pdf("C:\\Rmisc\\graphs\\amoeba.pdf")

amoeba1 <- read.fwf("C:\\data\\amoeba.txt", width=c(8,8), col.names=c("Trt", "Yield"))

fTrt <- factor(amoeba1$Trt, levels=1:5)

levels(fTrt) <- c("None", "H", "F", "HF", "FH")

amoeba <- data.frame(amoeba1, fTrt)

attach(amoeba)

kruskal.test(Yield~fTrt)

amoeba1.aov <- aov(Yield~fTrt)

summary(amoeba1.aov)


# Obtain Tukey's Comparisons among levels of treatment

TukeyHSD(amoeba1.aov, "fTrt")

# Obtain Bonferroni's Comparisons among levels of treatment (does not use MSE from ANOVA and not pooled df)

pairwise.t.test(Yield, fTrt, p.adj="bonf")

# Histogram of Residuals and Plot Residuals versus Time order

hist(residuals(amoeba1.aov), breaks=seq(-75,75,15))

plot(residuals(amoeba1.aov), type="o")

# Bartlett's test for equal variances

bartlett.test(Yield~fTrt)




dev.off()