R/makejagsIPDADnetmeta.R

In htx-r/GenericModelNMA:

#%%%%%%%%%%%%%%%%%#%%%%%%%%%%%%%%%%%#%%%%%%%%%%%%%%%%%#%%%%%%%%%%%%%%%%%#%%%%%%%%%%%%%%%%%
## JAGSdata: The whole dataset with IPDdata and ADdata in order to use it JAGS model
#%%%%%%%%%%%%%%%%%#%%%%%%%%%%%%%%%%%#%%%%%%%%%%%%%%%%%#%%%%%%%%%%%%%%%%%#%%%%%%%%%%%%%%%%%
makejagsIPDADnetmeta <- function(IPDdata,ADdata=NULL){
  if(is.null(ADdata)){# from IPD data we get the following
  studyid <- eval(substitute(studyid), IPDdata)
  y <- eval(substitute(y), IPDdata)
  treat <- eval(substitute(treat), IPDdata)
  baseline <- eval(substitute(baseline), IPDdata)

  # treatment indices matrix
  t <- tmat
  # additional needed numbers
  na <- na # number of arms
  nt <- length(levels(factor(treat))) # number of treatments
  nIPD <- length(unique(studyid)) # number of IPD studies
  ref <- unique(baseline) # the reference treatment index}
  jagsdataIPDADnetmeta <- list(y=y,treat=treat,baseline=baseline,studyid=studyid,
                           t=t,np=np,na=na,nt=nt,nIPD=nIPD,ref=ref)
  return(jagsdataIPDADnetmeta)
  }else{ # IPD and AD
    studyid <- eval(substitute(studyid), IPDdata)
    y <- eval(substitute(y), IPDdata)
    treat <- eval(substitute(treat), IPDdata)
    baseline <- eval(substitute(baseline), IPDdata)

    # treatment indices matrix
    t <- tmat

    # additional needed numbers
    na <- na # number of arms
    nt <- length(levels(factor(treat))) # number of treatments
    nIPD <- length(unique(studyid)) # number of IPD studies
    ref <- unique(baseline) # the reference treatment index}

    # additionally for AD
    nAD <- nAD
    r <- rmat
    n <- nmat

    jagsdataIPDADnetmeta <- list(y=y,treat=treat,baseline=baseline,studyid=studyid,
                                 t=t,np=np,na=na,nt=nt,nIPD=nIPD,ref=ref,
                                 nAD=nAD,r=r,n=n)

    return(jagsdataIPDADnetmeta)
  }
}
#

makejagsIPDADnetmeta <- function(){
  IPDdata <- data$IPDdata
  ADdata <- data$ADdata
  IPDdata$studyid <- eval(substitute(studyid), IPDdata)
  IPDdata$y <- eval(substitute(y), IPDdata)
  IPDdata$treat <- eval(substitute(treat), IPDdata)
  rt <- eval(substitute(rt), ADdata)
  nt <- eval(substitute(nt), ADdata)
  rc <- eval(substitute(rc), ADdata)
  nc <- eval(substitute(nc), ADdata)
  ADdata$studyid.a <- eval(substitute(studyid.a), ADdata)
studyid <- as.numeric(as.factor(studyid))
treat <- as.numeric(as.factor(treat))
  }
#
# MakeJAGSdataIPDADnetmeta <- function(IPDdata=SimulatedIPDADmeta()$IPDdata,ADdata=SimulatedIPDADmeta()$ADdata) {
#
#   # IPD
#
#   J.IPD_i <- as.vector(table(IPDdata$study.IPD))
#   N.IPD <- length(unique(IPDdata$study.IPD))
#
#   #
#   Y <- matrix(NA,N.IPD,max(J.IPD_i))
#   for (i in 1:N.IPD) {
#     Y[i,1:J.IPD_i[i]] <- IPDdata$Y_ij[IPDdata$study.IPD == i]
#   }
#
#   t <- matrix(NA,N.IPD,max(J.IPD_i))
#   for (i in 1:N.IPD) {
#     t[i,1:J.IPD_i[i]] <- IPDdata$t[IPDdata$study.IPD == i]
#   }
#
#   ## AD
#   rc <- ADdata$rc
#   rt <- ADdata$rt
#   nc_i <- ADdata$nc
#   nt_i <- ADdata$nt
#   N.AD <- length(unique(ADdata$study.AD))
#   IPDADmetareg_dataJAGS<- list(Y=Y,t = t,J.IPD_i=J.IPD_i,
#                                rc=rc,rt=rt,nc=nc_i,nt=nt_i,N.AD=N.AD,N.IPD=N.IPD)
#   return(IPDADmetareg_dataJAGS)
# }
#
# #JAGSdataIPDADmeta()