mirror of
https://github.com/msberends/AMR.git
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459 lines
17 KiB
R
Executable File
459 lines
17 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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# functions from dplyr, will perhaps become poorman
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distinct <- function(.data, ..., .keep_all = FALSE) {
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check_is_dataframe(.data)
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if ("grouped_data" %in% class(.data)) {
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distinct.grouped_data(.data, ..., .keep_all = .keep_all)
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} else {
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distinct.default(.data, ..., .keep_all = .keep_all)
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}
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}
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distinct.default <- function(.data, ..., .keep_all = FALSE) {
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names <- rownames(.data)
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rownames(.data) <- NULL
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if (length(deparse_dots(...)) == 0) {
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selected <- .data
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} else {
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selected <- select(.data, ...)
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}
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rows <- as.integer(rownames(unique(selected)))
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if (isTRUE(.keep_all)) {
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res <- .data[rows, , drop = FALSE]
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} else {
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res <- selected[rows, , drop = FALSE]
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}
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rownames(res) <- names[rows]
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res
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}
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distinct.grouped_data <- function(.data, ..., .keep_all = FALSE) {
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apply_grouped_function(.data, "distinct", ..., .keep_all = .keep_all)
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}
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filter_join_worker <- function(x, y, by = NULL, type = c("anti", "semi")) {
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type <- match.arg(type, choices = c("anti", "semi"), several.ok = FALSE)
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if (is.null(by)) {
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by <- intersect(names(x), names(y))
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join_message(by)
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}
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rows <- interaction(x[, by]) %in% interaction(y[, by])
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if (type == "anti") rows <- !rows
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res <- x[rows, , drop = FALSE]
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rownames(res) <- NULL
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res
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}
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# No export, no Rd
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addin_insert_in <- function() {
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stopifnot_installed_package("rstudioapi")
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get("insertText", envir = asNamespace("rstudioapi"))(" %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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stopifnot_installed_package("rstudioapi")
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get("insertText", envir = asNamespace("rstudioapi"))(" %like% ")
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}
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check_dataset_integrity <- function() {
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tryCatch({
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check_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
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"class", "order", "family", "genus",
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"species", "subspecies", "rank",
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"col_id", "species_id", "source",
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"ref", "prevalence", "snomed") %in% colnames(microorganisms),
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na.rm = TRUE) & NROW(microorganisms) == NROW(MO_lookup)
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check_antibiotics <- all(c("ab", "atc", "cid", "name", "group",
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"atc_group1", "atc_group2", "abbreviations",
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"synonyms", "oral_ddd", "oral_units",
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"iv_ddd", "iv_units", "loinc") %in% colnames(antibiotics),
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na.rm = TRUE)
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}, error = function(e)
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stop('Please use the command \'library("AMR")\' before using this function, to load the required reference data.', call. = FALSE)
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)
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if (!check_microorganisms | !check_antibiotics) {
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stop("Data set `microorganisms` or data set `antibiotics` is overwritten by your global environment and prevents the AMR package from working correctly. Please rename your object before using this function.", call. = FALSE)
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}
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invisible(TRUE)
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}
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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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x <- as.data.frame(x, stringsAsFactors = FALSE)
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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 ("mo" %in% colnames(x) &
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suppressWarnings(
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all(x$mo %in% c(NA,
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microorganisms$mo,
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microorganisms.translation$mo_old)))) {
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found <- "mo"
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} else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$")) {
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found <- colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$"][1]
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} else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|bacterie)")) {
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found <- colnames(x)[colnames(x) %like% "^(microorganism|organism|bacteria|bacterie)"][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(pull(x, found)) %in% c("Date", "POSIXct"))) {
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stop(font_red(paste0("ERROR: Found column `", font_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 seq_len(ncol(x))) {
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if (any(class(pull(x, 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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# -- UTI (urinary tract infection)
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if (type == "uti") {
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if (any(colnames(x) == "uti")) {
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found <- colnames(x)[colnames(x) == "uti"][1]
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} else if (any(colnames(x) %like% "(urine|urinary)")) {
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found <- colnames(x)[colnames(x) %like% "(urine|urinary)"][1]
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}
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if (!is.null(found)) {
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# this column should contain logicals
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if (!is.logical(x[, found, drop = TRUE])) {
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message(font_red(paste0("NOTE: Column `", font_bold(found), "` found as input for `col_", type,
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"`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.")))
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found <- NULL
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}
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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 `", font_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", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
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}
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message(font_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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sapply(package, function(x)
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tryCatch(get(".packageName", envir = asNamespace(x)),
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error = function(e) stop("package '", x, "' required but not installed.",
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"\nTry to install it with: install.packages(\"", x, "\")",
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call. = FALSE)))
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return(invisible())
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}
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stopifnot_msg <- function(expr, msg) {
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if (!isTRUE(expr)) {
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stop(msg, call. = FALSE)
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}
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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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class_integrity_check <- function(value, type, check_vector) {
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if (!all(value[!is.na(value)] %in% check_vector)) {
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warning(paste0("invalid ", type, ", NA generated"), call. = FALSE)
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value[!value %in% check_vector] <- NA
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}
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value
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}
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# transforms data set to data.frame with only ASCII values, to comply with CRAN policies
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dataset_UTF8_to_ASCII <- function(df) {
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trans <- function(vect) {
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iconv(vect, from = "UTF-8", to = "ASCII//TRANSLIT")
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}
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df <- as.data.frame(df, stringsAsFactors = FALSE)
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for (i in seq_len(NCOL(df))) {
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col <- df[, i]
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if (is.list(col)) {
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col <- lapply(col, function(j) trans(j))
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df[, i] <- list(col)
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} else {
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if (is.factor(col)) {
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levels(col) <- trans(levels(col))
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} else if (is.character(col)) {
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col <- trans(col)
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} else {
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col
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}
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df[, i] <- col
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}
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}
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df
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}
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# replace crayon::has_color
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has_colour <- function() {
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if (Sys.getenv("TERM") == "dumb") {
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return(FALSE)
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}
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if (tolower(Sys.info()["sysname"]) == "windows") {
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if (Sys.getenv("ConEmuANSI") == "ON" | Sys.getenv("CMDER_ROOT") != "") {
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return(TRUE)
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} else {
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return(FALSE)
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}
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}
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"COLORTERM" %in% names(Sys.getenv()) | grepl("^screen|^xterm|^vt100|color|ansi|cygwin|linux",
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Sys.getenv("TERM"),
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ignore.case = TRUE,
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perl = TRUE)
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}
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# the crayon colours
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try_colour <- function(..., before, after, collapse = " ") {
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txt <- paste0(unlist(list(...)), collapse = collapse)
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if (isTRUE(has_colour())) {
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if (is.null(collapse)) {
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paste0(before, txt, after, collapse = NULL)
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} else {
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paste0(before, txt, after, collapse = "")
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}
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} else {
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txt
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}
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}
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font_black <- function(..., collapse = " ") {
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try_colour(..., before = "\033[38;5;232m", after = "\033[39m", collapse = collapse)
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}
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font_blue <- function(..., collapse = " ") {
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try_colour(..., before = "\033[34m", after = "\033[39m", collapse = collapse)
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}
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font_green <- function(..., collapse = " ") {
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try_colour(..., before = "\033[32m", after = "\033[39m", collapse = collapse)
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}
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font_magenta <- function(..., collapse = " ") {
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try_colour(..., before = "\033[35m", after = "\033[39m", collapse = collapse)
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}
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font_red <- function(..., collapse = " ") {
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try_colour(..., before = "\033[31m", after = "\033[39m", collapse = collapse)
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}
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font_silver <- function(..., collapse = " ") {
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try_colour(..., before = "\033[90m", after = "\033[39m", collapse = collapse)
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}
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font_white <- function(..., collapse = " ") {
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try_colour(..., before = "\033[37m", after = "\033[39m", collapse = collapse)
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}
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font_yellow <- function(..., collapse = " ") {
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try_colour(..., before = "\033[33m", after = "\033[39m", collapse = collapse)
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}
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font_subtle <- function(..., collapse = " ") {
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try_colour(..., before = "\033[38;5;246m", after = "\033[39m", collapse = collapse)
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}
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font_grey <- function(..., collapse = " ") {
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try_colour(..., before = "\033[38;5;249m", after = "\033[39m", collapse = collapse)
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}
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font_green_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[42m", after = "\033[49m", collapse = collapse)
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}
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font_red_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[41m", after = "\033[49m", collapse = collapse)
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}
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font_yellow_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[43m", after = "\033[49m", collapse = collapse)
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}
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font_bold <- function(..., collapse = " ") {
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try_colour(..., before = "\033[1m", after = "\033[22m", collapse = collapse)
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}
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font_italic <- function(..., collapse = " ") {
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try_colour(..., before = "\033[3m", after = "\033[23m", collapse = collapse)
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}
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font_underline <- function(..., collapse = " ") {
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try_colour(..., before = "\033[4m", after = "\033[24m", collapse = collapse)
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}
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font_stripstyle <- function(x) {
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# from crayon:::ansi_regex
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gsub("(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]", "", x, perl = TRUE)
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}
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progress_estimated <- function(n = 1, n_min = 0, ...) {
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if (n >= n_min) {
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pb <- utils::txtProgressBar(max = n, style = 3)
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pb$tick <- function() {
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pb$up(pb$getVal() + 1)
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}
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pb
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} else {
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pb <- list()
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pb$tick <- function() {
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invisible()
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}
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pb$kill <- function() {
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invisible()
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}
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structure(pb, class = "txtProgressBar")
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}
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}
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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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x <- as.double(x)
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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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values_trans <- val[val != as.integer(val) & !is.na(val)]
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val[val != as.integer(val) & !is.na(val)] <- paste0(values_trans,
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strrep("0",
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max(0,
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digits - nchar(
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format(
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as.double(
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gsub(".*[.](.*)$",
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"\\1",
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values_trans)),
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scientific = FALSE)))))
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}
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as.double(val)
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}
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# percentage from our other package: 'cleaner'
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percentage <- function(x, digits = NULL, ...) {
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# getdecimalplaces() function
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getdecimalplaces <- function(x, minimum = 0, maximum = 3) {
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if (maximum < minimum) {
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maximum <- minimum
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}
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if (minimum > maximum) {
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minimum <- maximum
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}
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max_places <- max(unlist(lapply(strsplit(sub("0+$", "",
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as.character(x * 100)), ".", fixed = TRUE),
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function(y) ifelse(length(y) == 2, nchar(y[2]), 0))), na.rm = TRUE)
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max(min(max_places,
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maximum, na.rm = TRUE),
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minimum, na.rm = TRUE)
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}
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# format_percentage() function
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format_percentage <- function(x, digits = NULL, ...) {
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if (is.null(digits)) {
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digits <- getdecimalplaces(x)
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}
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# round right: percentage(0.4455) and format(as.percentage(0.4455), 1) should return "44.6%", not "44.5%"
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x_formatted <- format(round2(as.double(x), digits = digits + 2) * 100,
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scientific = FALSE,
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digits = digits,
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nsmall = digits,
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...)
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x_formatted <- paste0(x_formatted, "%")
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x_formatted[!grepl(pattern = "^[0-9.,e-]+$", x = x)] <- NA_character_
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x_formatted
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}
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# the actual working part
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x <- as.double(x)
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if (is.null(digits)) {
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# max one digit if undefined
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digits <- getdecimalplaces(x, minimum = 0, maximum = 1)
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}
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format_percentage(structure(.Data = as.double(x),
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class = c("percentage", "numeric")),
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digits = digits, ...)
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}
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# prevent dependency on package 'backports'
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# these functions were not available in previous versions of R (last checked: R 4.0.0)
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# see here for the full list: https://github.com/r-lib/backports
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strrep <- function(x, times) {
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x <- as.character(x)
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if (length(x) == 0L)
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return(x)
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unlist(.mapply(function(x, times) {
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if (is.na(x) || is.na(times))
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return(NA_character_)
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if (times <= 0L)
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return("")
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paste0(replicate(times, x), collapse = "")
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}, list(x = x, times = times), MoreArgs = list()), use.names = FALSE)
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}
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trimws <- function(x, which = c("both", "left", "right")) {
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which <- match.arg(which)
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mysub <- function(re, x) sub(re, "", x, perl = TRUE)
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if (which == "left")
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return(mysub("^[ \t\r\n]+", x))
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if (which == "right")
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return(mysub("[ \t\r\n]+$", x))
|
|
mysub("[ \t\r\n]+$", mysub("^[ \t\r\n]+", x))
|
|
}
|
|
isFALSE <- function(x) {
|
|
is.logical(x) && length(x) == 1L && !is.na(x) && !x
|
|
}
|
|
deparse1 <- function(expr, collapse = " ", width.cutoff = 500L, ...) {
|
|
paste(deparse(expr, width.cutoff, ...), collapse = collapse)
|
|
}
|