mirror of https://github.com/msberends/AMR.git
414 lines
21 KiB
R
Executable File
414 lines
21 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(tbl, type) {
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# try to find columns based on type
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found <- NULL
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colnames(tbl) <- trimws(colnames(tbl))
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# -- mo
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if (type == "mo") {
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if ("mo" %in% lapply(tbl, class)) {
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found <- colnames(tbl)[lapply(tbl, class) == "mo"][1]
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} else if (any(colnames(tbl) %like% "^(mo|microorganism|organism|bacteria)")) {
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found <- colnames(tbl)[colnames(tbl) %like% "^(mo|microorganism|organism|bacteria)"][1]
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} else if (any(colnames(tbl) %like% "species")) {
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found <- colnames(tbl)[colnames(tbl) %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(tbl) %like% "^key.*(ab|antibiotics)")) {
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found <- colnames(tbl)[colnames(tbl) %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(tbl) %like% "^(specimen date|specimen_date|spec_date)")) {
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# WHONET support
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found <- colnames(tbl)[colnames(tbl) %like% "^(specimen date|specimen_date|spec_date)"][1]
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if (!any(class(tbl %>% 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(tbl)) {
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if (any(class(tbl %>% pull(i)) %in% c("Date", "POSIXct"))) {
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found <- colnames(tbl)[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(tbl) %like% "^(identification |patient|patid)")) {
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found <- colnames(tbl)[colnames(tbl) %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(tbl) %like% "(specimen type|spec_type)")) {
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found <- colnames(tbl)[colnames(tbl) %like% "(specimen type|spec_type)"][1]
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} else if (any(colnames(tbl) %like% "^(specimen)")) {
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found <- colnames(tbl)[colnames(tbl) %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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get_ab_col <- function(columns, ab) {
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columns[names(columns) == ab]
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}
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get_column_abx <- function(tbl,
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soft_dependencies = NULL,
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hard_dependencies = NULL,
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verbose = FALSE,
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AMC = guess_ab_col(),
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AMK = guess_ab_col(),
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AMX = guess_ab_col(),
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AMP = guess_ab_col(),
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AZM = guess_ab_col(),
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AZL = guess_ab_col(),
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ATM = guess_ab_col(),
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RID = guess_ab_col(),
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FEP = guess_ab_col(),
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CTX = guess_ab_col(),
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FOX = guess_ab_col(),
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CED = guess_ab_col(),
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CAZ = guess_ab_col(),
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CRO = guess_ab_col(),
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CXM = guess_ab_col(),
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CHL = guess_ab_col(),
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CIP = guess_ab_col(),
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CLR = guess_ab_col(),
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CLI = guess_ab_col(),
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FLC = guess_ab_col(),
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COL = guess_ab_col(),
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CZO = guess_ab_col(),
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DAP = guess_ab_col(),
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DOX = guess_ab_col(),
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ETP = guess_ab_col(),
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ERY = guess_ab_col(),
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FOS = guess_ab_col(),
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FUS = guess_ab_col(),
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GEN = guess_ab_col(),
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IPM = guess_ab_col(),
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KAN = guess_ab_col(),
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LVX = guess_ab_col(),
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LIN = guess_ab_col(),
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LNZ = guess_ab_col(),
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MEM = guess_ab_col(),
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MTR = guess_ab_col(),
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MEZ = guess_ab_col(),
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MNO = guess_ab_col(),
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MFX = guess_ab_col(),
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NAL = guess_ab_col(),
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NEO = guess_ab_col(),
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NET = guess_ab_col(),
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NIT = guess_ab_col(),
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NOR = guess_ab_col(),
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NOV = guess_ab_col(),
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OFX = guess_ab_col(),
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OXA = guess_ab_col(),
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PEN = guess_ab_col(),
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PIP = guess_ab_col(),
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TZP = guess_ab_col(),
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PLB = guess_ab_col(),
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PRI = guess_ab_col(),
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QDA = guess_ab_col(),
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RIF = guess_ab_col(),
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RXT = guess_ab_col(),
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SIS = guess_ab_col(),
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TEC = guess_ab_col(),
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TCY = guess_ab_col(),
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TIC = guess_ab_col(),
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TGC = guess_ab_col(),
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TOB = guess_ab_col(),
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TMP = guess_ab_col(),
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SXT = guess_ab_col(),
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VAN = guess_ab_col()) {
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# check columns
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if (identical(AMC, as.name("guess_ab_col"))) AMC <- guess_ab_col(tbl, "AMC", verbose = verbose)
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if (identical(AMK, as.name("guess_ab_col"))) AMK <- guess_ab_col(tbl, "AMK", verbose = verbose)
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if (identical(AMX, as.name("guess_ab_col"))) AMX <- guess_ab_col(tbl, "AMX", verbose = verbose)
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if (identical(AMP, as.name("guess_ab_col"))) AMP <- guess_ab_col(tbl, "AMP", verbose = verbose)
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if (identical(AZM, as.name("guess_ab_col"))) AZM <- guess_ab_col(tbl, "AZM", verbose = verbose)
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if (identical(AZL, as.name("guess_ab_col"))) AZL <- guess_ab_col(tbl, "AZL", verbose = verbose)
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if (identical(ATM, as.name("guess_ab_col"))) ATM <- guess_ab_col(tbl, "ATM", verbose = verbose)
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if (identical(RID, as.name("guess_ab_col"))) RID <- guess_ab_col(tbl, "RID", verbose = verbose)
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if (identical(FEP, as.name("guess_ab_col"))) FEP <- guess_ab_col(tbl, "FEP", verbose = verbose)
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if (identical(CTX, as.name("guess_ab_col"))) CTX <- guess_ab_col(tbl, "CTX", verbose = verbose)
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if (identical(FOX, as.name("guess_ab_col"))) FOX <- guess_ab_col(tbl, "FOX", verbose = verbose)
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if (identical(CED, as.name("guess_ab_col"))) CED <- guess_ab_col(tbl, "CED", verbose = verbose)
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if (identical(CAZ, as.name("guess_ab_col"))) CAZ <- guess_ab_col(tbl, "CAZ", verbose = verbose)
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if (identical(CRO, as.name("guess_ab_col"))) CRO <- guess_ab_col(tbl, "CRO", verbose = verbose)
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if (identical(CXM, as.name("guess_ab_col"))) CXM <- guess_ab_col(tbl, "CXM", verbose = verbose)
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if (identical(CHL, as.name("guess_ab_col"))) CHL <- guess_ab_col(tbl, "CHL", verbose = verbose)
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if (identical(CIP, as.name("guess_ab_col"))) CIP <- guess_ab_col(tbl, "CIP", verbose = verbose)
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if (identical(CLR, as.name("guess_ab_col"))) CLR <- guess_ab_col(tbl, "CLR", verbose = verbose)
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if (identical(CLI, as.name("guess_ab_col"))) CLI <- guess_ab_col(tbl, "CLI", verbose = verbose)
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if (identical(FLC, as.name("guess_ab_col"))) FLC <- guess_ab_col(tbl, "FLC", verbose = verbose)
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if (identical(COL, as.name("guess_ab_col"))) COL <- guess_ab_col(tbl, "COL", verbose = verbose)
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if (identical(CZO, as.name("guess_ab_col"))) CZO <- guess_ab_col(tbl, "CZO", verbose = verbose)
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if (identical(DAP, as.name("guess_ab_col"))) DAP <- guess_ab_col(tbl, "DAP", verbose = verbose)
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if (identical(DOX, as.name("guess_ab_col"))) DOX <- guess_ab_col(tbl, "DOX", verbose = verbose)
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if (identical(ETP, as.name("guess_ab_col"))) ETP <- guess_ab_col(tbl, "ETP", verbose = verbose)
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if (identical(ERY, as.name("guess_ab_col"))) ERY <- guess_ab_col(tbl, "ERY", verbose = verbose)
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if (identical(FOS, as.name("guess_ab_col"))) FOS <- guess_ab_col(tbl, "FOS", verbose = verbose)
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if (identical(FUS, as.name("guess_ab_col"))) FUS <- guess_ab_col(tbl, "FUS", verbose = verbose)
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if (identical(GEN, as.name("guess_ab_col"))) GEN <- guess_ab_col(tbl, "GEN", verbose = verbose)
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if (identical(IPM, as.name("guess_ab_col"))) IPM <- guess_ab_col(tbl, "IPM", verbose = verbose)
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if (identical(KAN, as.name("guess_ab_col"))) KAN <- guess_ab_col(tbl, "KAN", verbose = verbose)
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if (identical(LVX, as.name("guess_ab_col"))) LVX <- guess_ab_col(tbl, "LVX", verbose = verbose)
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if (identical(LIN, as.name("guess_ab_col"))) LIN <- guess_ab_col(tbl, "LIN", verbose = verbose)
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if (identical(LNZ, as.name("guess_ab_col"))) LNZ <- guess_ab_col(tbl, "LNZ", verbose = verbose)
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if (identical(MEM, as.name("guess_ab_col"))) MEM <- guess_ab_col(tbl, "MEM", verbose = verbose)
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if (identical(MTR, as.name("guess_ab_col"))) MTR <- guess_ab_col(tbl, "MTR", verbose = verbose)
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if (identical(MEZ, as.name("guess_ab_col"))) MEZ <- guess_ab_col(tbl, "MEZ", verbose = verbose)
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if (identical(MNO, as.name("guess_ab_col"))) MNO <- guess_ab_col(tbl, "MNO", verbose = verbose)
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if (identical(MFX, as.name("guess_ab_col"))) MFX <- guess_ab_col(tbl, "MFX", verbose = verbose)
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if (identical(NAL, as.name("guess_ab_col"))) NAL <- guess_ab_col(tbl, "NAL", verbose = verbose)
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if (identical(NEO, as.name("guess_ab_col"))) NEO <- guess_ab_col(tbl, "NEO", verbose = verbose)
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if (identical(NET, as.name("guess_ab_col"))) NET <- guess_ab_col(tbl, "NET", verbose = verbose)
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if (identical(NIT, as.name("guess_ab_col"))) NIT <- guess_ab_col(tbl, "NIT", verbose = verbose)
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if (identical(NOR, as.name("guess_ab_col"))) NOR <- guess_ab_col(tbl, "NOR", verbose = verbose)
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if (identical(NOV, as.name("guess_ab_col"))) NOV <- guess_ab_col(tbl, "NOV", verbose = verbose)
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if (identical(OFX, as.name("guess_ab_col"))) OFX <- guess_ab_col(tbl, "OFX", verbose = verbose)
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if (identical(OXA, as.name("guess_ab_col"))) OXA <- guess_ab_col(tbl, "OXA", verbose = verbose)
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if (identical(PEN, as.name("guess_ab_col"))) PEN <- guess_ab_col(tbl, "PEN", verbose = verbose)
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if (identical(PIP, as.name("guess_ab_col"))) PIP <- guess_ab_col(tbl, "PIP", verbose = verbose)
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if (identical(TZP, as.name("guess_ab_col"))) TZP <- guess_ab_col(tbl, "TZP", verbose = verbose)
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if (identical(PLB, as.name("guess_ab_col"))) PLB <- guess_ab_col(tbl, "PLB", verbose = verbose)
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if (identical(PRI, as.name("guess_ab_col"))) PRI <- guess_ab_col(tbl, "PRI", verbose = verbose)
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if (identical(QDA, as.name("guess_ab_col"))) QDA <- guess_ab_col(tbl, "QDA", verbose = verbose)
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if (identical(RIF, as.name("guess_ab_col"))) RIF <- guess_ab_col(tbl, "RIF", verbose = verbose)
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if (identical(RXT, as.name("guess_ab_col"))) RXT <- guess_ab_col(tbl, "RXT", verbose = verbose)
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if (identical(SIS, as.name("guess_ab_col"))) SIS <- guess_ab_col(tbl, "SIS", verbose = verbose)
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if (identical(TEC, as.name("guess_ab_col"))) TEC <- guess_ab_col(tbl, "TEC", verbose = verbose)
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if (identical(TCY, as.name("guess_ab_col"))) TCY <- guess_ab_col(tbl, "TCY", verbose = verbose)
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if (identical(TIC, as.name("guess_ab_col"))) TIC <- guess_ab_col(tbl, "TIC", verbose = verbose)
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if (identical(TGC, as.name("guess_ab_col"))) TGC <- guess_ab_col(tbl, "TGC", verbose = verbose)
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if (identical(TOB, as.name("guess_ab_col"))) TOB <- guess_ab_col(tbl, "TOB", verbose = verbose)
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if (identical(TMP, as.name("guess_ab_col"))) TMP <- guess_ab_col(tbl, "TMP", verbose = verbose)
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if (identical(SXT, as.name("guess_ab_col"))) SXT <- guess_ab_col(tbl, "SXT", verbose = verbose)
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if (identical(VAN, as.name("guess_ab_col"))) VAN <- guess_ab_col(tbl, "VAN", verbose = verbose)
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columns_available <- c(AMC = AMC, AMK = AMK, AMX = AMX, AMP = AMP, AZM = AZM,
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AZL = AZL, ATM = ATM, RID = RID, FEP = FEP, CTX = CTX,
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FOX = FOX, CED = CED, CAZ = CAZ, CRO = CRO, CXM = CXM,
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CHL = CHL, CIP = CIP, CLR = CLR, CLI = CLI, FLC = FLC,
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COL = COL, CZO = CZO, DAP = DAP, DOX = DOX, ETP = ETP,
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ERY = ERY, FOS = FOS, FUS = FUS, GEN = GEN, IPM = IPM,
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KAN = KAN, LVX = LVX, LIN = LIN, LNZ = LNZ, MEM = MEM,
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MTR = MTR, MEZ = MEZ, MNO = MNO, MFX = MFX, NAL = NAL,
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NEO = NEO, NET = NET, NIT = NIT, NOR = NOR, NOV = NOV,
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OFX = OFX, OXA = OXA, PEN = PEN, PIP = PIP, TZP = TZP,
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PLB = PLB, PRI = PRI, QDA = QDA, RIF = RIF, RXT = RXT,
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SIS = SIS, TEC = TEC, TCY = TCY, TIC = TIC, TGC = TGC,
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TOB = TOB, TMP = TMP, SXT = SXT, VAN = VAN)
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if (!is.null(hard_dependencies)) {
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if (!all(hard_dependencies %in% names(columns_available[!is.na(columns_available)]))) {
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# missing a hard dependency will return NA and consequently the data will not be analysed
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missing <- hard_dependencies[!hard_dependencies %in% names(columns_available[!is.na(columns_available)])]
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generate_warning_abs_missing(missing, any = FALSE)
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return(NA)
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}
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}
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if (!is.null(soft_dependencies)) {
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if (!all(soft_dependencies %in% names(columns_available[!is.na(columns_available)]))) {
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# missing a soft dependency may lower the reliability
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missing <- soft_dependencies[!soft_dependencies %in% names(columns_available[!is.na(columns_available)])]
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missing <- paste0("`", missing, "` (", ab_name(missing, tolower = TRUE), ")")
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warning('Reliability might be improved if these antimicrobial results would be available too: ', paste(missing, collapse = ", "),
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immediate. = TRUE,
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call. = FALSE)
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}
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}
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#deps <- c(soft_dependencies, hard_dependencies)
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#if (length(deps) > 0) {
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# columns_available[names(columns_available) %in% deps]
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#} else {
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columns_available
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#}
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}
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generate_warning_abs_missing <- function(missing, any = FALSE) {
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missing <- paste0("`", missing, "` (", ab_name(missing, tolower = TRUE), ")")
|
|
if (any == TRUE) {
|
|
any_txt <- c(" any of", "is")
|
|
} else {
|
|
any_txt <- c("", "are")
|
|
}
|
|
warning(paste0("Introducing NAs since", any_txt[1], " these antimicrobials ", any_txt[2], " required: ",
|
|
paste(missing, collapse = ", ")),
|
|
immediate. = TRUE,
|
|
call. = FALSE)
|
|
}
|
|
|
|
|
|
stopifnot_installed_package <- function(package) {
|
|
if (!package %in% base::rownames(utils::installed.packages())) {
|
|
stop("this function requires the ", package, " package.", call. = FALSE)
|
|
}
|
|
}
|
|
|
|
# translate strings based on inst/translations.tsv
|
|
#' @importFrom dplyr %>% filter
|
|
t <- function(from, language = get_locale()) {
|
|
# if (getOption("AMR_locale", "en") != language) {
|
|
# language <- getOption("AMR_locale", "en")
|
|
# }
|
|
|
|
if (is.null(language)) {
|
|
return(from)
|
|
}
|
|
if (language %in% c("en", "")) {
|
|
return(from)
|
|
}
|
|
|
|
df_trans <- utils::read.table(file = system.file("translations.tsv", package = "AMR"),
|
|
sep = "\t",
|
|
stringsAsFactors = FALSE,
|
|
header = TRUE,
|
|
blank.lines.skip = TRUE,
|
|
fill = TRUE,
|
|
strip.white = TRUE,
|
|
encoding = "UTF-8",
|
|
fileEncoding = "UTF-8",
|
|
na.strings = c(NA, "", NULL))
|
|
|
|
if (!language %in% df_trans$lang) {
|
|
stop("Unsupported language: '", language, "' - use one of: ",
|
|
paste0("'", sort(unique(df_trans$lang)), "'", collapse = ", "),
|
|
call. = FALSE)
|
|
}
|
|
|
|
df_trans <- df_trans %>% filter(lang == language)
|
|
|
|
# default case sensitive if value if 'ignore.case' is missing:
|
|
df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
|
|
# default not using regular expressions (fixed = TRUE) if 'fixed' is missing:
|
|
df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
|
|
|
|
# check if text to look for is in one of the patterns
|
|
any_form_in_patterns <- tryCatch(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
|
|
error = function(e) {
|
|
warning("Translation not possible. Please open an issue on GitLab (https://gitlab.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
|
|
return(FALSE)
|
|
})
|
|
if (NROW(df_trans) == 0 | !any_form_in_patterns) {
|
|
return(from)
|
|
}
|
|
|
|
for (i in 1:nrow(df_trans)) {
|
|
from <- gsub(x = from,
|
|
pattern = df_trans$pattern[i],
|
|
replacement = df_trans$replacement[i],
|
|
fixed = df_trans$fixed[i],
|
|
ignore.case = df_trans$ignore.case[i])
|
|
}
|
|
|
|
# force UTF-8 for diacritics
|
|
base::enc2utf8(from)
|
|
|
|
}
|