data<-read.table("matrixalldataspp.txt",header=TRUE,sep="\t",dec=".")

stabC<-data[data$treatmentext=="control",]
stabF<-data[data$treatmentext=="fertilized",]

log_longterm_stabC<-log10(stabC$longterm_stab)
log_yeartoyear_stabC<-log10(stabC$yeartoyear_stab)
log_longterm_stabF<-log10(stabF$longterm_stab)
log_yeartoyear_stabF<-log10(stabF$yeartoyear_stab)

data2<-cbind(stabC,log_longterm_stabC,log_longterm_stabF,log_yeartoyear_stabC,log_yeartoyear_stabF)

#Correlation between long-term species stability in control and fertilized plots:

cor.test(data2$log_longterm_stabC,data2$log_longterm_stabF)


#Correlation between year-to-year species stability in control and fertilized plots:

cor.test(data2$log_yeartoyear_stabC,data2$log_yeartoyear_stabF)


#T-test between long-term species stability in control and fertilized plots:

ttestCandF<-t.test(data2$log_longterm_stabC,data2$log_longterm_stabF,paired=TRUE)
ttestCandF


#T-test between year-to-year species stability in control and fertilized plots:

ttestCandFt3<-t.test(data2$log_yeartoyear_stabC,data2$log_yeartoyear_stabF,paired=TRUE)
ttestCandFt3


#Correlation between long-term and year-to-year species stability in control plots:

cor.test(data2$log_longterm_stabC,data2$log_yeartoyear_stabC)


#Correlation between long-term and year-to-year species stability in fertilized plots:

cor.test(data2$log_longterm_stabF,data2$log_yeartoyear_stabF)


#T-test between long-term and year-to-year species stability in control plots:

ttestCtrendandt3<-t.test(data2$log_longterm_stabC,data2$log_yeartoyear_stabC,paired=TRUE)
ttestCtrendandt3


#T-test between long-term and year-to-year species stability in fertilized plots:

ttestFtrendandt3<-t.test(data2$log_longterm_stabF,data2$log_yeartoyear_stabF,paired=TRUE)
ttestFtrendandt3