#Biostatistics 390

#GLM & DUMMY VARIABLES
#COMPARING TWO-SAMPLE T-TEST WITH GLM:
ZAR=read.table("ZarEX8.1R.txt")
ZAR
attach(ZAR)
Y=data
X=group

#PERFORMING TWO-SAMPLE TWO-SIDED t-TEST:
t.test(Y~X,alternative="two.sided",var.equal=TRUE, conf.level=0.95)
detach(ZAR)

#PERFORMING EQUIVALENT GLM REGRESSION:
ZAR2=read.table("ZarEX8.1bR.txt")
ZAR2
attach(ZAR2)
Y=data
X=group
summary(lm(Y~X))
detach(ZAR2)

#COMPARING ONE-WAY ANOVA AS GLM:
ZAR3=read.table("ZarEX10.1R.txt")
ZAR3
attach(ZAR3)
Y=weights
X=factor(feed)
LM=lm(Y~X)
model.matrix(LM)
anova(LM)

USEFUL CONTRASTS IN R FOR UNORDERED FACTORS:

#TREATMENT CONTRASTS (DEFAULT)
LM=lm(Y~X)
contrasts(X)
model.matrix(LM)
summary(LM)

#CELL MEANS CONTRASTS:
LM=lm(Y~X-1) #Note use of -1 
contrasts(X)
model.matrix(LM)
summary(LM)