# code to read the spruce data
#  fit a two-sample t-test using lm()
#  then estimate variances for nested random effects

spruce <- read.table('spruce.txt',header=T,as.is=T)

# create factor variables for both trt and chamber
spruce$trt.f <- as.factor(spruce$trt)
spruce$chamber.f <- as.factor(spruce$chamber)

# box plot
boxplot(size~chamber.f,data=spruce)

# dot plot in observation order
plot(spruce$size)

# fit a linear model, assuming one random error
spruce.lm <- lm(size~trt.f, data=spruce)
summary(spruce)

# fit a linear mixed effects model, assuming two nested errors
spruce.lme <- lme(size~trt.f,random=~+1|chamber.f,data=spruce)
summary(spruce.lme)