(v0.7.1.9059) bug_drug_combinations

2025-07-08 15:21:58 +02:00 · 2019-08-25 22:53:22 +02:00
parent 7c069145ac
commit e46cb0399f
23 changed files with 1081 additions and 230 deletions
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@ -0,0 +1,107 @@
+# ==================================================================== #
+# 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 printable format, see Examples.
+#' @inheritParams eucast_rules
+#' @inheritParams rsi_df
+#' @importFrom dplyr rename
+#' @importFrom tidyr spread
+#' @importFrom clean freq
+#' @export
+#' @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(septic_patients)
+#' x
+#' format(x)
+#' }
+bug_drug_combinations <- function(x, col_mo = NULL, minimum = 30) {
+  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 %>%
+    mutate(col_mo = x %>% pull(col_mo)) %>% 
+    filter(mo %in% (clean::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("bugdrug", class(x)))
+}
+
+#' @importFrom dplyr everything rename
+#' @importFrom tidyr spread
+#' @exportMethod format.bugdrug
+#' @export
+format.bugdrug <- function(x, combine_SI = TRUE, add_ab_group = TRUE, ...) {
+  if (combine_SI == TRUE) {
+    x$isolates <- x$R
+  } else {
+    x$isolates <- x$R + x$I
+  }
+  y <- x %>%
+    mutate(mo = mo_name(mo),
+           txt = paste0(AMR:::percent(isolates / total, force_zero = TRUE), 
+                            " (", trimws(format(isolates, big.mark = ",")), "/", 
+                            trimws(format(total, big.mark = ",")), ")")) %>% 
+    select(ab, mo, txt) %>% 
+    spread(mo, txt) %>%
+    mutate_all(~ifelse(is.na(.), "", .)) %>% 
+    mutate(ab = paste0(ab_name(ab), " (", as.ab(ab), ", ", ab_atc(ab), ")"),
+           ab_group = ab_group(ab)) %>% 
+    select(ab_group, ab, everything()) %>% 
+    arrange(ab_group, ab) %>% 
+    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)
+  }
+  y <- y %>% rename("Group" = ab_group,
+                    "Antibiotic" = ab)
+  y
+}
+
+#' @exportMethod print.bugdrug
+#' @export
+#' @importFrom crayon blue
+print.bugdrug <- function(x, ...) {
+  print(as.data.frame(x, stringsAsFactors = FALSE))
+  message(blue("NOTE: Use 'format()' on this result to get a format that is ready for export or printing."))
+}