runLOO_jm = function(i,Tstart,predict_times,data,id){

  tryCatch({

    RD = data[which(data$PatientID %in% id[-i,1]),]

    ND = data[which(data$PatientID %in% id[i,1]),]

    RD.id = RD[which(!duplicated(RD$PatientID)), ]

    lmeFit1 <- lme( logAF ~ ns(TestDate,2),data=RD,random = ~  ns(TestDate,2) | PatientID,

                    control = lmeControl(opt = "optim",msMaxIter =1000))

    coxFit1 <- coxph(Surv(DFS,DFS_status)~TP53+T_stage,data=RD.id,x = TRUE)

    iForm <- list(fixed = ~ 0 + TestDate + ins(TestDate, 2), random = ~ 0 + TestDate + ins(TestDate, 2),

                  indFixed = 1:3, indRandom = 1:3)

    JM.RD <-jointModelBayes(lmeFit1, coxFit1, timeVar = "TestDate",

                            param = "td-extra", extraForm = iForm

    )

    NDn = ND[which(ND$TestDate<=Tstart),]

    survfit <- survfitJM(JM.RD, newdata = NDn,idVar = "PatientID",type="SurvProb",

                         survTimes = predict_times )

    survsum = survfit$summaries[[1]]

    res = cbind( ND,

           prob1=round(survsum[1,"Median"],4), # at 12 months

           prob2=round(survsum[2,"Median"],4) # at 15 months

    )

    return(res)

  },

  error=function(e) { print(e);return(NULL)}

  )

}

runLOO_cox = function(i,Tstart,predict_times,data,id){

  tryCatch({

    library(pec)

    RD = data[which(data$PatientID %in% id[-i,1]),]

    ND = data[which(data$PatientID %in% id[i,1]),]

    RD.id = RD[which(!duplicated(RD$PatientID)), ]

    dataLM <- JMbayes:::dataLM

    D1 = dataLM(RD, Tstart, idVar ="PatientID" ,respVar = "Test_status", timeVar = "TestDate", 

                evTimeVar = "DFS")

    # landmarking cox

    CoxLM1 <- coxph(Surv(DFS, DFS_status) ~ Test_status+T_stage+TP53, x=TRUE,

                    data = D1)

    NDn = tail(ND[which(ND$TestDate<=Tstart),],1)

    pred_lm1 = predictSurvProb(CoxLM1,newdata = NDn, times = predict_times)

    res = cbind( ND,

                 cox1_prob1=round(pred_lm1[[1]],4),

                 cox1_prob2=round(pred_lm1[[2]],4)

                 )

    return(res)

  },

  error=function(e) { print(e);return(NULL)}

  )

}

###### test #########

data = mydata

id = mydata.id

runLOO_jm(1,Tstart,predict_times,mydata,mydata.id)