GenericModelNMA:

library(devtools)
library(R2jags)
install_github("htx-r/CleaningData",force=TRUE)
install_github("htx-r/NMApredictionsRiskModel", force = TRUE)
install_github("htx-r/GenericModelNMA", force = TRUE)

library(NMApredictionsRiskModel)
library(CleaningData)
library(GenericModelNMA)
###### Give your path of data
mydatapath="/Users/tasneem/Desktop/TasnimPhD/multiple sclerosis/IPD data from 6 Biogen trials"

####################################  DATA   ###########################################
#########################################################################################
#### load data
cleanBIOGENtrials<-cleanBIOGENtrials.fun(mydatapath)
adsl01<-cleanBIOGENtrials$adsl01


adsl01_2 <- adsl01[adsl01$STUDYID%in%c('DEFINE','CONFIRM','AFFIRM'),]
#as.numeric(table(as.numeric(as.factor(adsl01_2$STUDYID))))

## IPDAD netmeta
jagsdataIPDADnetmeta <- list(
  N.IPD=3,
  Np=sum(as.numeric(table(as.numeric(as.factor(adsl01_2$STUDYID))))),
  studyid=as.numeric(as.factor(adsl01_2$STUDYID))-1,
  Y=adsl01_2$RELAPSE2year,
  treat= as.numeric(droplevels(as.factor(adsl01_2$TRT01A))),
naIPD = length(unique(droplevels(as.factor(adsl01_2$TRT01A)))),
base=rep(1,sum(as.numeric(table(as.numeric(as.factor(adsl01_2$STUDYID)))))),
naAD= 4,
rt = round(runif(10,20,100)),
n = round(runif(10,100,200)),
a.studyid = rep(1:10,each=2),
a.treat =c(1,2, 1,3, 1,3, 1,4, 2,3, 1,4, 1,4, 1,2, 2,3, 2,3),
a.base = rep(1,2*10),
max.treat = 4,
nAD=10
)
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)



## IPDAD netmetareg
jagsdataIPDADnetmetareg <- list(
  N.IPD=3,
  Np=sum(as.numeric(table(as.numeric(as.factor(adsl01_2$STUDYID))))),
  studyid=as.numeric(as.factor(adsl01_2$STUDYID))-1,
  Y=adsl01_2$RELAPSE2year,
  treat= as.numeric(droplevels(as.factor(adsl01_2$TRT01A))),
  naIPD = length(unique(droplevels(as.factor(adsl01_2$TRT01A)))),
  base=rep(1,sum(as.numeric(table(as.numeric(as.factor(adsl01_2$STUDYID)))))),
  naAD= 4,
  rt = round(runif(10,20,100)),
  n = round(runif(10,100,200)),
  a.studyid = rep(1:10,each=2),
  a.treat =c(1,2, 1,3, 1,3, 1,4, 2,3, 1,4, 1,4, 1,2, 2,3, 2,3),
  a.base = rep(1,2*10),
  max.treat = 4,
  nAD=10
)
IPDADnetmetaregJAGSmodel <- jags.parallel(data = jagsdataIPDADnetmetareg ,inits=NULL,parameters.to.save = c('d'),model.file = ModelIPDADnetmetareg,
                                       n.chains=2,n.iter = 100,n.burnin = 5,DIC=F,n.thin = 1)