f=c(24.1,23.9,24.4,24.4,23.5)
m=c(25.6,26.1,25.8,25.9,26)

# ANOVA w/o aov
G.mean=mean(c(f,m))
ss.total=sum((c(f,m)-G.mean)^2)
ss.tr=sum((mean(f)-G.mean)^2)*5+sum((mean(m)-G.mean)^2)*5
ss.error=sum((f-mean(f))^2)+sum((m-mean(m))^2)
ss.tr+ss.error
df.tr = 2 - 1
df.error = (4-1)*2
ms.tr = ss.tr /df.tr
ms.error = ss.error /df.error
1-pf(f.value,1,8)

# ANOVA w/ aov
dat<-data.frame(ssize=c(f,m),gender=c(rep("f",5),rep("m",5)))
dat.aov<-aov(ssize ~ gender, data=dat)
summary(dat.aov)

dat<-read.table("http://www.matsuka.info/data_folder/aov01.txt")
dat.aov<-aov(shoesize~club, dat)

# TukeyHSD w/o TukeyHSD command
qT<-qtukey(0.95, 3, 67)
HSD<-qT*sqrt((2.243*(1/23+1/24))/2)
means<-tapply(dat$shoesize,dat$club,mean)
abs(outer(means,means,"-"))
abs(outer(means,means,"-"))>HSD

# TukeyHSD
TukeyHSD(dat.aov)


dat<-read.csv("http://www.matsuka.info/data_folder/dktb312.csv")
dat.aov<-aov(result~method, data=dat)
summary(dat.aov)
source("http://www.matsuka.info/univ/course_folder/cutil.R")
adj.alpha(5,0.05)

# multiple t-test
dat.means<-tapply(dat$result,dat$method,mean)
new.alpha = 1-(1-0.05)^(1/5)
cont=c(-3,1,1,1)
bunshi=sum(cont*dat.means)
bunbo=sqrt(5.29*(sum((cont^2)/8)))
t.value=bunshi/bunbo
2*(1-pt(t.value,28)) > new.alpha

# bonferroni w/ cUTIL
cu.bonF1F(dat.aov,dat,c(-3,1,1,1),new.alpha)
cu.bonF1F(dat.aov,dat,c(-1,1,0,0),new.alpha)
cu.bonF1F(dat.aov,dat,c(-1,0,1,0),new.alpha)
cu.bonF1F(dat.aov,dat,c(-1,0,0,1),new.alpha)
cu.bonF1F(dat.aov,dat,c(0,-2,1,1),new.alpha)

# scheffe w/ cUTIL
new.f<-adj.f(4,3,28,0.05)
cu.scheffe1F(dat.aov,dat,c(-3,1,1,1))
cu.scheffe1F(dat.aov,dat,c(-1,0,1,0))
cu.scheffe1F(dat.aov,dat,c(-1,0,0,1))