# you need to set your default directory to the folder containing the file Tunjai_regeneration.txt
# OR paste the path to the file in addition to the file name


tj<-read.table(file="Tunjai_regeneration.txt", header=TRUE)
tj

colnames(tj)[9]<- "PercentEstab"
arcsine_establishment<- asin(sqrt(tj$PercentEstab /100))
tj<-cbind(tj, arcsine_establishment)
levels(tj$Size_categ)
levels(tj$Coat)
levels(tj$Shape)


### Arcsine squareroot transformation

is.ordered(tj$Size_categ)
tj$Size_categ<-ordered(tj$Size_categ, levels=c("S" ,"I", "L"))
tj$Coat<-ordered(tj$Coat, levels=c("Tn" ,"M", "Tk"))
is.ordered(tj$Size_categ)
boxplot(tj$arcsine_establishment ~ tj$Size_categ)


#modelA2<-aov(tj$arcsine_establishment ~ tj$Size_categ)
modelA<-lm(tj$arcsine_establishment ~ tj$Size_categ)
par(mfrow=c(2,2))
plot(modelA)
summary(modelA)

#modelA2<-aov(tj$arcsine_establishment ~ tj$Size_categ)
#modelA3<-aov(log(tj$arcsine_establishment) ~ tj$Size_categ)




modelB<-aov (tj$PercentEstab ~ tj$Size_categ)
summary(modelB)

### Logit transformation

tj$logit_establishment<-with(tj, log((PercentEstab/100)/(1-(PercentEstab/100))))
modelC<-aov(tj$logit_establishment ~ tj$Size_categ)
par(mfrow=c(2,2))
plot(modelC)
summary(modelC)