P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity
AMR/R/misc.R

212 lines
8.8 KiB
R
Executable File
Raw Blame History

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' Pattern Matching
#'
#' 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.
#' @inheritParams base::grep
#' @return A \code{logical} vector
#' @name like
#' @rdname like
#' @export
#' @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.
#' @examples
#' library(dplyr)
#' # get unique occurences of bacteria whose name start with 'Ent'
#' septic_patients %>%
#' left_join_microorganisms() %>%
#' filter(fullname %like% '^Ent') %>%
#' pull(fullname) %>%
#' unique()
"%like%" <- function(x, pattern) {
if (length(pattern) > 1) {
pattern <- pattern[1]
warning('only the first element of argument `pattern` used for `%like%`', call. = FALSE)
}
if (is.factor(x)) {
as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = TRUE)
} else {
base::grepl(pattern, x, ignore.case = TRUE)
}
}
# No export, no Rd
percent <- function(x, round = 1, force_zero = FALSE, ...) {
val <- base::round(x * 100, digits = round)
if (force_zero == TRUE & any(val == as.integer(val) & !is.na(val))) {
val[val == as.integer(val)] <- paste0(val[val == as.integer(val)], ".", strrep(0, round))
}
pct <- base::paste0(val, "%")
pct[pct == "NA%"] <- NA_character_
pct
}
check_available_columns <- function(tbl, col.list, info = TRUE) {
# check columns
col.list <- col.list[!is.na(col.list)]
names(col.list) <- col.list
col.list.bak <- col.list
# are they available as upper case or lower case then?
for (i in 1:length(col.list)) {
if (toupper(col.list[i]) %in% colnames(tbl)) {
col.list[i] <- toupper(col.list[i])
} else if (tolower(col.list[i]) %in% colnames(tbl)) {
col.list[i] <- tolower(col.list[i])
} else if (!col.list[i] %in% colnames(tbl)) {
col.list[i] <- NA
}
}
if (!all(col.list %in% colnames(tbl))) {
if (info == TRUE) {
warning('These columns do not exist and will be ignored: ',
col.list.bak[!(col.list %in% colnames(tbl))] %>% toString(),
'.\nTHIS MAY STRONGLY INFLUENCE THE OUTCOME.',
immediate. = TRUE,
call. = FALSE)
}
}
col.list
}
# Coefficient of variation (CV)
cv <- function(x, na.rm = TRUE) {
stats::sd(x, na.rm = na.rm) / base::abs(base::mean(x, na.rm = na.rm))
}
# Coefficient of dispersion, or coefficient of quartile variation (CQV).
# (Bonett et al., 2006: Confidence interval for a coefficient of quartile variation).
cqv <- function(x, na.rm = TRUE) {
cqv.x <-
(stats::quantile(x, 0.75, na.rm = na.rm, type = 6) - stats::quantile(x, 0.25, na.rm = na.rm, type = 6)) /
(stats::quantile(x, 0.75, na.rm = na.rm, type = 6) + stats::quantile(x, 0.25, na.rm = na.rm, type = 6))
unname(cqv.x)
}
# show bytes as kB/MB/GB
# size_humanreadable(123456) # 121 kB
# size_humanreadable(12345678) # 11.8 MB
size_humanreadable <- function(bytes, decimals = 1) {
bytes <- bytes %>% as.double()
# Adapted from:
# http://jeffreysambells.com/2012/10/25/human-readable-filesize-php
size <- c('B','kB','MB','GB','TB','PB','EB','ZB','YB')
factor <- floor((nchar(bytes) - 1) / 3)
# added slight improvement; no decimals for B and kB:
decimals <- rep(decimals, length(bytes))
decimals[size[factor + 1] %in% c('B', 'kB')] <- 0
out <- paste(sprintf(paste0("%.", decimals, "f"), bytes / (1024 ^ factor)), size[factor + 1])
out
}
# based on readr::parse_guess
tbl_parse_guess <- function(tbl,
date_names = 'en',
date_format = '%Y-%m-%d',
time_format = '%H:%M',
decimal_mark = '.',
tz = Sys.timezone(),
encoding = "UTF-8",
na = c("", "NA", "NULL")) {
date_format <- date_generic(date_format)
time_format <- date_generic(time_format)
# set col types with readr
for (i in 1:ncol(tbl)) {
if (!all(tbl %>% pull(i) %>% class() %in% c('list', 'matrix'))) {
tbl[, i] <- readr::parse_guess(x = tbl %>% pull(i) %>% as.character(),
na = na,
locale = readr::locale(date_names = date_names,
date_format = date_format,
time_format = time_format,
decimal_mark = decimal_mark,
encoding = encoding,
tz = tz,
asciify = FALSE))
}
if (any(tbl %>% pull(i) %>% class() %in% c('factor', 'character'))) {
# get values
distinct_val <- tbl %>% pull(i) %>% unique() %>% sort()
# remove ASCII escape character: https://en.wikipedia.org/wiki/Escape_character#ASCII_escape_character
tbl[, i] <- tbl %>% pull(i) %>% gsub('\033', ' ', ., fixed = TRUE)
# look for RSI, shouldn't all be "" and must be valid antibiotic interpretations
if (!all(distinct_val[!is.na(distinct_val)] == '')
& all(distinct_val[!is.na(distinct_val)] %in% c('', 'I', 'I;I', 'R', 'R;R', 'S', 'S;S'))) {
tbl[, i] <- tbl %>% pull(i) %>% as.rsi()
}
}
# convert to MIC class
if (colnames(tbl)[i] %like% '_mic$') {
tbl[, i] <- tbl %>% pull(i) %>% as.mic()
}
}
tbl
}
# transforms date format like "dddd d mmmm yyyy" to "%A %e %B %Y"
date_generic <- function(format) {
if (!grepl('%', format, fixed = TRUE)) {
# first months and minutes, after that everything is case INsensitive
format <- gsub('mmmm', '%B1', format, fixed = TRUE)
format <- gsub('mmm', '%b', format, fixed = TRUE)
format <- gsub('mm', '%m', format, fixed = TRUE)
format <- gsub('MM', '%M1', format, fixed = TRUE)
format <- format %>%
tolower() %>%
gsub('%b1', '%B', ., fixed = TRUE) %>%
gsub('%m1', '%M', ., fixed = TRUE)
# dates
format <- gsub('dddd', '%A', format, fixed = TRUE)
format <- gsub('ddd', '%a', format, fixed = TRUE)
format <- gsub('dd', '%!', format, fixed = TRUE)
format <- gsub('d', '%e', format, fixed = TRUE)
format <- gsub('%!', '%d', format, fixed = TRUE)
format <- gsub('ww', '%V', format, fixed = TRUE)
format <- gsub('w', '%V', format, fixed = TRUE)
format <- gsub('qq', 'Qq', format, fixed = TRUE) # so will be 'Q%%q' after this
format <- gsub('kk', 'Kq', format, fixed = TRUE)
format <- gsub('k', 'q', format, fixed = TRUE)
format <- gsub('q', '%%q', format, fixed = TRUE)
format <- gsub('yyyy_iso', '%G', format, fixed = TRUE)
format <- gsub('jjjj_iso', '%G', format, fixed = TRUE)
format <- gsub('yyyy', '%Y', format, fixed = TRUE)
format <- gsub('jjjj', '%Y', format, fixed = TRUE)
format <- gsub('yy_iso', '%g', format, fixed = TRUE)
format <- gsub('jj_iso', '%g', format, fixed = TRUE)
format <- gsub('yy', '%y', format, fixed = TRUE)
format <- gsub('jj', '%y', format, fixed = TRUE)
# time
format <- gsub('hh', '%H', format, fixed = TRUE)
format <- gsub('h', '%k', format, fixed = TRUE)
format <- gsub('ss', '%S', format, fixed = TRUE)
# seconds since the Epoch, 1970-01-01 00:00:00
format <- gsub('unix', '%s', format, fixed = TRUE)
# Equivalent to %Y-%m-%d (the ISO 8601 date format)
format <- gsub('iso', '%F', format, fixed = TRUE)
}
format
}
View Git Blame Copy Permalink