attach(anova.data)
plot(y)
abline(mean(y),0)
for(i in 1:14) lines(c(i,i), c(mean(y),y[i]))

plot(y)
lines(c(1,7.5),c(means[1],means[1]))
lines(c(7.5,14),c(means[2],means[2]))
for (i in 1:7) lines(c(i,i), c(means[1],y[i]))
for (i in 8:14) lines(c(i,i), c(means[2],y[i]))

model<-lm(y~f)
plot(y)
abline(mean(y),0)
points(predict(model),pch=16)
for (i in 1:14) lines(c(i,i), c(mean(y),predict(model)[i]))

attach(oneway)
names(oneway)

tapply(Growth,Photoperiod,mean)

Photoperiod<-ordered(Photoperiod,levels=c("Very.short","Short","Long","Very.long"))

tapply(Growth,Photoperiod,mean)
 
is.factor(Photoperiod)

model<-aov(Growth~Photoperiod)

summary(model)

model.tables(model)

tapply(Growth,Photoperiod,mean)

mean(Growth)

tapply(Growth,Photoperiod,mean)-mean(Growth)

rm(Growth, Photoperiod)

attach(twoway)
names(twoway)

tapply(Growth,Genotype,mean)

model2<-aov(Growth~Genotype+Photoperiod)

summary(model2)

attach(factorial)
names(factorial)

par(mfrow=c(1,2))
plot(diet,growth)
plot(coat,growth)

sum(growth)

sum(growth)^2

sum(growth^2)

tapply(growth,diet,sum)

tapply(growth,coat,sum)

tapply(growth,list(coat,diet),sum)

model<-aov(growth~diet*coat)
summary(model)
 
model2<-update(model, ~. - diet:coat)

anova(model,model2)

summary(model2)

model3<-update(model2, ~. -diet)
anova(model2,model3)

summary(model3)

tapply(growth,diet,mean)
   
diet2<-factor(1+(diet=="C"))
diet2

model4<-update(model3, ~. +diet2)

anova(model3,model4)

model5<-update(model4, ~. +diet2:coat)
anova(model4,model5)

summary(model4)

attach(daphnia)
names(daphnia)

par(mfrow=c(1,3))
plot(Water,Growth.rate)
plot(Detergent,Growth.rate)
plot(Daphnia,Growth.rate)

model<-aov(Growth.rate~Water*Detergent*Daphnia)
summary(model)

tapply(Growth.rate,list(Detergent,Daphnia),mean)

interaction.plot(Detergent,Daphnia,Growth.rate)

model.tables(model,type="adj.means",se=T)

factornames <- list(insects = c("plus", "minus"),
molluscs = c("plus", "minus"),
N = c("plus", "minus"),
P = c("plus", "minus"),
K = c("plus", "minus"))

experiment <- fac.design(rep(2,5), factor.names = factornames,
                       fraction =  ~ - insects:molluscs:N + N:P:K)
experiment

attach(Fungi)
names(Fungi)

model<-aov(Fungus.yield~Habitat)
summary(model)

plot(Habitat,Fungus.yield)

allcomp<-multicomp(model)
plot(allcomp)

allcomp

controlcomp<-multicomp(model,comparisons="mcc",control=5)
plot(controlcomp)



