mirror of https://github.com/msberends/AMR.git
325 lines
11 KiB
R
325 lines
11 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2020 Berends MS, Luz CF et al. #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
#' Filter isolates on result in antibiotic class
|
|
#'
|
|
#' Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
|
|
#' @inheritSection lifecycle Stable lifecycle
|
|
#' @param x a data set
|
|
#' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`AMR::antibiotics$group`][antibiotics]
|
|
#' @param result an antibiotic result: S, I or R (or a combination of more of them)
|
|
#' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"`
|
|
#' @param ... parameters passed on to `filter_at` from the `dplyr` package
|
|
#' @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.
|
|
#' @rdname filter_ab_class
|
|
#' @importFrom dplyr filter_at %>% select vars any_vars all_vars
|
|
#' @importFrom crayon bold blue
|
|
#' @export
|
|
#' @examples
|
|
#' library(dplyr)
|
|
#'
|
|
#' # filter on isolates that have any result for any aminoglycoside
|
|
#' example_isolates %>% filter_aminoglycosides()
|
|
#'
|
|
#' # this is essentially the same as (but without determination of column names):
|
|
#' example_isolates %>%
|
|
#' filter_at(.vars = vars(c("GEN", "TOB", "AMK", "KAN")),
|
|
#' .vars_predicate = any_vars(. %in% c("S", "I", "R")))
|
|
#'
|
|
#'
|
|
#' # filter on isolates that show resistance to ANY aminoglycoside
|
|
#' example_isolates %>% filter_aminoglycosides("R")
|
|
#'
|
|
#' # filter on isolates that show resistance to ALL aminoglycosides
|
|
#' example_isolates %>% filter_aminoglycosides("R", "all")
|
|
#'
|
|
#' # filter on isolates that show resistance to
|
|
#' # any aminoglycoside and any fluoroquinolone
|
|
#' example_isolates %>%
|
|
#' filter_aminoglycosides("R") %>%
|
|
#' filter_fluoroquinolones("R")
|
|
#'
|
|
#' # filter on isolates that show resistance to
|
|
#' # all aminoglycosides and all fluoroquinolones
|
|
#' example_isolates %>%
|
|
#' filter_aminoglycosides("R", "all") %>%
|
|
#' filter_fluoroquinolones("R", "all")
|
|
filter_ab_class <- function(x,
|
|
ab_class,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
scope <- scope[1L]
|
|
if (is.null(result)) {
|
|
result <- c("S", "I", "R")
|
|
}
|
|
# make result = "SI" work too:
|
|
result <- unlist(strsplit(result, ""))
|
|
|
|
if (!all(result %in% c("S", "I", "R"))) {
|
|
stop("`result` must be one or more of: S, I, R", call. = FALSE)
|
|
}
|
|
if (!all(scope %in% c("any", "all"))) {
|
|
stop("`scope` must be one of: any, all", call. = FALSE)
|
|
}
|
|
|
|
vars_df <- colnames(x)[tolower(colnames(x)) %in% tolower(ab_class_vars(ab_class))]
|
|
ab_group <- find_ab_group(ab_class)
|
|
|
|
if (length(vars_df) > 0) {
|
|
if (length(result) == 1) {
|
|
operator <- " is "
|
|
} else {
|
|
operator <- " is one of "
|
|
}
|
|
if (scope == "any") {
|
|
scope_txt <- " or "
|
|
scope_fn <- any_vars
|
|
} else {
|
|
scope_txt <- " and "
|
|
scope_fn <- all_vars
|
|
if (length(vars_df) > 1) {
|
|
operator <- gsub("is", "are", operator)
|
|
}
|
|
}
|
|
if (length(vars_df) > 1) {
|
|
scope <- paste(scope, "of columns ")
|
|
} else {
|
|
scope <- "column "
|
|
}
|
|
message(blue(paste0("Filtering on ", ab_group, ": ", scope,
|
|
paste(bold(paste0("`", vars_df, "`")), collapse = scope_txt), operator, toString(result))))
|
|
x %>%
|
|
filter_at(vars(vars_df),
|
|
scope_fn(. %in% result),
|
|
...)
|
|
} else {
|
|
warning(paste0("no antibiotics of class ", ab_group, " found, leaving data unchanged"), call. = FALSE)
|
|
x
|
|
}
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_aminoglycosides <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "aminoglycoside",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_carbapenems <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "carbapenem",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_cephalosporins <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "cephalosporin",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_1st_cephalosporins <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "cephalosporins (1st gen.)",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_2nd_cephalosporins <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "cephalosporins (2nd gen.)",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_3rd_cephalosporins <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "cephalosporins (3rd gen.)",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_4th_cephalosporins <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "cephalosporins (4th gen.)",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_5th_cephalosporins <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "cephalosporins (5th gen.)",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_fluoroquinolones <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "fluoroquinolone",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_glycopeptides <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "glycopeptide",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_macrolides <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "macrolide",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @rdname filter_ab_class
|
|
#' @export
|
|
filter_tetracyclines <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "tetracycline",
|
|
result = result,
|
|
scope = scope,
|
|
...)
|
|
}
|
|
|
|
#' @importFrom dplyr %>% filter_at vars any_vars select
|
|
ab_class_vars <- function(ab_class) {
|
|
ab_class <- gsub("[^a-z0-9]+", ".*", ab_class)
|
|
ab_vars <- AMR::antibiotics %>%
|
|
filter(group %like% ab_class) %>%
|
|
select(ab:name, abbreviations, synonyms) %>%
|
|
unlist() %>%
|
|
as.matrix() %>%
|
|
as.character() %>%
|
|
paste(collapse = "|") %>%
|
|
strsplit("|", fixed = TRUE) %>%
|
|
unlist() %>%
|
|
unique()
|
|
ab_vars <- ab_vars[!ab_vars %in% c(NA, "", "NA") & nchar(ab_vars) > 2]
|
|
if (length(ab_vars) == 0) {
|
|
# try again, searching atc_group1 and atc_group2 columns
|
|
ab_vars <- AMR::antibiotics %>%
|
|
filter_at(vars(c("atc_group1", "atc_group2")), any_vars(. %like% ab_class)) %>%
|
|
select(ab:name, abbreviations, synonyms) %>%
|
|
unlist() %>%
|
|
as.matrix() %>%
|
|
as.character() %>%
|
|
paste(collapse = "|") %>%
|
|
strsplit("|", fixed = TRUE) %>%
|
|
unlist() %>%
|
|
unique()
|
|
ab_vars <- ab_vars[!ab_vars %in% c(NA, "", "NA") & nchar(ab_vars) > 2]
|
|
}
|
|
ab_vars
|
|
}
|
|
|
|
#' @importFrom dplyr %>% filter pull
|
|
find_ab_group <- function(ab_class) {
|
|
ifelse(ab_class %in% c("aminoglycoside",
|
|
"carbapenem",
|
|
"cephalosporin",
|
|
"fluoroquinolone",
|
|
"glycopeptide",
|
|
"macrolide",
|
|
"tetracycline"),
|
|
paste0(ab_class, "s"),
|
|
AMR::antibiotics %>%
|
|
filter(ab %in% ab_class_vars(ab_class)) %>%
|
|
pull(group) %>%
|
|
unique() %>%
|
|
tolower() %>%
|
|
paste(collapse = "/")
|
|
)
|
|
}
|