R/doRev.R

In Paleantology/RevR: Interaction with "RevBayes" in R

#'Call RevBayes with Continuous Session History
#'
#'The basic Revticulate function for interacting with RevBayes
#'
#'This function allows users to make multiple calls to RevBayes, while maintaining a
#'persistent input history. This means that variables defined in one call can be referenced in
#'another call, giving the feel of a continuous RevBayes session.
#'
#'Because this function is the basis for repRev() and knitRev(), variables defined in RevBayes
#'with any of these functions can be referenced by any of the others.
#'
#'@param input character - Rev language expression to execute in RevBayes
#'
#'@param evaluate logical - If FALSE, input will be written to the .Revhistory file, but will not be interpreted in RevBayes. Default is FALSE.
#'
#'@param coerce logical - If TRUE, the output from RevBayes will be coerced into R format with coerceRev()
#'
#'@param viewCode logical - If TRUE, Rev code input and output will be displayed in the viewing pane. Mostly used for development purposes.
#'
#'@param timeout integer - Determines how long the system2() call should wait before timing out. Default is 5 seconds. For longer calls, see 'callRevFromTerminal()'
#'
#'@return now - RevBayes output, type varies. If coerce = TRUE, coerceRev() will attempt to convert RevBayes output into an equivalent R object. If else, the return type is character.
#'
#'@examples
#' \dontrun{
#' doRev("simTree(16)", coerce=FALSE)
#' doRev("a <- 10")
#' doRev("a * 100")
#'}
#'
#'@export
#'

doRev <- function(input, coerce = TRUE, evaluate = TRUE, viewCode = FALSE, timeout = 5){

  input <- unlist(input)

  if(!evaluate){
    cat(input, file = Sys.getenv("revHistory"), append = TRUE, sep = "\n")
    return("")
  }

  if(length(input) != 1)
    stop("Input length must equal one.")

  if(!all((str_count(input, c("\\(", "\\{", "\\[")) == str_count(input, c("\\)", "\\}", "\\]"))))){
    stop("RevBayes command must have an equal number of open and closing braces!")
  }

  allCode <- getRevHistory()

  try({

    first <- callRev(getRevHistory(), coerce = FALSE, timeout = timeout)
    cat(input, file = Sys.getenv("revHistory"), append = TRUE, sep = "\n")
    last <- callRev(getRevHistory(), coerce = FALSE, viewCode = viewCode, timeout = timeout)

  }, silent = TRUE)
  if(length(first) != 0)
    now <- last[-c(1:length(first))]
  else now <- last

  if(length(now) == 0)
    now <- ""

  if (any(str_detect(now, pattern = "Error:|error|Missing Variable:"))) {
    cat(allCode, file = Sys.getenv("revHistory"), append = FALSE, sep = "\n")
    if(coerce){
      cat(stringr::str_squish(now), file = stderr(), sep = "\n")
      return(invisible())
    }
  }

  if(coerce){
    now <- coerceRev(now)
    return(now)
  }

  if(length(now) > 1){
    if(str_squish(now[1]) == ""){
      now <- now[2:length(now)]
    }
  }

  return(now)
}