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

DF = read.csv('../../Data/ASCII_Comma/Chapter_12/linseed.txt', quote='\'', header=TRUE)
DF$Plot = as.factor(DF$Plot)

fit = aov(Yield ~ Plot * Variety, data=DF)
print(summary(fit))

fit = aov(Yield ~ Plot + Variety, data=DF)
print(summary(fit))

fit = aov(Yield ~ Variety, data=DF)
print(summary(fit))

#postscript("../../WriteUp/Graphics/Chapter12/prob_30_plotmeans.eps", onefile=FALSE, horizontal=FALSE)
plotmeans(Yield ~ Variety, data=DF)
#dev.off()

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

par(las=2)
par(mar=c(5, 8, 4, 2))
plot(TukeyHSD(fit))

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

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