eggs_and_nests.RdEgg data combined with data on nests
eggs_and_nests
A data frame
Taxonomic family
Taxonomic order
Genus and species
Index of how asymmetric an egg is
Index of how elliptical an egg is
Mean length of egg
nest type of species
author
ellipticity of bird in grams
....
if (FALSE) { library(ggplot2) library(ggpubr) ## Explore data graphically ### Plot boxplots ggpubr::ggboxplot(data = eggs_and_nests, y = "ellipticity", x = "nest", fill = "nest") ### Plot histograms ggpubr::gghistogram(data = eggs_and_nests, x = "ellipticity", title = "All data") ggpubr::gghistogram(data = eggs_and_nests, x = "ellipticity", facet.by = "nest", fill = "nest", title = "Faceted by nest") } ## Plot means with 95% confidence intervals #ggpubr::ggerrorplot(eggs_and_nests, # x = "nest", # y = "ellipticity", # desc_stat = "mean_ci", # add = "mean") ## 1-way ANOVA ### null model model.null <- lm(ellipticity ~ 1, data = eggs_and_nests) ### model of interest model.alt <- lm(ellipticity ~ nest, data = eggs_and_nests) ### compare models anova(model.null, model.alt)#> Analysis of Variance Table #> #> Model 1: ellipticity ~ 1 #> Model 2: ellipticity ~ nest #> Res.Df RSS Df Sum of Sq F Pr(>F) #> 1 721 3.5560 #> 2 716 3.2544 5 0.30153 13.268 2.212e-12 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1## Pairwise comparisons after 1-way ANOVA ### no corrections for multiple comparisons pairwise.t.test(x = eggs_and_nests$ellipticity, g = eggs_and_nests$nest, p.adjust.method = "none")#> #> Pairwise comparisons using t tests with pooled SD #> #> data: eggs_and_nests$ellipticity and eggs_and_nests$nest #> #> branches burrows Cup Dome ground surface #> burrows 0.97676 - - - - #> Cup 0.02170 1.5e-08 - - - #> Dome 0.05491 3.5e-06 0.00329 - - #> ground surface 0.46012 0.13746 1.4e-06 0.00042 - #> holes and crevices 0.31689 0.10739 0.04834 0.18610 0.55863 #> #> P value adjustment method: none### Bonferonni correction pairwise.t.test(x = eggs_and_nests$ellipticity, g = eggs_and_nests$nest, p.adjust.method = "bonferroni")#> #> Pairwise comparisons using t tests with pooled SD #> #> data: eggs_and_nests$ellipticity and eggs_and_nests$nest #> #> branches burrows Cup Dome ground surface #> burrows 1.0000 - - - - #> Cup 0.3256 2.3e-07 - - - #> Dome 0.8236 5.3e-05 0.0493 - - #> ground surface 1.0000 1.0000 2.1e-05 0.0062 - #> holes and crevices 1.0000 1.0000 0.7251 1.0000 1.0000 #> #> P value adjustment method: bonferroni## Tukey test ### re-fit model with aov() model.alt.aov <- aov(ellipticity ~ nest, data = eggs_and_nests) ### TukeyHSD() on model from aov() TukeyHSD(model.alt.aov)#> Tukey multiple comparisons of means #> 95% family-wise confidence level #> #> Fit: aov(formula = ellipticity ~ nest, data = eggs_and_nests) #> #> $nest #> diff lwr upr #> burrows-branches -0.001492308 -0.1478176897 0.14483307 #> Cup-branches -0.109886719 -0.2463740344 0.02660060 #> Dome-branches -0.092205357 -0.2292353178 0.04482460 #> ground surface-branches -0.036871429 -0.1794321827 0.10568933 #> holes and crevices-branches -0.055133333 -0.2124283927 0.10216173 #> Cup-burrows -0.108394411 -0.1624989507 -0.05428987 #> Dome-burrows -0.090713049 -0.1461722598 -0.03525384 #> ground surface-burrows -0.035379121 -0.1033650201 0.03260678 #> holes and crevices-burrows -0.053641026 -0.1487212527 0.04143920 #> Dome-Cup 0.017681362 0.0005526165 0.03481011 #> ground surface-Cup 0.073015290 0.0301229553 0.11590763 #> holes and crevices-Cup 0.054753385 -0.0243536274 0.13386040 #> ground surface-Dome 0.055333929 0.0107449704 0.09992289 #> holes and crevices-Dome 0.037072024 -0.0429676056 0.11711165 #> holes and crevices-ground surface -0.018261905 -0.1074398211 0.07091601 #> p adj #> burrows-branches 1.0000000 #> Cup-branches 0.1950900 #> Dome-branches 0.3889850 #> ground surface-branches 0.9770011 #> holes and crevices-branches 0.9174222 #> Cup-burrows 0.0000002 #> Dome-burrows 0.0000518 #> ground surface-burrows 0.6727661 #> holes and crevices-burrows 0.5907892 #> Dome-Cup 0.0384537 #> ground surface-Cup 0.0000208 #> holes and crevices-Cup 0.3561386 #> ground surface-Dome 0.0055542 #> holes and crevices-Dome 0.7719777 #> holes and crevices-ground surface 0.9920083 #>### Plot effect sizes #plotTukeysHSD(TukeyHSD(model.alt.aov))