mirror of https://github.com/msberends/AMR.git
114 lines
4.4 KiB
R
Executable File
114 lines
4.4 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 package 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 R package 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 version 2.0 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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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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# https://stackoverflow.com/a/12688836/4575331
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round2 <- function(x, n) (trunc((abs(x) * 10 ^ n) + 0.5) / 10 ^ n) * sign(x)
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val <- round2(x, round + 2) # 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 (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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