mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 16:46:13 +01:00
57 lines
2.1 KiB
R
57 lines
2.1 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# AUTHORS #
|
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# LICENCE #
|
|
# This program is free software; you can redistribute it and/or modify #
|
|
# it under the terms of the GNU General Public License version 2.0, #
|
|
# as published by the Free Software Foundation. #
|
|
# #
|
|
# This program is distributed in the hope that it will be useful, #
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
|
# GNU General Public License for more details. #
|
|
# ==================================================================== #
|
|
|
|
#' 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
|
|
#' @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
|
|
}
|