mirror of https://github.com/msberends/AMR.git
197 lines
7.6 KiB
R
Executable File
197 lines
7.6 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.gitab.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 and adds decimal zeroes until `digits` is reached
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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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# No export, no Rd
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percent <- function(x, round = 1, force_zero = FALSE, decimal.mark = getOption("OutDec"), ...) {
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decimal.mark.options <- getOption("OutDec")
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options(OutDec = ".")
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val <- round2(x, round + 2, force_zero = FALSE) # round up 0.5
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val <- round(x = val * 100, digits = round) # remove floating point error
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if (force_zero == TRUE) {
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if (any(val == as.integer(val) & !is.na(val))) {
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# add zeroes to all integers
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val[val == as.integer(as.character(val))] <- paste0(val[val == as.integer(val)], ".", strrep(0, round))
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}
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# add extra zeroes if needed
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val_decimals <- nchar(gsub(".*[.](.*)", "\\1", as.character(val)))
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val[val_decimals < round] <- paste0(val[val_decimals < round], strrep(0, max(0, round - val_decimals)))
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}
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pct <- base::paste0(val, "%")
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pct[pct %in% c("NA%", "NaN%")] <- NA_character_
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if (decimal.mark != ".") {
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pct <- gsub(".", decimal.mark, pct, fixed = TRUE)
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}
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options(OutDec = decimal.mark.options)
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pct
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}
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check_available_columns <- function(tbl, col.list, info = TRUE) {
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# check columns
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col.list <- col.list[!is.na(col.list) & !is.null(col.list)]
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names(col.list) <- col.list
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col.list.bak <- col.list
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# are they available as upper case or lower case then?
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for (i in 1:length(col.list)) {
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if (is.null(col.list[i]) | isTRUE(is.na(col.list[i]))) {
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col.list[i] <- NULL
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} else if (toupper(col.list[i]) %in% colnames(tbl)) {
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col.list[i] <- toupper(col.list[i])
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} else if (tolower(col.list[i]) %in% colnames(tbl)) {
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col.list[i] <- tolower(col.list[i])
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} else if (!col.list[i] %in% colnames(tbl)) {
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col.list[i] <- NULL
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}
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}
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if (!all(col.list %in% colnames(tbl))) {
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if (info == TRUE) {
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warning('These columns do not exist and will be ignored: ',
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col.list.bak[!(col.list %in% colnames(tbl))] %>% toString(),
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'.\nTHIS MAY STRONGLY INFLUENCE THE OUTCOME.',
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immediate. = TRUE,
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call. = FALSE)
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}
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}
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col.list
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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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#' @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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