referencesNMA/otherScripts/ModelIPDADnetmeta2.R

In htx-r/GenericModelNMA:

library(R2jags)
library(devtools)
install_github('htx-r/CleaningData',force = TRUE)
library(CleaningData)
## 4. Check if the calculated dummy variables are correct.
datapath="/Users/tasneem/Desktop/TasnimPhD/multiple sclerosis/IPD data from 6 Biogen trials"

cleanBIOGENtrials <- cleanBIOGENtrials.fun(datapath)
adarr_OBJREL <- cleanBIOGENtrials$adarr_OBJREL
adsl01 <- cleanBIOGENtrials$adsl01


ModelIPDADnetmeta <- function(){
  ######## NMA model
  for (i in 1:Np){
    dropout[i]~dbern(p.d[i] )
    logit(p.d[i])<-u0[studyid[i]]+(1-equals(treat[i],2))*Delta[i]+gamma[studyid[i]]*Risk[i]
    Delta[i]<-d[treat[i]]-d[2]
    }
  #### reference treatment= CBASP+medication = 2
  for (i in 1:Nstudies){
    u0[i]~dnorm(0,0.01)
    gamma[i]~dnorm(0,0.01)
    } # for prediction model MAKE SURE TO CHANGE THIS FOR SIMPLE IPD-NMA
  d[1]~dnorm(0,0.01)
  d[3]~dnorm(0,0.01)
  d[4]~dnorm(0,0.01)

  d[2]<-0

  }

adsl01_2 <- adsl01[adsl01$STUDYID%in%c('DEFINE','CONFIRM','AFFIRM'),]
#as.numeric(table(as.numeric(as.factor(adsl01_2$STUDYID))))
jagsdataIPDADnetmeta <- list(
  Nstudies=3,
  Npatients=as.numeric(table(as.numeric(as.factor(adsl01_2$STUDYID)))),
  Np=sum(as.numeric(table(as.numeric(as.factor(adsl01_2$STUDYID))))),
  studyid=as.numeric(as.factor(adsl01_2$STUDYID))-1,
  dropout=adsl01_2$RELAPSE2year,
  treat= as.numeric(droplevels(as.factor(adsl01_2$TRT01A))),
  Risk=rnorm(sum(as.numeric(table(as.numeric(as.factor(adsl01_2$STUDYID))))))

)
IPDADnetmetaJAGSmodel <- jags.parallel(data = jagsdataIPDADnetmeta ,inits=NULL,parameters.to.save = c('d'),model.file = ModelIPDADnetmeta,
                                    n.chains=2,n.iter = 100,n.burnin = 5,DIC=F,n.thin = 1)
str(jagsdataIPDADnetmeta)
## Freq  ------------------------------------------------------------------------
# Structure the dataset as the AcuteMania: Treatment name, r, n, studyid
AcuteManiaPair = pairwise(treat = treatment, event = r, n = n,
                          data = AcuteMania, studlab = studyid, sm = "OR")
net1 = netmeta(AcuteManiaPair, ref = "PLA", comb.fixed = FALSE, comb.random = TRUE)