beans <- read.table("/home/units/r.data/broadbeans.dat", header=T)
summary(beans)
attributes(beans)

attach(beans)

attributes(Type)

Concentration[Type=="Cut.shoot"]

t.test( x=Concentration[Type=="Cut.shoot"], y=Concentration[Type=="Rooted.plant"] )
t.test( Concentration ~ Type )

bartlett.test( Concentration ~ Type )

t.test( Concentration ~ Type, var.equal=TRUE)
t.test( Concentration ~ Type, var.equal=TRUE, alternative="greater")
beans.test <- t.test( Concentration ~ Type, var.equal=TRUE, alternative="greater")
names(beans.test)


plot(beans)
plot( Concentration ~ Type )

# Deal with potential outlier
sort( Concentration[Type=="Cut.shoot"] )
detach(beans)

beans <- beans[-4,]                         # A negative index *removes* the element
attach(beans)

plot( Concentration ~ Type )

t.test( Concentration ~ Type )
ks.test( x=Concentration[Type=="Cut.shoot"], y=Concentration[Type=="Rooted.plant"] )

detach(beans)


### Try another


barley <- read.table("/home/units/r.data/split-R.dat", header=T)
summary(barley)

attach(barley)

b.m1 <-  lm( Yield ~ Block + Variety + Manure )          # Wrong!
b.m1 <-  lm( Yield ~ factor(Block) + factor(Variety) + factor(Manure) )
b.m1

detach(barley)

barley$Block <- factor(barley$Block)
barley$Variety <- factor(barley$Variety)

attach(barley)
b.m1 <-  lm( Yield ~ factor(Block) + factor(Variety) + factor(Manure) )
b.m1

detach(barley)