R/runARGES.R

In CompareCausalNetworks: Interface to Diverse Estimation Methods of Causal Networks

runARGES <- function(X, parentsOf, variableSelMat, setOptions, directed, verbose, 
                   ...){
  
  
  package <- setOptions$package
  if(is.null(package)) package <- "huge"
  
  if(package == "huge"){
    method <- setOptions$method
    if(is.null(method)) method <- "mb"
    criterion <- setOptions$criterion
    if(is.null(criterion)) criterion <- "ric"
  }else if(package == "flare"){
    method <- setOptions$method
    if(is.null(method)) method <- "tiger"
    criterion <- setOptions$criterion
    if(is.null(criterion)) criterion <- "cv"
  }else{
    stop(paste("Package", package, "not supported for CIG estimation. Valid
               options are 'huge' or 'flare'."))
  }
  
  # estimate CIG
  if(is.null(variableSelMat)){
    if(package == "huge"){
      hugeObj <- huge::huge(X, method = method, verbose = FALSE)
      hugeSel <- huge::huge.select(hugeObj, criterion = criterion, verbose = FALSE)
      variableSelMat <- hugeSel$refit
    }else{
      flareObj <- flare::sugm(X, method = method, verbose = FALSE)  
      flareSel <- flare::sugm.select(flareObj,  criterion = criterion, verbose = FALSE)  
      variableSelMat <- flareSel$refit
    }
    
    variableSelMat <- as.matrix(variableSelMat)
    variableSelMat[variableSelMat == 1] <- TRUE
    variableSelMat[variableSelMat == 0] <- FALSE
  }
  
  # additional options for ARGES
  if(is.null(setOptions$adaptive)){
    setOptions$adaptive <- "vstructures" #ARGES-CIG
  }else{
    if(setOptions$adaptive == "none")
      setOptions$adaptive <- "vstructures" #ARGES-CIG
  }
  
  runGES(X, parentsOf, variableSelMat, setOptions, directed, verbose, 
         ...)
}