_color_manual(values=c("control" = "black", "CO" = "tan")) + scale_fill_manual(values=c("control" = "black", "CO" = "tan")) + theme(text = element_text(size=20))
graph.1
## `geom_smooth()` using formula = 'y ~ x'
graph.2
## `geom_smooth()` using formula = 'y ~ x'
ggsave("RMRxbold_temp.eps", graph.1, height = 6, width = 10, dpi = 320)
## `geom_smooth()` using formula = 'y ~ x'
## Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size):
## semi-transparency is not supported on this device: reported only once per page
ggsave("RMRxbold_temp.2.eps", graph.2, height = 6, width = 10, dpi = 320)
## `geom_smooth()` using formula = 'y ~ x'
## Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size):
## semi-transparency is not supported on this device: reported only once per page
ggsave("RMRxbold_temp.png", graph.1, height = 6, width = 10, dpi = 320)
## `geom_smooth()` using formula = 'y ~ x'
ggsave("RMRxbold_temp.2.png", graph.2, height = 6, width = 10, dpi = 320)
## `geom_smooth()` using formula = 'y ~ x'
AS model
ggplot(Behaviour_and_resp, aes(x=Bold, y=AS, colour=Parental_treatment)) + theme_classic() + geom_smooth(method = lm) + facet_grid(~Juv_treat)
## `geom_smooth()` using formula = 'y ~ x'
lmer.bold.AS = lmer(AS ~ Parental_treatment * Temp * Control_CO2 * Bold + (1 | Parental_number) + (1 | Chamber_ID), data = Behaviour_and_resp)
model analysis
summary(lmer.bold.AS)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## AS ~ Parental_treatment * Temp * Control_CO2 * Bold + (1 | Parental_number) +
## (1 | Chamber_ID)
## Data: Behaviour_and_resp
##
## REML criterion at convergence: 6453.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.07859 -0.66859 -0.08868 0.58651 2.89525
##
## Random effects:
## Groups Name Variance Std.Dev.
## Parental_number (Intercept) 607.5 24.65
## Chamber_ID (Intercept) 4854.4 69.67
## Residual 15622.7 124.99
## Number of obs: 544, groups: Parental_number, 24; Chamber_ID, 4
##
## Fixed effects:
## Estimate Std. Error
## (Intercept) 721.05 103.78
## Parental_treatmentCCCH -189.08 126.85
## Parental_treatmentHHCC -192.03 120.02
## Parental_treatmentCCHC -160.15 123.08
## Parental_treatmentHHHC -249.90 132.73
## Tempzero -373.27 130.49
## Control_CO2control -312.68 122.41
## Bold -63.85 27.72
## Parental_treatmentCCCH:Tempzero 221.24 169.61
## Parental_treatmentHHCC:Tempzero 357.57 178.83
## Parental_treatmentCCHC:Tempzero 292.42 166.71
## Parental_treatmentHHHC:Tempzero 333.35 175.10
## Parental_treatmentCCCH:Control_CO2control 203.98 162.21
## Parental_treatmentHHCC:Control_CO2control 462.56 168.35
## Parental_treatmentCCHC:Control_CO2control 202.96 154.72
## Parental_treatmentHHHC:Control_CO2control 402.91 176.87
## Tempzero:Control_CO2control 379.24 166.33
## Parental_treatmentCCCH:Bold 44.32 35.30
## Parental_treatmentHHCC:Bold 42.77 33.73
## Parental_treatmentCCHC:Bold 35.37 34.58
## Parental_treatmentHHHC:Bold 49.66 37.77
## Tempzero:Bold 85.41 38.17
## Control_CO2control:Bold 66.14 35.49
## Parental_treatmentCCCH:Tempzero:Control_CO2control -159.64 218.14
## Parental_treatmentHHCC:Tempzero:Control_CO2control -676.38 237.55
## Parental_treatmentCCHC:Tempzero:Control_CO2control -346.56 216.61
## Parental_treatmentHHHC:Tempzero:Control_CO2control -486.51 232.45
## Parental_treatmentCCCH:Tempzero:Bold -48.82 49.65
## Parental_treatmentHHCC:Tempzero:Bold -86.54 51.69
## Parental_treatmentCCHC:Tempzero:Bold -61.45 48.58
## Parental_treatmentHHHC:Tempzero:Bold -72.15 52.55
## Parental_treatmentCCCH:Control_CO2control:Bold -38.97 46.32
## Parental_treatmentHHCC:Control_CO2control:Bold -104.00 47.19
## Parental_treatmentCCHC:Control_CO2control:Bold -42.30 44.60
## Parental_treatmentHHHC:Control_CO2control:Bold -63.35 51.79
## Tempzero:Control_CO2control:Bold -89.49 50.08
## Parental_treatmentCCCH:Tempzero:Control_CO2control:Bold 36.49 65.67
## Parental_treatmentHHCC:Tempzero:Control_CO2control:Bold 174.09 69.41
## Parental_treatmentCCHC:Tempzero:Control_CO2control:Bold 74.86 64.60
## Parental_treatmentHHHC:Tempzero:Control_CO2control:Bold 84.49 70.54
## df t value
## (Intercept) 161.74 6.948
## Parental_treatmentCCCH 456.41 -1.491
## Parental_treatmentHHCC 466.47 -1.600
## Parental_treatmentCCHC 473.45 -1.301
## Parental_treatmentHHHC 461.82 -1.883
## Tempzero 490.65 -2.861
## Control_CO2control 499.85 -2.554
## Bold 487.78 -2.303
## Parental_treatmentCCCH:Tempzero 493.95 1.304
## Parental_treatmentHHCC:Tempzero 501.06 1.999
## Parental_treatmentCCHC:Tempzero 500.25 1.754
## Parental_treatmentHHHC:Tempzero 501.01 1.904
## Parental_treatmentCCCH:Control_CO2control 499.88 1.258
## Parental_treatmentHHCC:Control_CO2control 500.88 2.748
## Parental_treatmentCCHC:Control_CO2control 500.37 1.312
## Parental_treatmentHHHC:Control_CO2control 490.86 2.278
## Tempzero:Control_CO2control 500.86 2.280
## Parental_treatmentCCCH:Bold 486.40 1.255
## Parental_treatmentHHCC:Bold 497.21 1.268
## Parental_treatmentCCHC:Bold 496.82 1.023
## Parental_treatmentHHHC:Bold 494.50 1.315
## Tempzero:Bold 496.07 2.237
## Control_CO2control:Bold 495.40 1.864
## Parental_treatmentCCCH:Tempzero:Control_CO2control 500.91 -0.732
## Parental_treatmentHHCC:Tempzero:Control_CO2control 500.83 -2.847
## Parental_treatmentCCHC:Tempzero:Control_CO2control 500.94 -1.600
## Parental_treatmentHHHC:Tempzero:Control_CO2control 500.62 -2.093
## Parental_treatmentCCCH:Tempzero:Bold 499.60 -0.983
## Parental_treatmentHHCC:Tempzero:Bold 501.04 -1.674
## Parental_treatmentCCHC:Tempzero:Bold 500.92 -1.265
## Parental_treatmentHHHC:Tempzero:Bold 500.29 -1.373
## Parental_treatmentCCCH:Control_CO2control:Bold 496.38 -0.841
## Parental_treatmentHHCC:Control_CO2control:Bold 499.68 -2.204
## Parental_treatmentCCHC:Control_CO2control:Bold 501.11 -0.948
## Parental_treatmentHHHC:Control_CO2control:Bold 481.24 -1.223
## Tempzero:Control_CO2control:Bold 500.97 -1.787
## Parental_treatmentCCCH:Tempzero:Control_CO2control:Bold 501.05 0.556
## Parental_treatmentHHCC:Tempzero:Control_CO2control:Bold 500.95 2.508
## Parental_treatmentCCHC:Tempzero:Control_CO2control:Bold 500.66 1.159
## Parental_treatmentHHHC:Tempzero:Control_CO2control:Bold 500.02 1.198
## Pr(>|t|)
## (Intercept) 8.6e-11 ***
## Parental_treatmentCCCH 0.13677
## Parental_treatmentHHCC 0.11029
## Parental_treatmentCCHC 0.19381
## Parental_treatmentHHHC 0.06036 .
## Tempzero 0.00441 **
## Control_CO2control 0.01094 *
## Bold 0.02169 *
## Parental_treatmentCCCH:Tempzero 0.19271
## Parental_treatmentHHCC:Tempzero 0.04610 *
## Parental_treatmentCCHC:Tempzero 0.08004 .
## Parental_treatmentHHHC:Tempzero 0.05751 .
## Parental_treatmentCCCH:Control_CO2control 0.20916
## Parental_treatmentHHCC:Control_CO2control 0.00622 **
## Parental_treatmentCCHC:Control_CO2control 0.19022
## Parental_treatmentHHHC:Control_CO2control 0.02315 *
## Tempzero:Control_CO2control 0.02303 *
## Parental_treatmentCCCH:Bold 0.20993
## Parental_treatmentHHCC:Bold 0.20540
## Parental_treatmentCCHC:Bold 0.30699
## Parental_treatmentHHHC:Bold 0.18926
## Tempzero:Bold 0.02570 *
## Control_CO2control:Bold 0.06293 .
## Parental_treatmentCCCH:Tempzero:Control_CO2control 0.46462
## Parental_treatmentHHCC:Tempzero:Control_CO2control 0.00459 **
## Parental_treatmentCCHC:Tempzero:Control_CO2control 0.11025
## Parental_treatmentHHHC:Tempzero:Control_CO2control 0.03686 *
## Parental_treatmentCCCH:Tempzero:Bold 0.32589
## Parental_treatmentHHCC:Tempzero:Bold 0.09475 .
## Parental_treatmentCCHC:Tempzero:Bold 0.20643
## Parental_treatmentHHHC:Tempzero:Bold 0.17036
## Parental_treatmentCCCH:Control_CO2control:Bold 0.40054
## Parental_treatmentHHCC:Control_CO2control:Bold 0.02801 *
## Parental_treatmentCCHC:Control_CO2control:Bold 0.34336
## Parental_treatmentHHHC:Control_CO2control:Bold 0.22184
## Tempzero:Control_CO2control:Bold 0.07456 .
## Parental_treatmentCCCH:Tempzero:Control_CO2control:Bold 0.57862
## Parental_treatmentHHCC:Tempzero:Control_CO2control:Bold 0.01245 *
## Parental_treatmentCCHC:Tempzero:Control_CO2control:Bold 0.24714
## Parental_treatmentHHHC:Tempzero:Control_CO2control:Bold 0.23160
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation matrix not shown by default, as p = 40 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it
Anova(lmer.bold.AS)
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: AS
## Chisq Df Pr(>Chisq)
## Parental_treatment 1.0702 4 0.898963
## Temp 6.7119 1 0.009577 **
## Control_CO2 0.5300 1 0.466606
## Bold 2.4494 1 0.117570
## Parental_treatment:Temp 2.9648 4 0.563731
## Parental_treatment:Control_CO2 8.2652 4 0.082333 .
## Temp:Control_CO2 0.0454 1 0.831244
## Parental_treatment:Bold 0.6814 4 0.953599
## Temp:Bold 4.2750 1 0.038677 *
## Control_CO2:Bold 0.5978 1 0.439432
## Parental_treatment:Temp:Control_CO2 10.1758 4 0.037569 *
## Parental_treatment:Temp:Bold 1.8354 4 0.765999
## Parental_treatment:Control_CO2:Bold 0.8542 4 0.931038
## Temp:Control_CO2:Bold 0.6545 1 0.418494
## Parental_treatment:Temp:Control_CO2:Bold 7.3474 4 0.118632
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
post model checks
performance::check_model(lmer.bold.AS, check="homogeneity")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
performance::check_model(lmer.bold.AS, check="outliers")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
performance::check_model(lmer.bold.AS, check="qq")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
performance::check_model(lmer.bold.AS, check="normality")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
performance::check_model(lmer.bold.AS, check="linearity")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
performance::check_model(lmer.bold.AS, check="pp_check")
## Model has interaction terms. VIFs might be inflated.
## You may check multicollinearity among predictors of a model without
## interaction terms.
plot(lmer.bold.AS)
hist(residuals(lmer.bold.AS), col="darkgray")
shapiro.test(residuals(lmer.bold.AS))
##
## Shapiro-Wilk normality test
##
## data: residuals(lmer.bold.AS)
## W = 0.98574, p-value = 3.638e-05
qqnorm(resid(lmer.bold.AS))
qqline(resid(lmer.bold.AS))
library(sjPlot)
plot_model(lmer.bold.AS, type = "diag")
## [[1]]
## `geom_smooth()` using formula = 'y ~ x'
##
## [[2]]
## [[2]]$Parental_number
## `geom_smooth()` using formula = 'y ~ x'
##
## [[2]]$Chamber_ID
## `geom_smooth()` using formula = 'y ~ x'
##
##
## [[3]]
##
## [[4]]
## `geom_smooth()` using formula = 'y ~ x'
outlierTest(lmer.bold.AS)
## No Studentized residuals with Bonferroni p < 0.05
## Largest |rstudent|:
## rstudent unadjusted p-value Bonferroni p
## 189 3.057359 0.0023525 NA
library(DHARMa)
plot(simulateResiduals(lmer.bold.AS))
emmeans(lmer.bold.AS, pairwise ~ Temp, adjust="tukey")
## NOTE: Results may be misleading due to involvement in interactions
## $emmeans
## Temp emmean SE df lower.CL upper.CL
## elevated 467 36.1 3.30 357 576
## zero 432 36.0 3.27 323 542
##
## Results are averaged over the levels of: Parental_treatment, Control_CO2
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## elevated - zero 34 11.2 492 3.034 0.0025
##
## Results are averaged over the levels of: Parental_treatment, Control_CO2
## Degrees-of-freedom method: kenward-roger
plot(emmeans(lmer.bold.AS, pairwise ~ Temp, adjust="tukey"))
## NOTE: Results may be misleading due to involvement in interactions
emmeans(lmer.bold.AS, pairwise ~ Parental_treatment * Temp * Control_CO2, adjust="tukey")
## NOTE: Results may be misleading due to involvement in interactions
## $emmeans
## Parental_treatment Temp Control_CO2 emmean SE df lower.CL upper.CL
## CCCC elevated CO 519 45.2 7.94 415 623
## CCCH elevated CO 470 44.6 7.61 366 574
## HHCC elevated CO 462 43.3 6.75 359 565
## CCHC elevated CO 471 44.9 7.77 367 575
## HHHC elevated CO 426 45.4 8.14 322 531
## CCCC zero CO 416 44.1 7.24 313 520
## CCCH zero CO 434 44.9 7.78 330 538
## HHCC zero CO 443 43.8 7.07 340 546
## CCHC zero CO 466 44.4 7.44 362 569
## HHHC zero CO 428 46.5 8.95 323 534
## CCCC elevated control 416 43.2 6.66 313 519
## CCCH elevated control 447 45.0 7.87 343 552
## HHCC elevated control 492 44.8 7.70 388 596
## CCHC elevated control 436 42.9 6.53 333 540
## HHHC elevated control 525 47.2 9.37 419 631
## CCCC zero control 409 43.4 6.78 305 512
## CCCH zero control 463 43.4 6.80 360 566
## HHCC zero control 444 42.3 6.17 341 547
## CCHC zero control 418 42.9 6.53 315 521
## HHHC zero control 404 45.1 7.91 300 508
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio
## CCCC elevated CO - CCCH elevated CO 48.716 40.0 131.9 1.218
## CCCC elevated CO - HHCC elevated CO 56.557 38.6 116.4 1.467
## CCCC elevated CO - CCHC elevated CO 48.142 40.3 133.4 1.196
## CCCC elevated CO - HHHC elevated CO 92.617 40.9 116.7 2.265
## CCCC elevated CO - CCCC zero CO 102.747 36.2 497.9 2.835
## CCCC elevated CO - CCCH zero CO 84.855 40.4 126.1 2.103
## CCCC elevated CO - HHCC zero CO 75.814 39.1 120.7 1.938
## CCCC elevated CO - CCHC zero CO 53.100 39.8 126.9 1.335
## CCCC elevated CO - HHHC zero CO 90.539 42.2 129.5 2.148
## CCCC elevated CO - CCCC elevated control 103.196 34.9 489.7 2.960
## CCCC elevated CO - CCCH elevated control 71.360 40.5 133.5 1.763
## CCCC elevated CO - HHCC elevated control 26.587 40.2 130.2 0.662
## CCCC elevated CO - CCHC elevated control 82.367 38.1 112.2 2.160
## CCCC elevated CO - HHHC elevated control -6.456 42.8 125.7 -0.151
## CCCC elevated CO - CCCC zero control 110.150 35.1 489.7 3.139
## CCCC elevated CO - CCCH zero control 55.756 38.7 115.9 1.442
## CCCC elevated CO - HHCC zero control 75.036 37.5 106.2 2.002
## CCCC elevated CO - CCHC zero control 101.002 38.1 112.9 2.648
## CCCC elevated CO - HHHC zero control 114.580 40.6 113.2 2.824
## CCCH elevated CO - HHCC elevated CO 7.841 37.9 116.9 0.207
## CCCH elevated CO - CCHC elevated CO -0.574 39.6 134.5 -0.014
## CCCH elevated CO - HHHC elevated CO 43.901 40.3 117.4 1.089
## CCCH elevated CO - CCCC zero CO 54.032 38.8 125.5 1.392
## CCCH elevated CO - CCCH zero CO 36.139 36.7 500.7 0.983
## CCCH elevated CO - HHCC zero CO 27.098 38.5 121.2 0.704
## CCCH elevated CO - CCHC zero CO 4.385 39.2 128.1 0.112
## CCCH elevated CO - HHHC zero CO 41.823 41.6 130.1 1.006
## CCCH elevated CO - CCCC elevated control 54.480 37.7 114.8 1.444
## CCCH elevated CO - CCCH elevated control 22.645 36.8 493.5 0.616
## CCCH elevated CO - HHCC elevated control -22.129 39.6 131.1 -0.559
## CCCH elevated CO - CCHC elevated control 33.651 37.5 112.5 0.898
## CCCH elevated CO - HHHC elevated control -55.172 42.2 126.2 -1.307
## CCCH elevated CO - CCCC zero control 61.434 38.0 115.9 1.618
## CCCH elevated CO - CCCH zero control 7.040 34.7 490.0 0.203
## CCCH elevated CO - HHCC zero control 26.320 36.9 106.6 0.714
## CCCH elevated CO - CCHC zero control 52.286 37.5 113.3 1.395
## CCCH elevated CO - HHHC zero control 65.865 40.0 113.5 1.648
## HHCC elevated CO - CCHC elevated CO -8.415 38.2 118.5 -0.220
## HHCC elevated CO - HHHC elevated CO 36.060 38.9 103.1 0.928
## HHCC elevated CO - CCCC zero CO 46.190 37.3 108.9 1.239
## HHCC elevated CO - CCCH zero CO 28.297 38.3 111.2 0.739
## HHCC elevated CO - HHCC zero CO 19.257 33.4 485.7 0.576
## HHCC elevated CO - CCHC zero CO -3.457 37.7 111.5 -0.092
## HHCC elevated CO - HHHC zero CO 33.981 40.1 115.2 0.847
## HHCC elevated CO - CCCC elevated control 46.639 36.2 99.1 1.288
## HHCC elevated CO - CCCH elevated control 14.803 38.4 118.8 0.385
## HHCC elevated CO - HHCC elevated control -29.971 34.8 490.7 -0.862
## HHCC elevated CO - CCHC elevated control 25.810 36.0 97.1 0.718
## HHCC elevated CO - HHHC elevated control -63.014 40.9 113.0 -1.542
## HHCC elevated CO - CCCC zero control 53.593 36.5 100.5 1.470
## HHCC elevated CO - CCCH zero control -0.801 36.5 100.5 -0.022
## HHCC elevated CO - HHCC zero control 18.479 31.6 485.5 0.586
## HHCC elevated CO - CCHC zero control 44.445 36.0 97.7 1.236
## HHCC elevated CO - HHHC zero control 58.023 38.5 99.5 1.507
## CCHC elevated CO - HHHC elevated CO 44.475 40.6 118.7 1.096
## CCHC elevated CO - CCCC zero CO 54.605 39.1 127.1 1.397
## CCHC elevated CO - CCCH zero CO 36.712 40.0 128.4 0.918
## CCHC elevated CO - HHCC zero CO 27.672 38.8 123.0 0.714
## CCHC elevated CO - CCHC zero CO 4.958 36.3 493.4 0.137
## CCHC elevated CO - HHHC zero CO 42.396 41.8 131.5 1.014
## CCHC elevated CO - CCCC elevated control 55.054 38.0 116.6 1.448
## CCHC elevated CO - CCCH elevated control 23.218 40.2 136.5 0.578
## CCHC elevated CO - HHCC elevated control -21.556 39.8 132.8 -0.541
## CCHC elevated CO - CCHC elevated control 34.225 34.3 486.4 0.997
## CCHC elevated CO - HHHC elevated control -54.599 42.5 127.7 -1.286
## CCHC elevated CO - CCCC zero control 62.008 38.2 117.7 1.621
## CCHC elevated CO - CCCH zero control 7.614 38.3 118.4 0.199
## CCHC elevated CO - HHCC zero control 26.894 37.2 108.4 0.724
## CCHC elevated CO - CCHC zero control 52.860 34.4 486.7 1.536
## CCHC elevated CO - HHHC zero control 66.438 40.2 115.1 1.651
## HHHC elevated CO - CCCC zero CO 10.130 39.7 110.5 0.255
## HHHC elevated CO - CCCH zero CO -7.762 40.6 112.4 -0.191
## HHHC elevated CO - HHCC zero CO -16.803 39.5 107.3 -0.426
## HHHC elevated CO - CCHC zero CO -39.517 40.1 112.8 -0.986
## HHHC elevated CO - HHHC zero CO -2.078 38.7 490.7 -0.054
## HHHC elevated CO - CCCC elevated control 10.579 38.7 101.7 0.273
## HHHC elevated CO - CCCH elevated control -21.257 40.8 119.0 -0.521
## HHHC elevated CO - HHCC elevated control -66.030 40.5 116.1 -1.630
## HHHC elevated CO - CCHC elevated control -10.250 38.5 99.8 -0.266
## HHHC elevated CO - HHHC elevated control -99.073 39.3 494.4 -2.524
## HHHC elevated CO - CCCC zero control 17.533 38.9 102.8 0.450
## HHHC elevated CO - CCCH zero control -36.861 39.0 103.0 -0.945
## HHHC elevated CO - HHCC zero control -17.581 37.8 94.2 -0.465
## HHHC elevated CO - CCHC zero control 8.385 38.5 100.4 0.218
## HHHC elevated CO - HHHC zero control 21.963 36.9 487.0 0.594
## CCCC zero CO - CCCH zero CO -17.893 39.2 119.5 -0.457
## CCCC zero CO - HHCC zero CO -26.933 37.9 113.7 -0.711
## CCCC zero CO - CCHC zero CO -49.647 38.5 119.7 -1.289
## CCCC zero CO - HHHC zero CO -12.209 41.0 123.0 -0.298
## CCCC zero CO - CCCC elevated control 0.449 33.7 490.2 0.013
## CCCC zero CO - CCCH elevated control -31.387 39.3 127.0 -0.799
## CCCC zero CO - HHCC elevated control -76.161 39.0 123.8 -1.952
## CCCC zero CO - CCHC elevated control -20.380 36.9 105.4 -0.553
## CCCC zero CO - HHHC elevated control -109.204 41.7 120.2 -2.619
## CCCC zero CO - CCCC zero control 7.403 34.0 492.6 0.218
## CCCC zero CO - CCCH zero control -46.991 37.4 108.5 -1.257
## CCCC zero CO - HHCC zero control -27.711 36.1 98.5 -0.767
## CCCC zero CO - CCHC zero control -1.745 36.9 105.8 -0.047
## CCCC zero CO - HHHC zero control 11.833 39.4 106.8 0.301
## CCCH zero CO - HHCC zero CO -9.041 38.9 115.9 -0.233
## CCCH zero CO - CCHC zero CO -31.754 39.5 122.1 -0.803
## CCCH zero CO - HHHC zero CO 5.684 41.9 124.5 0.136
## CCCH zero CO - CCCC elevated control 18.341 38.1 109.8 0.481
## CCCH zero CO - CCCH elevated control -13.494 37.1 498.8 -0.364
## CCCH zero CO - HHCC elevated control -58.268 39.9 125.4 -1.459
## CCCH zero CO - CCHC elevated control -2.488 37.9 107.7 -0.066
## CCCH zero CO - HHHC elevated control -91.311 42.6 121.5 -2.146
## CCCH zero CO - CCCC zero control 25.296 38.4 111.0 0.659
## CCCH zero CO - CCCH zero control -29.098 35.0 498.1 -0.831
## CCCH zero CO - HHCC zero control -9.818 37.2 101.7 -0.264
## CCCH zero CO - CCHC zero control 16.148 37.9 108.5 0.426
## CCCH zero CO - HHHC zero control 29.726 40.3 109.0 0.737
## HHCC zero CO - CCHC zero CO -22.714 38.2 116.3 -0.594
## HHCC zero CO - HHHC zero CO 14.725 40.7 119.7 0.362
## HHCC zero CO - CCCC elevated control 27.382 36.8 103.5 0.744
## HHCC zero CO - CCCH elevated control -4.454 39.0 123.1 -0.114
## HHCC zero CO - HHCC elevated control -49.227 35.2 488.0 -1.397
## HHCC zero CO - CCHC elevated control 6.553 36.5 101.4 0.179
## HHCC zero CO - HHHC elevated control -82.270 41.4 116.5 -1.988
## HHCC zero CO - CCCC zero control 34.336 37.0 104.6 0.927
## HHCC zero CO - CCCH zero control -20.058 37.1 105.1 -0.541
## HHCC zero CO - HHCC zero control -0.778 32.3 489.9 -0.024
## HHCC zero CO - CCHC zero control 25.188 36.5 101.9 0.689
## HHCC zero CO - HHHC zero control 38.766 39.1 103.4 0.992
## CCHC zero CO - HHHC zero CO 37.438 41.3 125.4 0.906
## CCHC zero CO - CCCC elevated control 50.096 37.5 109.9 1.336
## CCHC zero CO - CCCH elevated control 18.260 39.6 129.4 0.461
## CCHC zero CO - HHCC elevated control -26.514 39.4 126.4 -0.673
## CCHC zero CO - CCHC elevated control 29.267 33.8 487.8 0.866
## CCHC zero CO - HHHC elevated control -59.557 42.0 122.5 -1.417
## CCHC zero CO - CCCC zero control 57.050 37.7 111.1 1.513
## CCHC zero CO - CCCH zero control 2.656 37.8 111.0 0.070
## CCHC zero CO - HHCC zero control 21.936 36.5 101.0 0.600
## CCHC zero CO - CCHC zero control 47.902 33.8 488.3 1.418
## CCHC zero CO - HHHC zero control 61.480 39.7 109.1 1.548
## HHHC zero CO - CCCC elevated control 12.657 40.0 114.1 0.316
## HHHC zero CO - CCCH elevated control -19.178 42.0 131.8 -0.456
## HHHC zero CO - HHCC elevated control -63.952 41.7 128.7 -1.532
## HHHC zero CO - CCHC elevated control -8.172 39.8 112.2 -0.206
## HHHC zero CO - HHHC elevated control -96.995 40.6 497.6 -2.388
## HHHC zero CO - CCCC zero control 19.612 40.2 115.3 0.487
## HHHC zero CO - CCCH zero control -34.782 40.3 115.3 -0.864
## HHHC zero CO - HHCC zero control -15.502 39.1 106.3 -0.396
## HHHC zero CO - CCHC zero control 10.464 39.8 112.9 0.263
## HHHC zero CO - HHHC zero control 24.042 38.4 491.2 0.627
## CCCC elevated control - CCCH elevated control -31.836 38.2 116.7 -0.833
## CCCC elevated control - HHCC elevated control -76.609 37.9 113.4 -2.020
## CCCC elevated control - CCHC elevated control -20.829 35.7 95.1 -0.583
## CCCC elevated control - HHHC elevated control -109.652 40.7 111.1 -2.694
## CCCC elevated control - CCCC zero control 6.954 32.6 486.9 0.213
## CCCC elevated control - CCCH zero control -47.440 36.3 98.7 -1.306
## CCCC elevated control - HHCC zero control -28.160 35.0 88.8 -0.804
## CCCC elevated control - CCHC zero control -2.194 35.7 95.5 -0.061
## CCCC elevated control - HHHC zero control 11.384 38.3 97.8 0.297
## CCCH elevated control - HHCC elevated control -44.774 40.1 133.0 -1.118
## CCCH elevated control - CCHC elevated control 11.007 38.0 114.7 0.290
## CCCH elevated control - HHHC elevated control -77.817 42.7 128.0 -1.823
## CCCH elevated control - CCCC zero control 38.790 38.4 117.7 1.009
## CCCH elevated control - CCCH zero control -15.604 35.2 493.7 -0.443
## CCCH elevated control - HHCC zero control 3.676 37.3 108.2 0.098
## CCCH elevated control - CCHC zero control 29.642 38.0 115.1 0.781
## CCCH elevated control - HHHC zero control 43.220 40.4 115.1 1.069
## HHCC elevated control - CCHC elevated control 55.780 37.7 111.1 1.481
## HHCC elevated control - HHHC elevated control -33.043 42.4 124.8 -0.780
## HHCC elevated control - CCCC zero control 83.564 38.1 114.4 2.190
## HHCC elevated control - CCCH zero control 29.170 38.3 115.2 0.762
## HHCC elevated control - HHCC zero control 48.450 33.5 489.1 1.444
## HHCC elevated control - CCHC zero control 74.416 37.7 111.9 1.975
## HHCC elevated control - HHHC zero control 87.994 40.2 112.2 2.191
## CCHC elevated control - HHHC elevated control -88.823 40.4 109.1 -2.197
## CCHC elevated control - CCCC zero control 27.783 36.0 96.2 0.772
## CCHC elevated control - CCCH zero control -26.611 36.1 97.0 -0.737
## CCHC elevated control - HHCC zero control -7.331 34.8 87.1 -0.211
## CCHC elevated control - CCHC zero control 18.635 31.8 482.7 0.586
## CCHC elevated control - HHHC zero control 32.214 38.1 96.0 0.846
## HHHC elevated control - CCCC zero control 116.607 40.9 112.0 2.850
## HHHC elevated control - CCCH zero control 62.213 41.0 112.8 1.517
## HHHC elevated control - HHCC zero control 81.493 39.9 104.3 2.043
## HHHC elevated control - CCHC zero control 107.459 40.5 109.8 2.655
## HHHC elevated control - HHHC zero control 121.037 38.8 492.3 3.119
## CCCC zero control - CCCH zero control -54.394 36.5 99.9 -1.488
## CCCC zero control - HHCC zero control -35.114 35.3 90.1 -0.995
## CCCC zero control - CCHC zero control -9.148 36.0 96.5 -0.254
## CCCC zero control - HHHC zero control 4.430 38.6 98.8 0.115
## CCCH zero control - HHCC zero control 19.280 35.3 90.0 0.546
## CCCH zero control - CCHC zero control 45.246 36.1 97.1 1.255
## CCCH zero control - HHHC zero control 58.824 38.6 99.2 1.523
## HHCC zero control - CCHC zero control 25.966 34.8 87.2 0.747
## HHCC zero control - HHHC zero control 39.544 37.4 90.4 1.057
## CCHC zero control - HHHC zero control 13.578 38.1 96.3 0.357
## p.value
## 0.9996
## 0.9953
## 0.9997
## 0.7539
## 0.3351
## 0.8492
## 0.9196
## 0.9986
## 0.8252
## 0.2584
## 0.9661
## 1.0000
## 0.8173
## 1.0000
## 0.1688
## 0.9962
## 0.8943
## 0.4761
## 0.3544
## 1.0000
## 1.0000
## 0.9999
## 0.9976
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9961
## 1.0000
## 1.0000
## 1.0000
## 0.9989
## 0.9856
## 1.0000
## 1.0000
## 0.9974
## 0.9825
## 1.0000
## 1.0000
## 0.9994
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9990
## 1.0000
## 1.0000
## 1.0000
## 0.9915
## 0.9950
## 1.0000
## 1.0000
## 0.9994
## 0.9933
## 0.9999
## 0.9975
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9960
## 1.0000
## 1.0000
## 1.0000
## 0.9991
## 0.9854
## 1.0000
## 1.0000
## 0.9931
## 0.9822
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9845
## 1.0000
## 0.5660
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9991
## 1.0000
## 1.0000
## 1.0000
## 0.9146
## 1.0000
## 0.4975
## 1.0000
## 0.9993
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9957
## 1.0000
## 0.8260
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9979
## 1.0000
## 0.9008
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9985
## 1.0000
## 1.0000
## 1.0000
## 0.9969
## 0.9932
## 1.0000
## 1.0000
## 0.9974
## 0.9911
## 1.0000
## 1.0000
## 0.9923
## 1.0000
## 0.6698
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.8874
## 1.0000
## 0.4431
## 1.0000
## 0.9988
## 1.0000
## 1.0000
## 1.0000
## 0.9999
## 1.0000
## 0.9533
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9999
## 0.9946
## 1.0000
## 0.7999
## 1.0000
## 0.9967
## 0.9055
## 0.7992
## 0.7956
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.3375
## 0.9930
## 0.8764
## 0.4714
## 0.1777
## 0.9942
## 1.0000
## 1.0000
## 1.0000
## 1.0000
## 0.9993
## 0.9924
## 1.0000
## 0.9999
## 1.0000
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 20 estimates
plot(emmeans(lmer.bold.AS, pairwise ~ Parental_treatment * Temp * Control_CO2, adjust="tukey"))
## NOTE: Results may be misleading due to involvement in interactions
plot data
library(broom.mixed)
aa <- augment(lmer.bold.AS)
aa
## # A tibble: 544 × 18
## AS Parental_treatment Temp Control_CO2 Bold Parental_number Chamber_ID
## <dbl> <fct> <fct> <fct> <dbl> <fct> <fct>
## 1 376. HHHC zero control 4 65 A
## 2 307. HHHC elevat… control 4 65 D
## 3 309. HHHC zero control 1 9b D
## 4 475. CCCC zero control 1 92b C
## 5 380. CCCH elevat… control 1 5 B
## 6 654. HHCC elevat… CO 1 81 A
## 7 434. CCCC zero control 1 92 C
## 8 812. CCCH elevat… control 2 94 A
## 9 440. HHHC zero control 2 9b B
## 10 366. CCCC zero CO 2 92b C
## # ℹ 534 more rows
## # ℹ 11 more variables: .fitted <dbl>, .resid <dbl>, .hat <dbl>, .cooksd <dbl>,
## # .fixed <dbl>, .mu <dbl>, .offset <dbl>, .sqrtXwt <dbl>, .sqrtrwt <dbl>,
## # .weights <dbl>, .wtres <dbl>
graph.b <- ggplot(aa, aes(x=Bold, y=.fitted)) + geom_jitter(aes (x=Bold, y=.fitted),height = .2, width = .2, alpha=0.3) + theme_classic() + geom_smooth(method = lm, se=TRUE) + stat_regline_equation(label.y= c(750), label.x= (c(1))) +stat_cor(aes(label = paste(..rr.label.., ..p.label.., sep = "~`,`~")), label.y= c(750), label.x= c(2)) + theme(text = element_text(size=20))
graph.b
## `geom_smooth()` using formula = 'y ~ x'
graph.a <- ggplot(aa, aes(x=Bold, y=.fitted, colour=Temp, fill= Temp)) + geom_jitter(aes (x=Bold, y=.fitted, colour = Temp),height = .2, width = .2, alpha=0.3) + theme_classic() + geom_smooth(method = lm, se=TRUE) + stat_regline_equation(label.y= c(750, 780), label.x= (c(1))) + stat_cor(aes(label = paste(..rr.label.., ..p.label.., sep = "~`,`~")), label.y= c(750, 780), label.x= (c(2.5))) + theme(text = element_text(size=20))
graph.a
## `geom_smooth()` using formula = 'y ~ x'
ggsave("ASxbold_temp.eps", graph.a, height = 6, width = 10, dpi = 320)
## `geom_smooth()` using formula = 'y ~ x'
## Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size):
## semi-transparency is not supported on this device: reported only once per page
ggsave("ASxbold_temp.b.eps", graph.b, height = 6, width = 10, dpi = 320)
## `geom_smooth()` using formula = 'y ~ x'
## Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size):
## semi-transparency is not supported on this device: reported only once per page