R/pc_helper.R

In causalMGM: Causal Learning of Mixed Graphical Models

get_directed_graph <- function(ds, graph, PC){

  # Check alpha value is valid
  check_alpha <- function(alpha){
    if(alpha < 0 || alpha > 1){
      print("Error: alpha values must be between 0 and 1")
      return(FALSE)
    } else {
      return(TRUE)
    }
  }

  get_new_alpha <- function(alpha){
    prompt <- paste("Please enter the alpha value you would like to use: ")
    alpha <- readline(prompt)
    if(!check_alpha(alpha)){
      get_alpha(alpha)
    } else {
      return(alpha)
    }
  }

  check_alpha_change <- function(response, alpha){
    if(identical(response, "y")){
      alpha <- get_new_alpha(alpha)
    }
    return(alpha)
  }

  get_alpha <- function(alpha){
    response <- readline(prompt="The default alpha value is 0.05. To change this alpha value, enter 'y': ")
    alpha <- check_alpha_change(response, alpha)
    return(alpha)
  }

  check_preferLinear <- function(preferLinear){
    linear_response <- readline(prompt="If you prefer to use linear regression, enter 'y': ")
    if(identical(linear_response, 'y')){
      preferLinear <- TRUE
    } else{
      preferLinear <- FALSE
    }
    return(preferLinear)
  }
  alpha <- 0.05
  alpha <- as.numeric(get_alpha(alpha))
  preferLinear <- TRUE
  preferLinear <- check_preferLinear(preferLinear)


  IndTest <- J("edu/pitt/csb/mgm/IndTestMultinomialAJ")
  indt <- new(IndTest, ds, alpha, preferLinear)
  pc <- new(PC, indt)

  .jcall(pc, "V", "setInitialGraph", graph)
  pc_graph <- .jcall(pc, "Ledu/cmu/tetrad/graph/Graph;", "search")
  pc_output <- .jcall(pc_graph, "Ljava/lang/String;", "toString")

  # Generate random number
  rn <- randnum()

  output_filename <- paste("causalMGM_directedgraph_",rn,".txt", sep="")

  # Write string to output file
  lapply(strsplit(pc_output[1], "\n"), write, output_filename)

  outputfile_path <- paste(getwd(), output_filename, sep=.Platform$file.sep)
  end_message <- paste("The output has been saved to", outputfile_path)
  print(end_message)

  return(pc_graph)
}