# Diagnostics for the final model fitted in Chapter 3, using R

library(lattice)
trellis.device(color=F)

# Generate Figure 3.4

res <- resid(model3.3.reml.fit)
ratred <- data.frame(ratpup, res)
ratred
histogram(~res | factor(trtgrp), data=ratred, layout=c(2,1), aspect = 2 , xlab = "Residual") 

# Generate Figure 3.5

qqnorm(model3.3.reml.fit, ~resid(.) | factor(trtgrp), layout=c(2,1), aspect = 2, id = 0.05) 

# Generate Figure 3.6 
 
plot(model3.3.reml.fit, resid(.) ~ fitted(.) | factor(trtgrp), layout=c(2,1), aspect=2, abline=0)

# Generate Figure 3.7 (note: these are conditional residuals)

attach(ratpup)

ranklit <- litsize+0.01*litter
sort(ranklit)
ranklit
ranklit <- factor(ranklit)

levels(ranklit) <- c( "1","2", "3","4","5","6","7","8","9","10", "11","12", "13","14","15","16","17","18","19","20", "21","22","23","24","25","26","27")

ranklit

bwplot(resid(model3.3.reml.fit) ~ ranklit, data=model3.3.reml.fit, ylab="residual", xlab="litter")

# Influence diagnostics are not currently available.