R/nmajagsranks_bin_B.R

In esm-ispm-unibe-ch/rankingagreement:

### jags models for binary outcomes - positive outcome

nmajagsranks_bin_B <- function(netdata) {

  #transform the data into a list suitable for JAGS analysis
  NMAdataBinary=make.jagsNMA.data(studyid=id, t=t,
                                  r=r, n=n,
                                  data=netdata, type="binary", reference = min(netdata$t))



  #run Jags and create a jags object
  NMAinJAGS<- jags.parallel(data = NMAdataBinary, inits = NULL,
                            parameters.to.save = c("ORref","tau", "SUCRA"),
                            n.chains = 2, n.iter = 10000,
                            n.burnin = 1000,DIC=F, n.thin=2,
                            model.file = modelNMABinary.SUCRA_B)

  #check chain mixing
  traceplot(NMAinJAGS,varname="tau", ask=F)


  SUCRAjags_ranks <- (NMAdataBinary$nt+1) - rank(NMAinJAGS$BUGSoutput$mean$SUCRA)
  SUCRAjags <- NMAinJAGS$BUGSoutput$mean$SUCRA
  return(round(cbind("SUCRA jags"= SUCRAjags, "SUCRAjags ranks" = SUCRAjags_ranks), digits = 3))
}