R/pipe_function.R

In emilio-berti/taxclean: Clean taxonomy using regex, taxize, and rgbif

#' @param x package name for the taxClean function (tc_...).
#' @param first if first package to be called.
#' @param after_gnr if called after rgnparser.
#' @param write if to write intermediate results to csv files.
pipe_function <- function(
  x,
  first = FALSE,
  after_gnr = FALSE,
  write
) {
  if (first) {
    if (write) {
      pipe <- paste0("tc_", x, "(d, write = TRUE)")
    } else {
      pipe <- paste0("tc_", x, "(d)")
    }
  } else if (after_gnr) {
    if (write) {
      pipe <- paste0("tc_", x, "(d, write = TRUE)")
    } else {
      pipe <- paste0("tc_", x, "(d)")
    }
  } else {
    if (write) {
      pipe <- paste0("tc_", x, "(ans$search_name[is.na(ans$scientific_name)], write = TRUE)")
    } else {
      pipe <- paste0("tc_", x, "(ans$search_name[is.na(ans$scientific_name)])")
    }
  }
  return(pipe)
}