#install.packages("rms")

library(rms)

setwd("n")

non_tumor<-read.table("input.txt",header=T,sep="\t")
 
#non_tumor$Use_of_GC<-factor(non_tumor$Use_of_GC,labels=c("No","Yes"))
#non_tumor$Use_of_NSAIDs<-factor(non_tumor$Use_of_NSAIDs,labels=c("No","Yes"))
#non_tumor$Number_of_questions<-factor(non_tumor$Number_of_questions,labels=c("0","1",">=2"))
#non_tumor$Education_level<-factor(non_tumor$Education_level,labels=c("Primary","Secondary","Higher"))
#non_tumor$Distance<-factor(non_tumor$Distance,labels=c("No","Yes"))

ddist <- datadist(non_tumor)
options(datadist="ddist")

mylog<-lrm(Status~Use_of_GC + Use_of_NSAIDs + Number_of_questions + Education_level + Distance,data=non_tumor,x=T,y=T)

mycal<-calibrate(mylog,method="boot",B=1000)

pdf("Calibration.pdf")
plot(mycal,xlab="Nomogram-predicted probability of nonadherence",ylab="Actual diagnosed nonadherence (proportion)",sub=F)
dev.off()