mirror of https://github.com/msberends/AMR.git
321 lines
11 KiB
R
321 lines
11 KiB
R
# ==================================================================== #
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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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#' Filter isolates on result in antimicrobial class
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#'
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#' Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.
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#' @inheritSection lifecycle Stable lifecycle
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#' @param x a data set
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#' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`antibiotics$group`][antibiotics]
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#' @param result an antibiotic result: S, I or R (or a combination of more of them)
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#' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"`
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#' @param ... parameters passed on to `filter_at` from the `dplyr` package
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#' @details The `group` column in [antibiotics] data set will be searched for `ab_class` (case-insensitive). If no results are found, the `atc_group1` and `atc_group2` columns will be searched. Next, `x` will be checked for column names with a value in any abbreviations, codes or official names found in the [antibiotics] data set.
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#' @rdname filter_ab_class
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#' @export
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#' @examples
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#' \dontrun{
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#' library(dplyr)
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#'
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#' # filter on isolates that have any result for any aminoglycoside
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#' example_isolates %>% filter_aminoglycosides()
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#'
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#' # this is essentially the same as (but without determination of column names):
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#' example_isolates %>%
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#' filter_at(.vars = vars(c("GEN", "TOB", "AMK", "KAN")),
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#' .vars_predicate = any_vars(. %in% c("S", "I", "R")))
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#'
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#'
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#' # filter on isolates that show resistance to ANY aminoglycoside
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#' example_isolates %>% filter_aminoglycosides("R")
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#'
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#' # filter on isolates that show resistance to ALL aminoglycosides
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#' example_isolates %>% filter_aminoglycosides("R", "all")
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#'
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#' # filter on isolates that show resistance to
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#' # any aminoglycoside and any fluoroquinolone
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#' example_isolates %>%
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#' filter_aminoglycosides("R") %>%
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#' filter_fluoroquinolones("R")
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#'
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#' # filter on isolates that show resistance to
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#' # all aminoglycosides and all fluoroquinolones
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#' example_isolates %>%
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#' filter_aminoglycosides("R", "all") %>%
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#' filter_fluoroquinolones("R", "all")
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#' }
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filter_ab_class <- function(x,
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ab_class,
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result = NULL,
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scope = "any",
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...) {
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check_dataset_integrity()
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if (!is.data.frame(x)) {
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stop("`x` must be a data frame.", call. = FALSE)
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}
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# save to return later
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x_class <- class(x)
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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scope <- scope[1L]
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if (is.null(result)) {
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result <- c("S", "I", "R")
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}
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# make result = "SI" work too:
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result <- unlist(strsplit(result, ""))
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if (!all(result %in% c("S", "I", "R"))) {
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stop("`result` must be one or more of: S, I, R", call. = FALSE)
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}
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if (!all(scope %in% c("any", "all"))) {
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stop("`scope` must be one of: any, all", call. = FALSE)
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}
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# get only columns with class ab, mic or disk - those are AMR results
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vars_df <- colnames(x)[sapply(x, function(y) is.rsi(y) | is.mic(y) | is.disk(y))]
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vars_df_ab <- suppressWarnings(as.ab(vars_df))
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# get the columns with a group names in the chosen ab class
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vars_df <- vars_df[which(ab_group(vars_df_ab) %like% ab_class |
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ab_atc_group1(vars_df_ab) %like% ab_class |
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ab_atc_group2(vars_df_ab) %like% ab_class)]
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ab_group <- find_ab_group(ab_class)
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if (length(vars_df) > 0) {
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if (length(result) == 1) {
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operator <- " is "
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} else {
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operator <- " is one of "
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}
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if (scope == "any") {
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scope_txt <- " or "
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scope_fn <- any
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} else {
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scope_txt <- " and "
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scope_fn <- all
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if (length(vars_df) > 1) {
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operator <- gsub("is", "are", operator)
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}
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}
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if (length(vars_df) > 1) {
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scope <- paste(scope, "of columns ")
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} else {
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scope <- "column "
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}
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message(font_blue(paste0("Filtering on ", ab_group, ": ", scope,
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paste0(font_bold(paste0("`", vars_df, "`"), collapse = NULL), collapse = scope_txt), operator, toString(result))))
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filtered <<- as.logical(by(x, seq_len(nrow(x)),
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function(row) scope_fn(unlist(row[, vars_df]) %in% result, na.rm = TRUE)))
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x <- x[which(filtered), , drop = FALSE]
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} else {
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message(font_blue(paste0("NOTE: no antimicrobial agents of class ", ab_group,
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" (such as ", find_ab_names(ab_group),
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") found, data left unchanged.")))
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}
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class(x) <- x_class
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x
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}
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#' @rdname filter_ab_class
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#' @export
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filter_aminoglycosides <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "aminoglycoside",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_carbapenems <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "carbapenem",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporin",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_1st_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporins (1st gen.)",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_2nd_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporins (2nd gen.)",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_3rd_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporins (3rd gen.)",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_4th_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporins (4th gen.)",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_5th_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporins (5th gen.)",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_fluoroquinolones <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "fluoroquinolone",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_glycopeptides <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "glycopeptide",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_macrolides <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "macrolide",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_tetracyclines <- function(x,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(x = x,
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ab_class = "tetracycline",
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result = result,
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scope = scope,
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...)
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}
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find_ab_group <- function(ab_class) {
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ifelse(ab_class %in% c("aminoglycoside",
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"carbapenem",
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"cephalosporin",
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"fluoroquinolone",
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"glycopeptide",
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"macrolide",
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"tetracycline"),
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paste0(ab_class, "s"),
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antibiotics %>%
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subset(group %like% ab_class |
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atc_group1 %like% ab_class |
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atc_group2 %like% ab_class) %>%
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pull(group) %>%
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unique() %>%
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tolower() %>%
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paste(collapse = "/")
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)
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}
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find_ab_names <- function(ab_group) {
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drugs <- antibiotics[which(antibiotics$group %like% ab_group), "name"]
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paste0(ab_name(sample(drugs, size = min(4, length(drugs)), replace = FALSE),
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tolower = TRUE, language = NULL),
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collapse = ", ")
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}
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