mirror of https://github.com/msberends/AMR.git
260 lines
9.5 KiB
R
Executable File
260 lines
9.5 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) 2018-2020 Berends MS, Luz CF et al. #
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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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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' @importFrom rlang enquos as_label
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dots2vars <- function(...) {
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# this function is to give more informative output about
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# variable names in count_* and proportion_* functions
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paste(
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unlist(
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lapply(enquos(...),
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function(x) {
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l <- as_label(x)
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if (l != ".") {
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l
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} else {
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character(0)
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}
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})
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),
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collapse = ", ")
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}
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#' @importFrom dplyr %>% pull all_vars any_vars filter_all funs mutate_all
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#' @importFrom cleaner percentage
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rsi_calc <- function(...,
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ab_result,
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minimum = 0,
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as_percent = FALSE,
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only_all_tested = FALSE,
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only_count = FALSE) {
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data_vars <- dots2vars(...)
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if (!is.numeric(minimum)) {
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stop("`minimum` must be numeric", call. = FALSE)
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}
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if (!is.logical(as_percent)) {
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stop("`as_percent` must be logical", call. = FALSE)
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}
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if (!is.logical(only_all_tested)) {
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stop("`only_all_tested` must be logical", call. = FALSE)
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}
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dots_df <- ...elt(1) # it needs this evaluation
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dots <- base::eval(base::substitute(base::alist(...)))
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if ("also_single_tested" %in% names(dots)) {
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stop("`also_single_tested` was replaced by `only_all_tested`. Please read Details in the help page (`?proportion`) as this may have a considerable impact on your analysis.", call. = FALSE)
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}
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ndots <- length(dots)
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if ("data.frame" %in% class(dots_df)) {
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# data.frame passed with other columns, like: example_isolates %>% proportion_S(amcl, gent)
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dots <- as.character(dots)
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dots <- dots[dots != "."]
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if (length(dots) == 0 | all(dots == "df")) {
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# for complete data.frames, like example_isolates %>% select(amcl, gent) %>% proportion_S()
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# and the old rsi function, that has "df" as name of the first parameter
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x <- dots_df
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} else {
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x <- dots_df[, dots]
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}
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} else if (ndots == 1) {
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# only 1 variable passed (can also be data.frame), like: proportion_S(example_isolates$amcl) and example_isolates$amcl %>% proportion_S()
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x <- dots_df
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} else {
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# multiple variables passed without pipe, like: proportion_S(example_isolates$amcl, example_isolates$gent)
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x <- NULL
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try(x <- as.data.frame(dots), silent = TRUE)
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if (is.null(x)) {
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# support for: with(example_isolates, proportion_S(amcl, gent))
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x <- as.data.frame(rlang::list2(...))
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}
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}
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if (is.null(x)) {
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warning("argument is NULL (check if columns exist): returning NA", call. = FALSE)
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return(NA)
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}
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print_warning <- FALSE
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ab_result <- as.rsi(ab_result)
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if (is.data.frame(x)) {
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rsi_integrity_check <- character(0)
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for (i in seq_len(ncol(x))) {
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# check integrity of columns: force rsi class
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if (!is.rsi(x %>% pull(i))) {
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rsi_integrity_check <- c(rsi_integrity_check, x %>% pull(i) %>% as.character())
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x[, i] <- suppressWarnings(x %>% pull(i) %>% as.rsi()) # warning will be given later
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print_warning <- TRUE
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}
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}
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if (length(rsi_integrity_check) > 0) {
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# this will give a warning for invalid results, of all input columns (so only 1 warning)
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rsi_integrity_check <- as.rsi(rsi_integrity_check)
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}
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if (only_all_tested == TRUE) {
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# THE NUMBER OF ISOLATES WHERE *ALL* ABx ARE S/I/R
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x <- apply(X = x %>% mutate_all(as.integer),
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MARGIN = 1,
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FUN = base::min)
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numerator <- sum(as.integer(x) %in% as.integer(ab_result), na.rm = TRUE)
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denominator <- length(x) - sum(is.na(x))
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} else {
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# THE NUMBER OF ISOLATES WHERE *ANY* ABx IS S/I/R
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other_values <- base::setdiff(c(NA, levels(ab_result)), ab_result)
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other_values_filter <- base::apply(x, 1, function(y) {
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base::all(y %in% other_values) & base::any(is.na(y))
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})
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numerator <- x %>% filter_all(any_vars(. %in% ab_result)) %>% nrow()
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denominator <- x %>% filter(!other_values_filter) %>% nrow()
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}
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} else {
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# x is not a data.frame
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if (!is.rsi(x)) {
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x <- as.rsi(x)
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print_warning <- TRUE
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}
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numerator <- sum(x %in% ab_result, na.rm = TRUE)
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denominator <- sum(x %in% levels(ab_result), na.rm = TRUE)
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}
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if (print_warning == TRUE) {
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warning("Increase speed by transforming to class `rsi` on beforehand: df %>% mutate_if(is.rsi.eligible, as.rsi)",
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call. = FALSE)
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}
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if (only_count == TRUE) {
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return(numerator)
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}
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if (denominator < minimum) {
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if (data_vars != "") {
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data_vars <- paste(" for", data_vars)
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}
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warning("Introducing NA: only ", denominator, " results available", data_vars, " (`minimum` was set to ", minimum, ").", call. = FALSE)
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fraction <- NA
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} else {
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fraction <- numerator / denominator
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}
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if (as_percent == TRUE) {
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percentage(fraction, digits = 1)
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} else {
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fraction
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}
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}
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#' @importFrom dplyr %>% summarise_if mutate select everything bind_rows arrange
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#' @importFrom tidyr pivot_longer
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rsi_calc_df <- function(type, # "proportion" or "count"
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data,
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translate_ab = "name",
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language = get_locale(),
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minimum = 30,
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as_percent = FALSE,
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combine_SI = TRUE,
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combine_IR = FALSE,
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combine_SI_missing = FALSE) {
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if (!"data.frame" %in% class(data)) {
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stop(paste0("`", type, "_df` must be called on a data.frame"), call. = FALSE)
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}
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if (isTRUE(combine_IR) & isTRUE(combine_SI_missing)) {
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combine_SI <- FALSE
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}
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if (isTRUE(combine_SI) & isTRUE(combine_IR)) {
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stop("either `combine_SI` or `combine_IR` can be TRUE, not both", call. = FALSE)
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}
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if (!any(sapply(data, is.rsi), na.rm = TRUE)) {
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stop("No columns with class 'rsi' found. See ?as.rsi.", call. = FALSE)
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}
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if (as.character(translate_ab) %in% c("TRUE", "official")) {
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translate_ab <- "name"
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}
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get_summaryfunction <- function(int, type) {
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# look for proportion_S, count_S, etc:
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int_fn <- get(paste0(type, "_", int), envir = asNamespace("AMR"))
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suppressWarnings(
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if (type == "proportion") {
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summ <- summarise_if(.tbl = data,
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.predicate = is.rsi,
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.funs = int_fn,
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minimum = minimum,
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as_percent = as_percent)
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} else if (type == "count") {
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summ <- summarise_if(.tbl = data,
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.predicate = is.rsi,
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.funs = int_fn)
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}
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)
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summ %>%
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mutate(interpretation = int) %>%
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select(interpretation, everything())
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}
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resS <- get_summaryfunction("S", type)
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resI <- get_summaryfunction("I", type)
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resR <- get_summaryfunction("R", type)
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resSI <- get_summaryfunction("SI", type)
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resIR <- get_summaryfunction("IR", type)
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data.groups <- group_vars(data)
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if (isFALSE(combine_SI) & isFALSE(combine_IR)) {
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res <- bind_rows(resS, resI, resR) %>%
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mutate(interpretation = factor(interpretation,
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levels = c("S", "I", "R"),
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ordered = TRUE))
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} else if (isTRUE(combine_IR)) {
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res <- bind_rows(resS, resIR) %>%
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mutate(interpretation = factor(interpretation,
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levels = c("S", "IR"),
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ordered = TRUE))
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} else if (isTRUE(combine_SI)) {
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res <- bind_rows(resSI, resR) %>%
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mutate(interpretation = factor(interpretation,
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levels = c("SI", "R"),
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ordered = TRUE))
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}
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res <- res %>%
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pivot_longer(-c(interpretation, data.groups), names_to = "antibiotic") %>%
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select(antibiotic, everything()) %>%
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arrange(antibiotic, interpretation)
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if (!translate_ab == FALSE) {
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res <- res %>% mutate(antibiotic = AMR::ab_property(antibiotic, property = translate_ab, language = language))
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}
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as.data.frame(res, stringsAsFactors = FALSE)
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}
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