Multiple Comparisons

### Use warpbreaks dataset
amod<-aov(breaks~tension, data=warpbreaks)

### 1-way ANOVA (exact)
library(multcomp)
summary(glht(amod, linfct=mcp(tension="Dunnett")))
summary(glht(amod, linfct=mcp(tension="Tukey")))

# CI
confint(glht(amod, linfct=mcp(tension="Dunnett")), level=0.9)

# create a contrast
contr<-rbind("M-L"=c(-1,1,0), "H-L"=c(-1,0,1), "H-M"=c(0,-1,1))
glht(amod, linfct=mcp(tension=contr))

# Tukey test
TukeyHSD(chickwts.out,"feed")

# Closed test
pairwise.t.test(warpbreaks$breaks, warpbreaks$tension, p.adj="none")
pairwise.t.test(warpbreaks$breaks, warpbreaks$tension, p.adj="bonf")
pairwise.t.test(warpbreaks$breaks, warpbreaks$tension, p.adj="hommel")