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AMR/R/bug_drug_combinations.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# 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. #
# #
# This R package was created for academic research and 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. #
# ==================================================================== #
#' Determine bug-drug combinations
#'
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a publicable/printable format, see Examples.
#' @inheritParams eucast_rules
#' @param combine_IR logical to indicate whether values R and I should be summed
#' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column
#' @param remove_intrinsic_resistant logical to indicate that rows with 100\% resistance for all tested antimicrobials must be removed from the table
#' @param FUN the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link{mo_shortname}}
#' @param translate_ab a character of length 1 containing column names of the \code{\link{antibiotics}} data set
#' @param ... arguments passed on to \code{FUN}
#' @inheritParams rsi_df
#' @inheritParams base::formatC
#' @importFrom dplyr %>% rename group_by select mutate filter summarise ungroup
#' @importFrom tidyr pivot_longer
#' @details The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
#'
#' The language of the output can be overwritten with \code{options(AMR_locale)}, please see \link{translate}.
#' @export
#' @rdname bug_drug_combinations
#' @return The function \code{bug_drug_combinations} returns a \code{data.frame} with columns "mo", "ab", "S", "I", "R" and "total".
#' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @inheritSection AMR Read more on our website!
#' @examples
#' \donttest{
#' x <- bug_drug_combinations(example_isolates)
#' x
#' format(x, translate_ab = "name (atc)")
#'
#' # Use FUN to change to transformation of microorganism codes
#' x <- bug_drug_combinations(example_isolates,
#' FUN = mo_gramstain)
#'
#' x <- bug_drug_combinations(example_isolates,
#' FUN = function(x) ifelse(x == "B_ESCHR_COLI",
#' "E. coli",
#' "Others"))
#' }
bug_drug_combinations <- function(x,
col_mo = NULL,
FUN = mo_shortname,
...) {
if (!is.data.frame(x)) {
stop("`x` must be a data frame.", call. = FALSE)
}
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo")
}
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
x <- x %>%
as.data.frame(stringsAsFactors = FALSE) %>%
mutate(mo = x %>%
pull(col_mo) %>%
FUN(...)) %>%
group_by(mo) %>%
select_if(is.rsi) %>%
pivot_longer(-mo, names_to = "ab") %>%
group_by(mo, ab) %>%
summarise(S = sum(value == "S", na.rm = TRUE),
I = sum(value == "I", na.rm = TRUE),
R = sum(value == "R", na.rm = TRUE)) %>%
ungroup() %>%
mutate(total = S + I + R) %>%
as.data.frame(stringsAsFactors = FALSE)
structure(.Data = x, class = c("bug_drug_combinations", class(x)))
}
#' @importFrom dplyr everything rename %>% ungroup group_by summarise mutate_all arrange everything lag
#' @importFrom tidyr pivot_wider
#' @importFrom cleaner percentage
#' @exportMethod format.bug_drug_combinations
#' @export
#' @rdname bug_drug_combinations
format.bug_drug_combinations <- function(x,
translate_ab = "name (ab, atc)",
language = get_locale(),
minimum = 30,
combine_SI = TRUE,
combine_IR = FALSE,
add_ab_group = TRUE,
remove_intrinsic_resistant = FALSE,
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ","),
...) {
x <- x %>% filter(total >= minimum)
if (remove_intrinsic_resistant == TRUE) {
x <- x %>% filter(R != total)
}
if (combine_SI == TRUE | combine_IR == FALSE) {
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I
}
give_ab_name <- function(ab, format, language) {
format <- tolower(format)
ab_txt <- rep(format, length(ab))
for (i in seq_len(length(ab_txt))) {
ab_txt[i] <- gsub("ab", ab[i], ab_txt[i])
ab_txt[i] <- gsub("cid", ab_cid(ab[i]), ab_txt[i])
ab_txt[i] <- gsub("group", ab_group(ab[i], language = language), ab_txt[i])
ab_txt[i] <- gsub("atc_group1", ab_atc_group1(ab[i], language = language), ab_txt[i])
ab_txt[i] <- gsub("atc_group2", ab_atc_group2(ab[i], language = language), ab_txt[i])
ab_txt[i] <- gsub("atc", ab_atc(ab[i]), ab_txt[i])
ab_txt[i] <- gsub("name", ab_name(ab[i], language = language), ab_txt[i])
ab_txt[i]
}
ab_txt
}
y <- x %>%
mutate(ab = as.ab(ab),
ab_txt = give_ab_name(ab = ab, format = translate_ab, language = language)) %>%
group_by(ab, ab_txt, mo) %>%
summarise(isolates = sum(isolates, na.rm = TRUE),
total = sum(total, na.rm = TRUE)) %>%
ungroup() %>%
mutate(txt = paste0(percentage(isolates / total, decimal.mark = decimal.mark, big.mark = big.mark),
" (", trimws(format(isolates, big.mark = big.mark)), "/",
trimws(format(total, big.mark = big.mark)), ")")) %>%
select(ab, ab_txt, mo, txt) %>%
arrange(mo) %>%
pivot_wider(names_from = mo, values_from = txt) %>%
mutate_all(~ifelse(is.na(.), "", .)) %>%
mutate(ab_group = ab_group(ab, language = language),
ab_txt) %>%
select(ab_group, ab_txt, everything(), -ab) %>%
arrange(ab_group, ab_txt) %>%
mutate(ab_group = ifelse(ab_group != lag(ab_group) | is.na(lag(ab_group)), ab_group, ""))
if (add_ab_group == FALSE) {
y <- y %>% select(-ab_group) %>% rename("Drug" = ab_txt)
colnames(y)[1] <- translate_AMR(colnames(y)[1], language = get_locale(), only_unknown = FALSE)
} else {
y <- y %>% rename("Group" = ab_group,
"Drug" = ab_txt)
colnames(y)[1:2] <- translate_AMR(colnames(y)[1:2], language = get_locale(), only_unknown = FALSE)
}
y
}
#' @exportMethod print.bug_drug_combinations
#' @export
#' @importFrom crayon blue
print.bug_drug_combinations <- function(x, ...) {
print(as.data.frame(x, stringsAsFactors = FALSE))
message(blue("NOTE: Use 'format()' on this result to get a publicable/printable format."))
}
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