file <- "http://www.uvm.edu/~rsingle/stat211/data/extra/ch5_MouseDiet.txt"
dat<-read.table(file, header=T, na.strings=c("NA",".")) 
diet <- dat$diet
reduc<- dat$reduction 

#split the screen
 par(mfrow=c(2,2))

#Checking assumptions
 hist(reduc[diet=="bean"], main="Bean diet")
 hist(reduc[diet=="oat"], main="Oat diet")
 qqnorm(reduc[diet=="bean"])
 qqnorm(reduc[diet=="oat"],main="QQ plot: oat")
  
#Separate Variance T-test 
 t.test(reduc[diet=="bean"],reduc[diet=="oat"])
 t.test(reduc~diet)
 t.test(reduc~diet, conf.level=.90)
 t.test(reduc~diet, alternative="less")
 
#Equal Variance T-test 
 t.test(reduc~diet, var.equal=TRUE)

 t.test(reduction~diet, data=dat, var.equal=TRUE)
 t.test(reduction~diet,           var.equal=TRUE)