mirror of https://github.com/msberends/AMR.git
114 lines
4.5 KiB
R
114 lines
4.5 KiB
R
# ==================================================================== #
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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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#' Pattern Matching
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#'
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#' Convenience function to compare a vector with a pattern, like \code{\link[base]{grep}}. It always returns a \code{logical} vector and is always case-insensitive.
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#' @inheritParams base::grep
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#' @return A \code{logical} vector
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#' @name like
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#' @rdname like
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#' @export
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#' @source Inherited from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default.
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#' @examples
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#' library(dplyr)
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#' # get unique occurences of bacteria whose name start with 'Ent'
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#' septic_patients %>%
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#' left_join_microorganisms() %>%
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#' filter(fullname %like% '^Ent') %>%
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#' pull(fullname) %>%
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#' unique()
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"%like%" <- function(x, pattern) {
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if (length(pattern) > 1) {
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pattern <- pattern[1]
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warning('only the first element of argument `pattern` used for `%like%`', call. = FALSE)
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}
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if (is.factor(x)) {
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as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = TRUE)
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} else {
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base::grepl(pattern, x, ignore.case = TRUE)
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}
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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 & any(val == as.integer(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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base::paste0(val, "%")
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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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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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cv.x <- sd(x, na.rm = na.rm) / abs(mean(x, na.rm = na.rm))
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cv.x
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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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cqv.x <-
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(quantile(x, 0.75, na.rm = na.rm, type = 6) - quantile(x, 0.25, na.rm = na.rm, type = 6)) /
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(quantile(x, 0.75, na.rm = na.rm, type = 6) + quantile(x, 0.25, na.rm = na.rm, type = 6))
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unname(cqv.x)
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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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