mirror of https://github.com/msberends/AMR.git
229 lines
8.6 KiB
R
Executable File
229 lines
8.6 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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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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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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#' @importFrom utils View
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addin_open_antibiotics <- function() {
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View(antibiotics)
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}
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# No export, no Rd
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#' @importFrom utils View
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addin_open_microorganisms <- function() {
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View(microorganisms)
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}
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# No export, no Rd
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#' @importFrom utils View
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addin_open_septic_patients <- function() {
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View(septic_patients)
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}
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# No export, no Rd
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percent <- function(x, round = 1, force_zero = FALSE, ...) {
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val <- base::round(x * 100, digits = round)
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if (force_zero == TRUE & any(val == as.integer(val) & !is.na(val))) {
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val[val == as.integer(val)] <- paste0(val[val == as.integer(val)], ".", strrep(0, round))
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}
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pct <- base::paste0(val, "%")
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pct[pct == "NA%"] <- NA_character_
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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)]
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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 (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] <- NA
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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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# based on readr::parse_guess
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tbl_parse_guess <- function(tbl,
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date_names = 'en',
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date_format = '%Y-%m-%d',
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time_format = '%H:%M',
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decimal_mark = '.',
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tz = "UTC",
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encoding = "UTF-8",
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remove_ASCII_escape_char = FALSE,
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na = c("", "NA", "NULL")) {
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date_format <- date_generic(date_format)
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time_format <- date_generic(time_format)
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# set col types with readr
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for (i in 1:ncol(tbl)) {
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if (!all(tbl %>% pull(i) %>% class() %in% c('list', 'matrix'))) {
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tbl[, i] <- readr::parse_guess(x = tbl %>% pull(i) %>% as.character(),
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na = na,
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locale = readr::locale(date_names = date_names,
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date_format = date_format,
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time_format = time_format,
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decimal_mark = decimal_mark,
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encoding = encoding,
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tz = tz,
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asciify = FALSE))
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}
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if (any(tbl %>% pull(i) %>% class() %in% c('factor', 'character'))) {
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if (remove_ASCII_escape_char == TRUE) {
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# remove ASCII escape character: https://en.wikipedia.org/wiki/Escape_character#ASCII_escape_character
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tbl[, i] <- tbl %>% pull(i) %>% gsub('\033', ' ', ., fixed = TRUE)
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}
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if (tbl %>% pull(i) %>% is.rsi.eligible()) {
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# look for RSI
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tbl[, i] <- as.rsi(tbl[, i])
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}
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}
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# convert to MIC class when ends on `_mic`
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if (colnames(tbl)[i] %like% '_mic$') {
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tbl[, i] <- as.mic(tbl[, i])
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}
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}
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tbl
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}
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#' @importFrom dplyr case_when
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Sys.locale <- function() {
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alreadyset <- getOption("AMR_locale")
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if (!is.null(alreadyset)) {
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if (tolower(alreadyset) %in% c("en", "de", "nl", "es", "fr", "pt", "it")) {
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return(tolower(alreadyset))
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}
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}
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sys <- base::Sys.getlocale()
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case_when(
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sys %like% '(Deutsch|German|de_)' ~ "de",
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sys %like% '(Nederlands|Dutch|nl_)' ~ "nl",
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sys %like% '(Espa.ol|Spanish|es_)' ~ "es",
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sys %like% '(Fran.ais|French|fr_)' ~ "fr",
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sys %like% '(Portugu.s|Portuguese|pt_)' ~ "pt",
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sys %like% '(Italiano|Italian|it_)' ~ "it",
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TRUE ~ "en"
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)
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}
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# transforms date format like "dddd d mmmm yyyy" to "%A %e %B %Y"
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date_generic <- function(format) {
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if (!grepl('%', format, fixed = TRUE)) {
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# first months and minutes, after that everything is case INsensitive
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format <- gsub('mmmm', '%B1', format, fixed = TRUE)
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format <- gsub('mmm', '%b', format, fixed = TRUE)
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format <- gsub('mm', '%m', format, fixed = TRUE)
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format <- gsub('MM', '%M1', format, fixed = TRUE)
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format <- format %>%
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tolower() %>%
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gsub('%b1', '%B', ., fixed = TRUE) %>%
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gsub('%m1', '%M', ., fixed = TRUE)
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# dates
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format <- gsub('dddd', '%A', format, fixed = TRUE)
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format <- gsub('ddd', '%a', format, fixed = TRUE)
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format <- gsub('dd', '%!', format, fixed = TRUE)
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format <- gsub('d', '%e', format, fixed = TRUE)
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format <- gsub('%!', '%d', format, fixed = TRUE)
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format <- gsub('ww', '%V', format, fixed = TRUE)
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format <- gsub('w', '%V', format, fixed = TRUE)
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format <- gsub('qq', 'Qq', format, fixed = TRUE) # so will be 'Q%%q' after this
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format <- gsub('kk', 'Kq', format, fixed = TRUE)
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format <- gsub('k', 'q', format, fixed = TRUE)
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format <- gsub('q', '%%q', format, fixed = TRUE)
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format <- gsub('yyyy_iso', '%G', format, fixed = TRUE)
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format <- gsub('jjjj_iso', '%G', format, fixed = TRUE)
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format <- gsub('yyyy', '%Y', format, fixed = TRUE)
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format <- gsub('jjjj', '%Y', format, fixed = TRUE)
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format <- gsub('yy_iso', '%g', format, fixed = TRUE)
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format <- gsub('jj_iso', '%g', format, fixed = TRUE)
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format <- gsub('yy', '%y', format, fixed = TRUE)
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format <- gsub('jj', '%y', format, fixed = TRUE)
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# time
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format <- gsub('hh', '%H', format, fixed = TRUE)
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format <- gsub('h', '%k', format, fixed = TRUE)
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format <- gsub('ss', '%S', format, fixed = TRUE)
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# seconds since the Epoch, 1970-01-01 00:00:00
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format <- gsub('unix', '%s', format, fixed = TRUE)
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# Equivalent to %Y-%m-%d (the ISO 8601 date format)
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format <- gsub('iso', '%F', format, fixed = TRUE)
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}
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format
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}
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