R/mnma.run.R

In vandy10s/mnma: Multivariate Network Meta-Analysis (NMA) within a Bayesian Framework

#' @title Run multivariate network meta-analysis (NMA) anlaysis
#' @description The function conducts bivariate NMA using a \code{mnma.model} object as an input. It uses \bold{OpenBUGS} software (through the \code{R2OpenBUGS} package).
#' @param input \code{mnma.model} class data, which can be generated using \code{mnma.model} function
#' @param inits  a list of initial values for \bold{OpenBUGS} model with \code{n.chains} elements; If \code{inits=NULL} (default), initial values are randomly generated by \bold{OpenBUGS}.
#' @param n.iter number of total iterations per chain (default: 5000)
#' @param n.burnin length of burnin per chain (default: 2000)
#' @param n.chains number of Markov chains (default: 1)
#' @param n.thin  thining rate (default: 1)
#' @param debug if FALSE (default), \strong{OpenBUGS} is closed automatically after running the \code{mnma.run} script. If TRUE, \strong{OpenBUGS} remains open with additional information.
#' @param codaPkg if FALSE (default), a \code{bugs} object is returned. Otherwise, file names of \strong{OpenBUGS} output are returned with TRUE.
#' @import R2OpenBUGS
#' @export
#' @references Efthimiou et al. (2015) Biostatistics 16(1):84-97
#' (\href{https://academic.oup.com/biostatistics/article/16/1/84/258780}{doi: 10.1093/biostatistics/kxu030})
#' @seealso \code{\link[R2OpenBUGS]{bugs}}
#' @return \code{mnma.result} class \code{bugs} result. See \code{\link[R2OpenBUGS]{bugs}} for details.
#' @examples \dontrun{
#' # Run after data transformation using mnma.model function.
#' res <- mnma.run(data, n.iter=3000, n.burnin=1000)
#' names(res)
#' # provides mean, standard deviation, and percentile information about log odds ratio
#' res$summary
#' }
#'
#'


mnma.run <- function(input, inits=NULL, n.iter=5000, n.burnin=2000, n.chains=1, n.thin=1, debug=FALSE, codaPkg=FALSE){

  input <- input$multivariate

  if (input$noa=="3arm"){
    models = model.file = system.file("bnma_3arm.txt",package="mnma")  # Fix the location
  } else if (input$noa=="2arm"){
    models = model.file = system.file("bnma_2arm.txt",package="mnma")  # Fix the location
  }

  if ( class(input) == "mnma.model"){

    data <- as.list(input$data)

    out.mul <- bugs(data=data,
                    inits=inits,
                    parameters.to.save= input$parameters,
                    n.iter=n.iter,
                    n.burnin=n.burnin,
                    n.thin=n.thin,
                    n.chains=n.chains,
                    model.file = models,
                    debug=debug,
                    codaPkg=codaPkg,
                    DIC = FALSE  # To have the results, we need to set this off.
    )

    class(out.mul) <- "mnma.result"
  }else{
    stop("Input data have to be 'mnma.model' class ")
  }
  return(out.mul)
}