IPDADmetaregAdjDesDATA.R

In htx-r/GenericModelNMA:

library(devtools)
library(R2jags)
install_github('htx-r/GenericModelNMA',force = T)
library(GenericModelNMA)

source('cleanData.R') # contains the FOUR different cleaned datasets
# data
# RCT-IPD
rct.ipd <-MSrelapse
# RCT-AD
rct.ad<-rct.ad[which(rct.ad$study=="Bornstein" | rct.ad$study=="Johnson"),]
# NRS-IPD
nrs.ipd <-nrs.ipd

# RCT-NRS-IPD-AD-NMA (naive approach)
rct.ipd2 <- rct.ipd[,c('STUDYID','RELAPSE2year','AGE','TRT01A')]
rct.nrs.ipd <- rbind.data.frame(rct.ipd2,nrs.ipd)

# RCT-NRS-IPD-AD NMA (design-adjusted)
jagsdataIPDADnetmetaregNRSdesAdj<- with(rct.nrs.ipd,list(
  nIPD=4,
  np=nrow(rct.nrs.ipd),
  studyid=as.numeric(factor(STUDYID)),
  y=as.numeric(RELAPSE2year)-1,
  x=as.numeric(AGE),
  xbar=unlist(sapply(unique(rct.nrs.ipd$STUDYID),function(i) rep(round(mean(rct.nrs.ipd[rct.nrs.ipd$STUDYID==i,'AGE'],na.rm = T),1),nrow(rct.nrs.ipd[rct.nrs.ipd$STUDYID==i,])))),
  t= rbind(c(4,1,NA,NA),c(4,1,2,NA),c(4,3,NA,NA), c(4,1,2,3),c(4,2,NA,NA),c(4,2,NA,NA)),
  na=c(2,3,2,4,2,2),
  treat=as.numeric(factor(TRT01A)),
  baseline=rep(4,nrow(rct.nrs.ipd)),
  bias=recode(STUDYID,'NRS'=1,.default=0),
  ref=4,
  nt=4,
  nAD=2,
  r=rbind(c(NA,11,NA,19),c(NA,89,NA,97)),
  n=rbind(c(NA,25,NA,25),c(NA,125,NA,126)),
  xbar.a =c(34.3,30)
)
)
jagsmodelIPDADnetmetaregNRSdesAdj <- jags.parallel(data = jagsdataIPDADnetmetaregNRSdesAdj,inits=NULL,parameters.to.save = c('d','tau','bb','bw','LOR'),model.file = modelIPDADnetmetaregNRSdesAdj,
                                                   n.chains=3,n.iter = 1000,n.burnin = 200,DIC=F,n.thin = 1)
jagsmodelIPDADnetmetaregNRSdesAdj