dat<-read.table("E://my file/BC project/Project II/KM estimates/data.txt",header=TRUE,sep="\t")

attach(dat)


## OS for whole group

# NO CI

OS_whole<-survfit(Surv(SURVP/365.25,STATP)~1,type="kaplan-meier")

plot(OS_whole,main="OS for whole group",conf.int=F,xlab="years",ylab="probability")


# 95% cI

OS_whole<-survfit(Surv(SURVP/365.25,STATP)~1,type="kaplan-meier",conf.type="log-log")

plot(OS_whole,main="OS for whole group",conf.int=T,xlab="years",ylab="probability")

mtext("with 95% confidence interval",side=3)


## EFS for whole group

# NO CI

EFS_whole<-survfit(Surv(SURVEFP/365.25,STATEFP)~1,type="kaplan-meier")

plot(EFS_whole,main="EFS for whole group",conf.int=F,xlab="years",ylab="probability")


# 95% CI

EFS_whole<-survfit(Surv(SURVEFP/365.25,STATEFP)~1,type="kaplan-meier",conf.type="log-log")

plot(EFS_whole,main="EFS for whole group",conf.int=T,xlab="years",ylab="probability")

mtext("with 95% confidence interval",side=3)


## OS for group split into allo/auto with log-rank comparison

OS_aa<-survdiff(Surv(SURVP,STATP)~TYPE,rho=0)