jmstB: Joint model for Bidirectional survival data using 'rstanarm'

In JMbdirect: Joint Model for Longitudinal and Multiple Time to Events Data

Joint model for Bidirectional survival data using rstanarm

Description

The function fits joint model for survival data with two events. It utilizes the rstanarm package for obtaining the model parameter estimates.

Usage

jmstB(
  dtlong,
  dtsurv,
  longm,
  survm,
  timeVar,
  id,
  nchain = 1,
  refresh = 1000,
  BIGdata = FALSE,
  samplesize = 200
)

Arguments

dtlong	longitudinal data
dtsurv	survival data with two event status along with event time
longm	longitudinal model e.g. list(serBilir~drug * year+(year|id),serBilir ~ drug * year+(year|id))
survm	survival model e.g. list(Surv(years,status2)~drug,Surv(time_2,status_2)~drug+age)
timeVar	time variable
id	ID variable
nchain	number of MCMC chain
refresh	number of refresh sample
BIGdata	logical argument TRUE or FALSE
samplesize	samplesize for bigdata

Value

Estimated model parameters of Joint model with bidirectional survival data

Author(s)

Atanu Bhattacharjee, Bhrigu Kumar Rajbongshi and Gajendra Kumar Vishwakarma

References

Goodrich, B., et al. "rstanarm: Bayesian applied regression modeling via Stan. R package version 2.17. 4." Online< http://mc-stan. org (2018).

Bhattacharjee, A., Rajbongshi, B. K., & Vishwakarma, G. K. (2024). jmBIG: enhancing dynamic risk prediction and personalized medicine through joint modeling of longitudinal and survival data in big routinely collected data. BMC Medical Research Methodology, 24(1), 172.

Examples

 
 ##
library(JMbayes2)
library(rstanarm)
st_pbcid<-function(){
  new_pbcid<-pbc2.id
  new_pbcid$time_2<-rexp(n=nrow(pbc2.id),1/10)
  cen_time<-runif(nrow(pbc2.id),min(new_pbcid$time_2),max(new_pbcid$time_2))
  status_2<-ifelse(new_pbcid$time_2<cen_time,1,0)
  new_pbcid$status_2<-status_2
  new_pbcid$time_2<-ifelse(new_pbcid$time_2<cen_time,new_pbcid$time_2,cen_time)
  new_pbcid$time_2<-ifelse(new_pbcid$time_2<new_pbcid$years,new_pbcid$years,
                           new_pbcid$time_2)
  new_pbcid
}
new_pbc2id<-st_pbcid()
pbc2$status_2<-rep(new_pbc2id$status_2,times=data.frame(table(pbc2$id))$Freq)
pbc2$time_2<-rep(new_pbc2id$time_2,times=data.frame(table(pbc2$id))$Freq)
pbc2_new<-pbc2[pbc2$id%in%c(1:50),]
new_pbc2id<-new_pbc2id[new_pbc2id$id%in%c(1:50),]
model_jmstBdirect<-jmstB(
  dtlong=pbc2_new,
  dtsurv = new_pbc2id,
  longm=list(serBilir~drug*year+(year|id),albumin~drug+year+(year|id)),
  survm=list(Surv(years,status2)~drug,Surv(time_2,status_2)~drug),
  timeVar="year",
  id='id',
  refresh=400,
  nchain=1)
model_jmstBdirect
##
 

JMbdirect documentation built on April 12, 2025, 1:55 a.m.