mirror of https://github.com/msberends/AMR.git
231 lines
8.4 KiB
R
Executable File
231 lines
8.4 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) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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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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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# 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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# No export, no Rd
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addin_insert_in <- function() {
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rstudioapi::insertText(" %in% ")
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}
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# No export, no Rd
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addin_insert_like <- function() {
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rstudioapi::insertText(" %like% ")
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}
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# No export, no Rd
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# works exactly like round(), but rounds `round(44.55, 1)` as 44.6 instead of 44.5
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# and adds decimal zeroes until `digits` is reached when force_zero = TRUE
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round2 <- function(x, digits = 0, force_zero = TRUE) {
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# https://stackoverflow.com/a/12688836/4575331
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val <- (trunc((abs(x) * 10 ^ digits) + 0.5) / 10 ^ digits) * sign(x)
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if (digits > 0 & force_zero == TRUE) {
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val[val != as.integer(val)] <- paste0(val[val != as.integer(val)],
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strrep("0", max(0, digits - nchar(gsub(".*[.](.*)$", "\\1", val[val != as.integer(val)])))))
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}
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val
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}
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# Coefficient of variation (CV)
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cv <- function(x, na.rm = TRUE) {
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stats::sd(x, na.rm = na.rm) / base::abs(base::mean(x, na.rm = na.rm))
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}
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# Coefficient of dispersion, or coefficient of quartile variation (CQV).
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# (Bonett et al., 2006: Confidence interval for a coefficient of quartile variation).
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cqv <- function(x, na.rm = TRUE) {
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fives <- stats::fivenum(x, na.rm = na.rm)
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(fives[4] - fives[2]) / (fives[4] + fives[2])
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}
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# show bytes as kB/MB/GB
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# size_humanreadable(123456) # 121 kB
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# size_humanreadable(12345678) # 11.8 MB
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size_humanreadable <- function(bytes, decimals = 1) {
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bytes <- bytes %>% as.double()
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# Adapted from:
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# http://jeffreysambells.com/2012/10/25/human-readable-filesize-php
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size <- c('B','kB','MB','GB','TB','PB','EB','ZB','YB')
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factor <- floor((nchar(bytes) - 1) / 3)
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# added slight improvement; no decimals for B and kB:
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decimals <- rep(decimals, length(bytes))
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decimals[size[factor + 1] %in% c('B', 'kB')] <- 0
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out <- paste(sprintf(paste0("%.", decimals, "f"), bytes / (1024 ^ factor)), size[factor + 1])
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out
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}
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percent_scales <- scales::percent
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# No export, no Rd
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# based on scales::percent
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percent <- function(x, round = 1, force_zero = FALSE, decimal.mark = getOption("OutDec"), ...) {
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x <- percent_scales(x = as.double(x),
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accuracy = 1 / 10 ^ round,
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decimal.mark = decimal.mark,
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...)
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if (force_zero == FALSE) {
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x <- gsub("([.]%|%%)", "%", paste0(gsub("0+%$", "", x), "%"))
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}
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x
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}
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#' @importFrom crayon blue bold red
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#' @importFrom dplyr %>% pull
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search_type_in_df <- function(x, type) {
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# try to find columns based on type
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found <- NULL
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colnames(x) <- trimws(colnames(x))
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# -- mo
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if (type == "mo") {
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if ("mo" %in% lapply(x, class)) {
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found <- colnames(x)[lapply(x, class) == "mo"][1]
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} else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria)s?$")) {
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found <- colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria)s?$"][1]
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} else if (any(colnames(x) %like% "species")) {
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found <- colnames(x)[colnames(x) %like% "species"][1]
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}
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}
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# -- key antibiotics
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if (type == "keyantibiotics") {
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if (any(colnames(x) %like% "^key.*(ab|antibiotics)")) {
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found <- colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics)"][1]
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}
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}
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# -- date
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if (type == "date") {
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if (any(colnames(x) %like% "^(specimen date|specimen_date|spec_date)")) {
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# WHONET support
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found <- colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"][1]
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if (!any(class(x %>% pull(found)) %in% c("Date", "POSIXct"))) {
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stop(red(paste0("ERROR: Found column `", bold(found), "` to be used as input for `col_", type,
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"`, but this column contains no valid dates. Transform its values to valid dates first.")),
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call. = FALSE)
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}
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} else {
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for (i in 1:ncol(x)) {
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if (any(class(x %>% pull(i)) %in% c("Date", "POSIXct"))) {
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found <- colnames(x)[i]
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break
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}
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}
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}
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}
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# -- patient id
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if (type == "patient_id") {
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if (any(colnames(x) %like% "^(identification |patient|patid)")) {
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found <- colnames(x)[colnames(x) %like% "^(identification |patient|patid)"][1]
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}
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}
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# -- specimen
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if (type == "specimen") {
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if (any(colnames(x) %like% "(specimen type|spec_type)")) {
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found <- colnames(x)[colnames(x) %like% "(specimen type|spec_type)"][1]
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} else if (any(colnames(x) %like% "^(specimen)")) {
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found <- colnames(x)[colnames(x) %like% "^(specimen)"][1]
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}
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}
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if (!is.null(found)) {
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msg <- paste0("NOTE: Using column `", bold(found), "` as input for `col_", type, "`.")
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if (type %in% c("keyantibiotics", "specimen")) {
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msg <- paste(msg, "Use", bold(paste0("col_", type), "= FALSE"), "to prevent this.")
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}
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message(blue(msg))
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}
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found
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}
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stopifnot_installed_package <- function(package) {
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# no "utils::installed.packages()" since it requires non-staged install since R 3.6.0
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# https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
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get(".packageName", envir = asNamespace(package))
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return(invisible())
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}
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# translate strings based on inst/translations.tsv
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#' @importFrom dplyr %>% filter
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translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
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# if (getOption("AMR_locale", "en") != language) {
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# language <- getOption("AMR_locale", "en")
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# }
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if (is.null(language)) {
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return(from)
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}
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if (language %in% c("en", "")) {
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return(from)
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}
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df_trans <- translations_file # internal data file
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if (!language %in% df_trans$lang) {
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stop("Unsupported language: '", language, "' - use one of: ",
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paste0("'", sort(unique(df_trans$lang)), "'", collapse = ", "),
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call. = FALSE)
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}
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df_trans <- df_trans %>% filter(lang == language)
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if (only_unknown == TRUE) {
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df_trans <- df_trans %>% filter(pattern %like% "unknown")
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}
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# default case sensitive if value if 'ignore.case' is missing:
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df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
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# default not using regular expressions (fixed = TRUE) if 'fixed' is missing:
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df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
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# check if text to look for is in one of the patterns
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any_form_in_patterns <- tryCatch(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
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error = function(e) {
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warning("Translation not possible. Please open an issue on GitLab (https://gitlab.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
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return(FALSE)
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})
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if (NROW(df_trans) == 0 | !any_form_in_patterns) {
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return(from)
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}
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for (i in 1:nrow(df_trans)) {
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from <- gsub(x = from,
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pattern = df_trans$pattern[i],
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replacement = df_trans$replacement[i],
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fixed = df_trans$fixed[i],
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ignore.case = df_trans$ignore.case[i])
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}
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# force UTF-8 for diacritics
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base::enc2utf8(from)
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}
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"%or%" <- function(x, y) {
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if (is.null(x) | is.null(y)) {
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if (is.null(x)) {
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return(y)
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} else {
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return(x)
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}
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}
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ifelse(!is.na(x),
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x,
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ifelse(!is.na(y), y, NA))
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}
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