# ==================================================================== # # 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 pull #' @importFrom tidyr spread #' @importFrom clean freq percentage #' @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 #' @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) #' #' # 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, minimum = 30, 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(...)) %>% filter(mo %in% (freq(mo) %>% filter(count >= minimum) %>% pull(item))) %>% group_by(mo) %>% AMR::rsi_df(translate_ab = FALSE, combine_SI = FALSE) %>% select(-value) %>% spread(interpretation, isolates) %>% mutate(total = S + I + R) %>% filter(total >= minimum) %>% rename(ab = antibiotic) 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 spread #' @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 == ",", ".", ","), ...) { if (remove_intrinsic_resistant == TRUE) { x <- x %>% filter(R != total) } if (combine_IR == FALSE | combine_SI == TRUE) { 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 1: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 %>% filter(total >= minimum) %>% 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) %>% spread(mo, 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.")) }