AMR/R/p.symbol.R

61 lines
2.4 KiB
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.gitab.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
}