AMR/R/p.symbol.R

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Analysis                              #
#                                                                      #
# SOURCE                                                               #
# https://gitlab.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
#                                                                      #
# This R package is free software; you can freely use and distribute   #
# it for both personal and commercial purposes under the terms of the  #
# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
# the Free Software Foundation.                                        #
#                                                                      #
# This R package was created for academic research and was publicly    #
# released in the hope that it will be useful, but it comes WITHOUT    #
# ANY WARRANTY OR LIABILITY.                                           #
# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
# ==================================================================== #

#' Symbol of a p value
#'
#' Return the symbol related to the p value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above \code{p = 1} will return \code{NA}.
#' @param p p value
#' @param emptychar text to show when \code{p > 0.1}
#' @return Text
#' @inheritSection AMR Read more on our website!
#' @export
p.symbol <- function(p, emptychar = " ") {
  setting.bak <- options()$scipen
  options(scipen = 999)
  s <- vector(mode = "character", length = length(p))
  for (i in 1:length(p)) {
    if (is.na(p[i])) {
      s[i] <- NA_character_
      next
    }
    if (p[i] > 1) {
      s[i] <- NA_character_
      next
    } else {
      p_test <- p[i]
    }

    if (p_test > 0.1) {
      s[i] <- emptychar
    } else if (p_test > 0.05) {
      s[i] <- '.'
    } else if (p_test > 0.01) {
      s[i] <- '*'
    } else if (p_test > 0.001) {
      s[i] <- '**'
    } else if (p_test >= 0) {
      s[i] <- '***'
    }
  }
  options(scipen = setting.bak)
  s
}