library("JM")
library("lattice")

Jointmodelpred<-function(Source="D",filename,var1="CA125",var2=0,var3=0,var4=0,cutpoint=2,predictsurvtime=36){
unkpath<-"X:\\predictSurv\\Y.csv"
unkpath.id<-"X:\\predictSurv\\Y.id.csv"
path <- sub("X",Source,unkpath)
path.id <- sub("X",Source,unkpath.id)
name<- sub("Y",filename,path)
name.id<- sub("Y",filename,path.id)

a <- read.csv(name)
b <- read.csv(name.id)

numbvar1<-which(names(a)==var1)
variable1<-a[,numbvar1]
add1<-dim(a)[2]+1
a[,add1]<-variable1
names(a)[add1]<-"variable1"

add2<-dim(a)[2]+1
a[,add2]<-rep(cutpoint,length(variable1))
names(a)[add2]<-"cutpoint"

fitLME<-lme((variable1)^0.5 ~ I((obstime<cutpoint)*obstime+(obstime>=cutpoint)*cutpoint)+I((obstime-cutpoint)*(obstime>cutpoint)) , random = ~ I((obstime<cutpoint)*obstime+(obstime>=cutpoint)*cutpoint) | patient , data=a ,control=lmeControl(returnObject=TRUE, msMaxIter=100,maxIter=100))
numbvar2<-which(names(b)==var2)
numbvar3<-which(names(b)==var3)
numbvar4<-which(names(b)==var4)
if(length(numbvar2)==0 && length(numbvar3)==0 && length(numbvar4)==0)
{
fitSURV <- coxph(Surv(Survivaltime, death) ~ 1, data = b, x = TRUE)
}else if
(length(numbvar2)==1 && length(numbvar3)==0)
{
variable2<-b[,numbvar2]
fitSURV <- coxph(Surv(Survivaltime, death) ~ variable2, data = b, x = TRUE)
}else if
(length(numbvar2)==1 && length(numbvar3)==1 && length(numbvar4)==0)
{
variable2<-b[,numbvar2]
variable3<-b[,numbvar3]
fitSURV <- coxph(Surv(Survivaltime, death) ~ variable2+variable3, data = b, x = TRUE)
}else if
(length(numbvar2)==1 && length(numbvar3)==1 && length(numbvar4)==1)
{
variable2<-b[,numbvar2]
variable3<-b[,numbvar3]
variable4<-b[,numbvar4]
fitSURV <- coxph(Surv(Survivaltime, death) ~ variable2+variable3+variable4, data = b, x = TRUE)
}else
{
stop("Please enter the variables from var2")
}
fit.JM<- jointModel(fitLME, fitSURV, timeVar = "obstime", method = "piecewise-PH-GH")

numbvar5<-which(names(b)==var1)
variable5<-b[,numbvar5]
j<-matrix(,(length(variable5)),1)
for(i in 1:(length(variable5))){
ND2 <- subset(a,patient==i)
predSurv <- survfitJM(fit.JM, newdata = ND2, idVar = "patient", survTimes= predictsurvtime) 
j[i]<-predSurv[[1]][[1]][1,2]
}
print(j)

}