library(rms)

setwd("")

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("<3km",">=3km"))

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

mylog<-lrm(MDR~CREA+Fever+	FIB+Invasiveoperation+
             LYMPH+	Age	+	DD	+APTT,data=non_tumor,x=T,y=T)

mylog

#install.packages("Hmisc")
library(Hmisc)

Cindex <- rcorrcens(non_tumor$Status~predict(mylog))
Cindex

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()