library(reshape2)
library(gplots)
library(multcomp)

DF = read.csv('../../Data/ASCII_Comma/Chapter_12/diet-and-longevity.txt', quote='\'', header=TRUE)

#postscript("../../WriteUp/Graphics/Chapter12/prob_33_boxplot.eps", onefile=FALSE, horizontal=FALSE)
boxplot(LIFETIME ~ DIET, data=DF)
#plotmeans(LIFETIME ~ DIET, data=DF)
#dev.off()

fit = aov(LIFETIME ~ DIET, data=DF)
print(summary(fit))

# A Tukey comparison of means test:
#
TukeyHSD(fit)

#postscript("../../WriteUp/Graphics/Chapter12/prob_33_TukeyHSD_plot.eps", onefile=FALSE, horizontal=FALSE)
par(las=2)
par(mar=c(5, 8, 4, 2))
plot(TukeyHSD(fit))
#dev.off()


# Use the multcomp package:
#
par(las=2)
par(mar=c(5, 4, 6, 2))
tuk = glht(fit, linfct=mcp(DIET='Tukey'))
plot(cld(tukr, level=0.05), col='lightgrey')

# A nonparametric test for one-way ANOVA:
#
print(kruskal.test(LIFETIME ~ DIET, data=DF))