mirror of
https://github.com/msberends/AMR.git
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72 lines
3.8 KiB
R
Executable File
72 lines
3.8 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' @importFrom cleaner freq
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#' @export
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cleaner::freq
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#' @exportMethod freq.mo
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#' @importFrom dplyr n_distinct
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#' @importFrom cleaner freq.default percentage
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#' @export
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#' @noRd
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freq.mo <- function(x, ...) {
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x_noNA <- as.mo(x[!is.na(x)]) # as.mo() to get the newest mo codes
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grams <- mo_gramstain(x_noNA, language = NULL)
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digits <- list(...)$digits
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if (is.null(digits)) {
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digits <- 2
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}
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freq.default(x = x, ...,
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.add_header = list(`Gram-negative` = paste0(format(sum(grams == "Gram-negative", na.rm = TRUE),
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big.mark = ",",
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decimal.mark = "."),
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" (", percentage(sum(grams == "Gram-negative", na.rm = TRUE) / length(grams), digits = digits),
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")"),
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`Gram-positive` = paste0(format(sum(grams == "Gram-positive", na.rm = TRUE),
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big.mark = ",",
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decimal.mark = "."),
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" (", percentage(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), digits = digits),
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")"),
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`No of genera` = n_distinct(mo_genus(x_noNA, language = NULL)),
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`No of species` = n_distinct(paste(mo_genus(x_noNA, language = NULL),
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mo_species(x_noNA, language = NULL)))))
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}
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#' @exportMethod freq.rsi
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#' @importFrom cleaner freq.default
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#' @export
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#' @noRd
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freq.rsi <- function(x, ...) {
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x_name <- deparse(substitute(x))
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x_name <- gsub(".*[$]", "", x_name)
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ab <- suppressMessages(suppressWarnings(AMR::as.ab(x_name)))
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if (!is.na(ab)) {
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freq.default(x = x, ...,
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.add_header = list(Drug = paste0(ab_name(ab), " (", ab, ", ", ab_atc(ab), ")"),
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group = ab_group(ab),
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`%SI` = AMR::susceptibility(x, minimum = 0, as_percent = TRUE)))
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} else {
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freq.default(x = x, ...,
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.add_header = list(`%SI` = AMR::susceptibility(x, minimum = 0, as_percent = TRUE)))
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}
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}
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