mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 22:22:03 +02:00
(v2.1.1.9111) add betalactams_with_inhibitor(), fixes #175
This commit is contained in:
191
R/ab_selectors.R
191
R/ab_selectors.R
@ -62,102 +62,88 @@
|
||||
#' \donttest{
|
||||
#' # dplyr -------------------------------------------------------------------
|
||||
#'
|
||||
#' if (require("dplyr")) {
|
||||
#' example_isolates %>% select(carbapenems())
|
||||
#' }
|
||||
#'
|
||||
#' if (require("dplyr")) {
|
||||
#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
|
||||
#' example_isolates %>% select(mo, aminoglycosides())
|
||||
#' }
|
||||
#'
|
||||
#' if (require("dplyr")) {
|
||||
#' # select only antibiotic columns with DDDs for oral treatment
|
||||
#' example_isolates %>% select(administrable_per_os())
|
||||
#' }
|
||||
#'
|
||||
#' if (require("dplyr")) {
|
||||
#' # get AMR for all aminoglycosides e.g., per ward:
|
||||
#' example_isolates %>%
|
||||
#' group_by(ward) %>%
|
||||
#' summarise(across(aminoglycosides(),
|
||||
#' resistance))
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # You can combine selectors with '&' to be more specific:
|
||||
#' example_isolates %>%
|
||||
#' select(penicillins() & administrable_per_os())
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # get AMR for only drugs that matter - no intrinsic resistance:
|
||||
#' example_isolates %>%
|
||||
#' filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>%
|
||||
#' group_by(ward) %>%
|
||||
#' summarise_at(not_intrinsic_resistant(),
|
||||
#' resistance)
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # get susceptibility for antibiotics whose name contains "trim":
|
||||
#' example_isolates %>%
|
||||
#' filter(first_isolate()) %>%
|
||||
#' group_by(ward) %>%
|
||||
#' summarise(across(ab_selector(name %like% "trim"), susceptibility))
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
|
||||
#' example_isolates %>%
|
||||
#' select(carbapenems())
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
|
||||
#' example_isolates %>%
|
||||
#' select(mo, aminoglycosides())
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # any() and all() work in dplyr's filter() too:
|
||||
#' example_isolates %>%
|
||||
#' filter(
|
||||
#' any(aminoglycosides() == "R"),
|
||||
#' all(cephalosporins_2nd() == "R")
|
||||
#' )
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # also works with c():
|
||||
#' example_isolates %>%
|
||||
#' filter(any(c(carbapenems(), aminoglycosides()) == "R"))
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # not setting any/all will automatically apply all():
|
||||
#' example_isolates %>%
|
||||
#' filter(aminoglycosides() == "R")
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
|
||||
#' example_isolates %>%
|
||||
#' select(mo, ab_class("mycobact"))
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # get bug/drug combinations for only glycopeptides in Gram-positives:
|
||||
#' example_isolates %>%
|
||||
#' filter(mo_is_gram_positive()) %>%
|
||||
#' select(mo, glycopeptides()) %>%
|
||||
#' bug_drug_combinations() %>%
|
||||
#' format()
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' data.frame(
|
||||
#' some_column = "some_value",
|
||||
#' J01CA01 = "S"
|
||||
#' ) %>% # ATC code of ampicillin
|
||||
#' select(penicillins()) # only the 'J01CA01' column will be selected
|
||||
#' }
|
||||
#' if (require("dplyr")) {
|
||||
#' # with recent versions of dplyr, this is all equal:
|
||||
#' x <- example_isolates[carbapenems() == "R", ]
|
||||
#' y <- example_isolates %>% filter(carbapenems() == "R")
|
||||
#' z <- example_isolates %>% filter(if_all(carbapenems(), ~ .x == "R"))
|
||||
#' identical(x, y) && identical(y, z)
|
||||
#' }
|
||||
#' library(dplyr, warn.conflicts = FALSE)
|
||||
#'
|
||||
#' example_isolates %>% select(carbapenems())
|
||||
#'
|
||||
#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
|
||||
#' example_isolates %>% select(mo, aminoglycosides())
|
||||
#'
|
||||
#' # you can combine selectors like you are used with tidyverse
|
||||
#' # e.g., for betalactams, but not the ones with an enzyme inhibitor:
|
||||
#' example_isolates |> select(betalactams(), -betalactams_with_inhibitor())
|
||||
#'
|
||||
#' # select only antibiotic columns with DDDs for oral treatment
|
||||
#' example_isolates %>% select(administrable_per_os())
|
||||
#'
|
||||
#' # get AMR for all aminoglycosides e.g., per ward:
|
||||
#' example_isolates %>%
|
||||
#' group_by(ward) %>%
|
||||
#' summarise(across(aminoglycosides(),
|
||||
#' resistance))
|
||||
#'
|
||||
#' # You can combine selectors with '&' to be more specific:
|
||||
#' example_isolates %>%
|
||||
#' select(penicillins() & administrable_per_os())
|
||||
#'
|
||||
#' # get AMR for only drugs that matter - no intrinsic resistance:
|
||||
#' example_isolates %>%
|
||||
#' filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>%
|
||||
#' group_by(ward) %>%
|
||||
#' summarise_at(not_intrinsic_resistant(),
|
||||
#' resistance)
|
||||
#'
|
||||
#' # get susceptibility for antibiotics whose name contains "trim":
|
||||
#' example_isolates %>%
|
||||
#' filter(first_isolate()) %>%
|
||||
#' group_by(ward) %>%
|
||||
#' summarise(across(ab_selector(name %like% "trim"), susceptibility))
|
||||
#'
|
||||
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
|
||||
#' example_isolates %>%
|
||||
#' select(carbapenems())
|
||||
#'
|
||||
#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
|
||||
#' example_isolates %>%
|
||||
#' select(mo, aminoglycosides())
|
||||
#'
|
||||
#' # any() and all() work in dplyr's filter() too:
|
||||
#' example_isolates %>%
|
||||
#' filter(
|
||||
#' any(aminoglycosides() == "R"),
|
||||
#' all(cephalosporins_2nd() == "R")
|
||||
#' )
|
||||
#'
|
||||
#' # also works with c():
|
||||
#' example_isolates %>%
|
||||
#' filter(any(c(carbapenems(), aminoglycosides()) == "R"))
|
||||
#'
|
||||
#' # not setting any/all will automatically apply all():
|
||||
#' example_isolates %>%
|
||||
#' filter(aminoglycosides() == "R")
|
||||
#'
|
||||
#' # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
|
||||
#' example_isolates %>%
|
||||
#' select(mo, ab_class("mycobact"))
|
||||
#'
|
||||
#' # get bug/drug combinations for only glycopeptides in Gram-positives:
|
||||
#' example_isolates %>%
|
||||
#' filter(mo_is_gram_positive()) %>%
|
||||
#' select(mo, glycopeptides()) %>%
|
||||
#' bug_drug_combinations() %>%
|
||||
#' format()
|
||||
#'
|
||||
#' data.frame(
|
||||
#' some_column = "some_value",
|
||||
#' J01CA01 = "S"
|
||||
#' ) %>% # ATC code of ampicillin
|
||||
#' select(penicillins()) # only the 'J01CA01' column will be selected
|
||||
#'
|
||||
#' # with recent versions of dplyr, this is all equal:
|
||||
#' x <- example_isolates[carbapenems() == "R", ]
|
||||
#' y <- example_isolates %>% filter(carbapenems() == "R")
|
||||
#' z <- example_isolates %>% filter(if_all(carbapenems(), ~ .x == "R"))
|
||||
#' identical(x, y) && identical(y, z)
|
||||
#'
|
||||
#'
|
||||
#' # base R ------------------------------------------------------------------
|
||||
@ -312,6 +298,13 @@ betalactams <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
|
||||
ab_select_exec("betalactams", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
betalactams_with_inhibitor <- function(only_sir_columns = FALSE, ...) {
|
||||
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("betalactams_with_inhibitor", only_sir_columns = only_sir_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
|
||||
@ -595,7 +588,7 @@ ab_select_exec <- function(function_name,
|
||||
only_treatable = FALSE,
|
||||
ab_class_args = NULL) {
|
||||
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
# but it only takes a couple of milliseconds
|
||||
# it only takes a couple of milliseconds, so no problem
|
||||
vars_df <- get_current_data(arg_name = NA, call = -3)
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df,
|
||||
@ -605,7 +598,7 @@ ab_select_exec <- function(function_name,
|
||||
|
||||
# untreatable drugs
|
||||
if (only_treatable == TRUE) {
|
||||
untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|nacubactam"), "ab", drop = TRUE]
|
||||
untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "(-high|EDTA|polysorbate|macromethod|screening|nacubactam)"), "ab", drop = TRUE]
|
||||
if (any(untreatable %in% names(ab_in_data))) {
|
||||
if (message_not_thrown_before(function_name, "ab_class", "untreatable")) {
|
||||
warning_(
|
||||
@ -644,7 +637,7 @@ ab_select_exec <- function(function_name,
|
||||
custom_ab <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$ab %in% AMR_env$custom_ab_codes), ]
|
||||
check_string <- paste0(custom_ab$group, custom_ab$atc_group1, custom_ab$atc_group2)
|
||||
if (function_name == "betalactams") {
|
||||
find_group <- "beta-lactams"
|
||||
find_group <- "beta[-]?lactams"
|
||||
} else if (function_name %like% "cephalosporins_") {
|
||||
find_group <- gsub("_(.*)$", paste0(" (\\1 gen.)"), function_name)
|
||||
} else {
|
||||
|
||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
Reference in New Issue
Block a user