mirror of https://github.com/msberends/AMR.git
938 lines
38 KiB
R
Executable File
938 lines
38 KiB
R
Executable File
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Antibiotic Selectors
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#'
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#' @description These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group (according to the [antibiotics] data set), without the need to define the columns or antibiotic abbreviations.
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#'
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#' In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up by [cephalosporins()].
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#' @param ab_class an antimicrobial class or a part of it, such as `"carba"` and `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
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#' @param filter an [expression] to be evaluated in the [antibiotics] data set, such as `name %like% "trim"`
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#' @param only_sir_columns a [logical] to indicate whether only columns of class `sir` must be selected (default is `FALSE`), see [as.sir()]
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#' @param only_treatable a [logical] to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`)
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#' @param ... ignored, only in place to allow future extensions
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#' @details
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#' These functions can be used in data set calls for selecting columns and filtering rows. They work with base \R, the Tidyverse, and `data.table`. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but are not limited to `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*.
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#'
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#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
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#'
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#' The [ab_class()] function can be used to filter/select on a manually defined antibiotic class. It searches for results in the [antibiotics] data set within the columns `group`, `atc_group1` and `atc_group2`.
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#' @section Full list of supported (antibiotic) classes:
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#'
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#' `r paste0(" * ", na.omit(sapply(DEFINED_AB_GROUPS, function(ab) ifelse(tolower(gsub("^AB_", "", ab)) %in% ls(envir = asNamespace("AMR")), paste0("[", tolower(gsub("^AB_", "", ab)), "()] can select: \\cr ", vector_and(paste0(ab_name(eval(parse(text = ab), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), " (", eval(parse(text = ab), envir = asNamespace("AMR")), ")"), quotes = FALSE, sort = TRUE)), character(0)), USE.NAMES = FALSE)), "\n", collapse = "")`
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#' @rdname antibiotic_class_selectors
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#' @name antibiotic_class_selectors
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#' @return (internally) a [character] vector of column names, with additional class `"ab_selector"`
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#' @export
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#' @inheritSection AMR Reference Data Publicly Available
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#' @examples
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#' # `example_isolates` is a data set available in the AMR package.
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#' # See ?example_isolates.
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#' example_isolates
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#'
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#'
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#' # Examples sections below are split into 'dplyr', 'base R', and 'data.table':
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#'
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#' \donttest{
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#' # dplyr -------------------------------------------------------------------
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#'
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#' if (require("dplyr")) {
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#' example_isolates %>% select(carbapenems())
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#' }
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#'
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#' if (require("dplyr")) {
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#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
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#' example_isolates %>% select(mo, aminoglycosides())
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#' }
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#'
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#' if (require("dplyr")) {
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#' # select only antibiotic columns with DDDs for oral treatment
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#' example_isolates %>% select(administrable_per_os())
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#' }
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#'
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#' if (require("dplyr")) {
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#' # get AMR for all aminoglycosides e.g., per ward:
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#' example_isolates %>%
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#' group_by(ward) %>%
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#' summarise(across(aminoglycosides(),
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#' resistance))
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#' }
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#' if (require("dplyr")) {
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#' # You can combine selectors with '&' to be more specific:
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#' example_isolates %>%
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#' select(penicillins() & administrable_per_os())
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#' }
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#' if (require("dplyr")) {
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#' # get AMR for only drugs that matter - no intrinsic resistance:
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#' example_isolates %>%
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#' filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>%
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#' group_by(ward) %>%
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#' summarise_at(not_intrinsic_resistant(),
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#' resistance)
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#' }
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#' if (require("dplyr")) {
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#' # get susceptibility for antibiotics whose name contains "trim":
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#' example_isolates %>%
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#' filter(first_isolate()) %>%
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#' group_by(ward) %>%
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#' summarise(across(ab_selector(name %like% "trim"), susceptibility))
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#' }
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#' if (require("dplyr")) {
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#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
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#' example_isolates %>%
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#' select(carbapenems())
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#' }
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#' if (require("dplyr")) {
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#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
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#' example_isolates %>%
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#' select(mo, aminoglycosides())
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#' }
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#' if (require("dplyr")) {
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#' # any() and all() work in dplyr's filter() too:
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#' example_isolates %>%
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#' filter(
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#' any(aminoglycosides() == "R"),
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#' all(cephalosporins_2nd() == "R")
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#' )
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#' }
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#' if (require("dplyr")) {
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#' # also works with c():
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#' example_isolates %>%
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#' filter(any(c(carbapenems(), aminoglycosides()) == "R"))
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#' }
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#' if (require("dplyr")) {
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#' # not setting any/all will automatically apply all():
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#' example_isolates %>%
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#' filter(aminoglycosides() == "R")
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#' }
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#' if (require("dplyr")) {
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#' # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
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#' example_isolates %>%
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#' select(mo, ab_class("mycobact"))
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#' }
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#' if (require("dplyr")) {
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#' # get bug/drug combinations for only glycopeptides in Gram-positives:
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#' example_isolates %>%
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#' filter(mo_is_gram_positive()) %>%
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#' select(mo, glycopeptides()) %>%
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#' bug_drug_combinations() %>%
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#' format()
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#' }
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#' if (require("dplyr")) {
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#' data.frame(
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#' some_column = "some_value",
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#' J01CA01 = "S"
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#' ) %>% # ATC code of ampicillin
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#' select(penicillins()) # only the 'J01CA01' column will be selected
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#' }
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#' if (require("dplyr")) {
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#' # with recent versions of dplyr, this is all equal:
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#' x <- example_isolates[carbapenems() == "R", ]
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#' y <- example_isolates %>% filter(carbapenems() == "R")
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#' z <- example_isolates %>% filter(if_all(carbapenems(), ~ .x == "R"))
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#' identical(x, y) && identical(y, z)
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#' }
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#'
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#'
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#' # base R ------------------------------------------------------------------
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#'
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#' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
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#' example_isolates[, carbapenems()]
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#'
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#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
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#' example_isolates[, c("mo", aminoglycosides())]
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#'
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#' # select only antibiotic columns with DDDs for oral treatment
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#' example_isolates[, administrable_per_os()]
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#'
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#' # filter using any() or all()
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#' example_isolates[any(carbapenems() == "R"), ]
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#' subset(example_isolates, any(carbapenems() == "R"))
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#'
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#' # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
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#' example_isolates[any(carbapenems()), ]
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#' example_isolates[all(carbapenems()), ]
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#'
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#' # filter with multiple antibiotic selectors using c()
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#' example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
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#'
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#' # filter + select in one go: get penicillins in carbapenem-resistant strains
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#' example_isolates[any(carbapenems() == "R"), penicillins()]
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#'
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#' # You can combine selectors with '&' to be more specific. For example,
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#' # penicillins() would select benzylpenicillin ('peni G') and
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#' # administrable_per_os() would select erythromycin. Yet, when combined these
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#' # drugs are both omitted since benzylpenicillin is not administrable per os
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#' # and erythromycin is not a penicillin:
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#' example_isolates[, penicillins() & administrable_per_os()]
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#'
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#' # ab_selector() applies a filter in the `antibiotics` data set and is thus
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#' # very flexible. For instance, to select antibiotic columns with an oral DDD
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#' # of at least 1 gram:
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#' example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
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#'
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#'
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#' # data.table --------------------------------------------------------------
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#'
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#' # data.table is supported as well, just use it in the same way as with
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#' # base R, but add `with = FALSE` if using a single AB selector.
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#'
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#' if (require("data.table")) {
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#' dt <- as.data.table(example_isolates)
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#'
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#' # this does not work, it returns column *names*
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#' dt[, carbapenems()]
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#' }
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#' if (require("data.table")) {
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#' # so `with = FALSE` is required
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#' dt[, carbapenems(), with = FALSE]
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#' }
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#'
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#' # for multiple selections or AB selectors, `with = FALSE` is not needed:
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#' if (require("data.table")) {
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#' dt[, c("mo", aminoglycosides())]
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#' }
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#' if (require("data.table")) {
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#' dt[, c(carbapenems(), aminoglycosides())]
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#' }
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#'
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#' # row filters are also supported:
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#' if (require("data.table")) {
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#' dt[any(carbapenems() == "S"), ]
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#' }
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#' if (require("data.table")) {
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#' dt[any(carbapenems() == "S"), penicillins(), with = FALSE]
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#' }
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#' }
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ab_class <- function(ab_class,
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only_sir_columns = FALSE,
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only_treatable = TRUE,
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...) {
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meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec(NULL, only_sir_columns = only_sir_columns, ab_class_args = ab_class, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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#' @details The [ab_selector()] function can be used to internally filter the [antibiotics] data set on any results, see *Examples*. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
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#' @export
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ab_selector <- function(filter,
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only_sir_columns = FALSE,
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only_treatable = TRUE,
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...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
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# but it only takes a couple of milliseconds
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vars_df <- get_current_data(arg_name = NA, call = -2)
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# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
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ab_in_data <- get_column_abx(vars_df,
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info = FALSE, only_sir_columns = only_sir_columns,
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sort = FALSE, fn = "ab_selector"
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)
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call <- substitute(filter)
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agents <- tryCatch(AMR_env$AB_lookup[which(eval(call, envir = AMR_env$AB_lookup)), "ab", drop = TRUE],
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error = function(e) stop_(e$message, call = -5)
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)
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agents <- ab_in_data[ab_in_data %in% agents]
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message_agent_names(
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function_name = "ab_selector",
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agents = agents,
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ab_group = NULL,
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examples = "",
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call = call
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)
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structure(unname(agents),
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class = c("ab_selector", "character")
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)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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aminoglycosides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec("aminoglycosides", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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aminopenicillins <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("aminopenicillins", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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antifungals <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("antifungals", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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antimycobacterials <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("antimycobacterials", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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betalactams <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec("betalactams", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec("carbapenems", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_1st <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_1st", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_2nd <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_2nd", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_3rd <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_3rd", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_4th <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_4th", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_5th <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_5th", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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fluoroquinolones <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("fluoroquinolones", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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glycopeptides <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("glycopeptides", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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lincosamides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec("lincosamides", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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lipoglycopeptides <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("lipoglycopeptides", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
macrolides <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("macrolides", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
nitrofurans <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("nitrofurans", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
oxazolidinones <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("oxazolidinones", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
penicillins <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("penicillins", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("polymyxins", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
quinolones <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("quinolones", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
rifamycins <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("rifamycins", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
streptogramins <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("streptogramins", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
tetracyclines <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("tetracyclines", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
trimethoprims <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("trimethoprims", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
ureidopenicillins <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
ab_select_exec("ureidopenicillins", only_sir_columns = only_sir_columns)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @details The [administrable_per_os()] and [administrable_iv()] functions also rely on the [antibiotics] data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the [antibiotics] data set.
|
|
#' @export
|
|
administrable_per_os <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
# 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
|
|
vars_df <- get_current_data(arg_name = NA, call = -2)
|
|
# 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,
|
|
info = FALSE, only_sir_columns = only_sir_columns,
|
|
sort = FALSE, fn = "administrable_per_os"
|
|
)
|
|
agents_all <- AMR_env$AB_lookup[which(!is.na(AMR_env$AB_lookup$oral_ddd)), "ab", drop = TRUE]
|
|
agents <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$ab %in% ab_in_data & !is.na(AMR_env$AB_lookup$oral_ddd)), "ab", drop = TRUE]
|
|
agents <- ab_in_data[ab_in_data %in% agents]
|
|
message_agent_names(
|
|
function_name = "administrable_per_os",
|
|
agents = agents,
|
|
ab_group = "administrable_per_os",
|
|
examples = paste0(
|
|
" (such as ",
|
|
vector_or(
|
|
ab_name(
|
|
sample(agents_all,
|
|
size = min(5, length(agents_all)),
|
|
replace = FALSE
|
|
),
|
|
tolower = TRUE,
|
|
language = NULL
|
|
),
|
|
quotes = FALSE
|
|
),
|
|
")"
|
|
)
|
|
)
|
|
structure(unname(agents),
|
|
class = c("ab_selector", "character")
|
|
)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @export
|
|
administrable_iv <- function(only_sir_columns = FALSE, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
|
# but it only takes a couple of milliseconds
|
|
vars_df <- get_current_data(arg_name = NA, call = -2)
|
|
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
|
ab_in_data <- get_column_abx(vars_df,
|
|
info = FALSE, only_sir_columns = only_sir_columns,
|
|
sort = FALSE, fn = "administrable_iv"
|
|
)
|
|
agents_all <- AMR_env$AB_lookup[which(!is.na(AMR_env$AB_lookup$iv_ddd)), "ab", drop = TRUE]
|
|
agents <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$ab %in% ab_in_data & !is.na(AMR_env$AB_lookup$iv_ddd)), "ab", drop = TRUE]
|
|
agents <- ab_in_data[ab_in_data %in% agents]
|
|
message_agent_names(
|
|
function_name = "administrable_iv",
|
|
agents = agents,
|
|
ab_group = "administrable_iv",
|
|
examples = ""
|
|
)
|
|
structure(unname(agents),
|
|
class = c("ab_selector", "character")
|
|
)
|
|
}
|
|
|
|
#' @rdname antibiotic_class_selectors
|
|
#' @inheritParams eucast_rules
|
|
#' @details The [not_intrinsic_resistant()] function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of *E. coli* and *K. pneumoniae* and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies `r format_eucast_version_nr(names(EUCAST_VERSION_EXPERT_RULES[1]))` to determine intrinsic resistance, using the [eucast_rules()] function internally. Because of this determination, this function is quite slow in terms of performance.
|
|
#' @export
|
|
not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, version_expertrules = 3.3, ...) {
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
# 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
|
|
vars_df <- get_current_data(arg_name = NA, call = -2)
|
|
# 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,
|
|
info = FALSE, only_sir_columns = only_sir_columns,
|
|
sort = FALSE, fn = "not_intrinsic_resistant"
|
|
)
|
|
# intrinsic vars
|
|
vars_df_R <- tryCatch(
|
|
sapply(
|
|
eucast_rules(vars_df,
|
|
col_mo = col_mo,
|
|
version_expertrules = version_expertrules,
|
|
rules = "expert",
|
|
info = FALSE
|
|
),
|
|
function(col) {
|
|
tryCatch(!any(is.na(col)) && all(col == "R"),
|
|
error = function(e) FALSE
|
|
)
|
|
}
|
|
),
|
|
error = function(e) stop_("in not_intrinsic_resistant(): ", e$message, call = FALSE)
|
|
)
|
|
|
|
agents <- ab_in_data[ab_in_data %in% names(vars_df_R[which(vars_df_R)])]
|
|
if (length(agents) > 0 &&
|
|
message_not_thrown_before("not_intrinsic_resistant", sort(agents))) {
|
|
agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
|
|
agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
|
|
need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
|
|
agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
|
|
message_(
|
|
"For `not_intrinsic_resistant()` removing ",
|
|
ifelse(length(agents) == 1, "column ", "columns "),
|
|
vector_and(agents_formatted, quotes = FALSE, sort = FALSE)
|
|
)
|
|
}
|
|
|
|
vars_df_R <- names(vars_df_R)[which(!vars_df_R)]
|
|
# find columns that are abx, but also intrinsic R
|
|
out <- unname(intersect(ab_in_data, vars_df_R))
|
|
structure(out,
|
|
class = c("ab_selector", "character")
|
|
)
|
|
}
|
|
|
|
ab_select_exec <- function(function_name,
|
|
only_sir_columns = FALSE,
|
|
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
|
|
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,
|
|
info = FALSE, only_sir_columns = only_sir_columns,
|
|
sort = FALSE, fn = function_name
|
|
)
|
|
|
|
# untreatable drugs
|
|
if (only_treatable == TRUE) {
|
|
untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|nacubactam"), "ab", drop = TRUE]
|
|
if (any(untreatable %in% names(ab_in_data))) {
|
|
if (message_not_thrown_before(function_name, "ab_class", "untreatable")) {
|
|
warning_(
|
|
"in `", function_name, "()`: some drugs were ignored since they cannot be used for treating patients: ",
|
|
vector_and(
|
|
ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
|
|
language = NULL,
|
|
tolower = TRUE
|
|
),
|
|
quotes = FALSE,
|
|
sort = TRUE
|
|
), ". They can be included using `", function_name, "(only_treatable = FALSE)`."
|
|
)
|
|
}
|
|
ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
|
|
}
|
|
}
|
|
|
|
if (length(ab_in_data) == 0) {
|
|
message_("No antimicrobial drugs found in the data.")
|
|
return(NULL)
|
|
}
|
|
|
|
if (is.null(ab_class_args) || isTRUE(function_name %in% c("antifungals", "antimycobacterials"))) {
|
|
ab_group <- NULL
|
|
if (isTRUE(function_name == "antifungals")) {
|
|
abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antifungals")]
|
|
} else if (isTRUE(function_name == "antimycobacterials")) {
|
|
abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antimycobacterials")]
|
|
} else {
|
|
# their upper case equivalent are vectors with class 'ab', created in data-raw/_pre_commit_checks.R
|
|
# carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
|
|
abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR"))
|
|
# manually added codes from add_custom_antimicrobials() must also be supported
|
|
if (length(AMR_env$custom_ab_codes) > 0) {
|
|
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$atc_group2)
|
|
if (function_name == "betalactams") {
|
|
find_group <- "beta-lactams"
|
|
} else if (function_name %like% "cephalosporins_") {
|
|
find_group <- gsub("_(.*)$", paste0(" (\\1 gen.)"), function_name)
|
|
} else {
|
|
find_group <- function_name
|
|
}
|
|
abx <- c(abx, custom_ab$ab[which(check_string %like% find_group)])
|
|
}
|
|
ab_group <- function_name
|
|
}
|
|
examples <- paste0(" (such as ", vector_or(
|
|
ab_name(sample(abx, size = min(2, length(abx)), replace = FALSE),
|
|
tolower = TRUE,
|
|
language = NULL
|
|
),
|
|
quotes = FALSE
|
|
), ")")
|
|
} else {
|
|
# this for the 'manual' ab_class() function
|
|
abx <- subset(
|
|
AMR_env$AB_lookup,
|
|
group %like% ab_class_args |
|
|
atc_group1 %like% ab_class_args |
|
|
atc_group2 %like% ab_class_args
|
|
)$ab
|
|
ab_group <- find_ab_group(ab_class_args)
|
|
function_name <- "ab_class"
|
|
examples <- paste0(" (such as ", find_ab_names(ab_class_args, 2), ")")
|
|
}
|
|
|
|
# get the columns with a group names in the chosen ab class
|
|
agents <- ab_in_data[names(ab_in_data) %in% abx]
|
|
|
|
message_agent_names(
|
|
function_name = function_name,
|
|
agents = agents,
|
|
ab_group = ab_group,
|
|
examples = examples,
|
|
ab_class_args = ab_class_args
|
|
)
|
|
|
|
structure(unname(agents),
|
|
class = c("ab_selector", "character")
|
|
)
|
|
}
|
|
|
|
#' @method print ab_selector
|
|
#' @export
|
|
#' @noRd
|
|
print.ab_selector <- function(x, ...) {
|
|
warning_("It should never be needed to print an antibiotic selector class. Are you using data.table? Then add the argument `with = FALSE`, see our examples at `?ab_selector`.",
|
|
immediate = TRUE)
|
|
cat("Class 'ab_selector'\n")
|
|
print(as.character(x), quote = FALSE)
|
|
}
|
|
|
|
#' @method c ab_selector
|
|
#' @export
|
|
#' @noRd
|
|
c.ab_selector <- function(...) {
|
|
structure(unlist(lapply(list(...), as.character)),
|
|
class = c("ab_selector", "character")
|
|
)
|
|
}
|
|
|
|
all_any_ab_selector <- function(type, ..., na.rm = TRUE) {
|
|
cols_ab <- c(...)
|
|
result <- cols_ab[toupper(cols_ab) %in% c("S", "SDD", "I", "R", "NI")]
|
|
if (length(result) == 0) {
|
|
message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "S", "I" or "R"')
|
|
result <- c("S", "SDD", "I", "R", "NI")
|
|
}
|
|
cols_ab <- cols_ab[!cols_ab %in% result]
|
|
df <- get_current_data(arg_name = NA, call = -3)
|
|
|
|
if (type == "all") {
|
|
scope_fn <- all
|
|
} else {
|
|
scope_fn <- any
|
|
}
|
|
|
|
x_transposed <- as.list(as.data.frame(t(df[, cols_ab, drop = FALSE]), stringsAsFactors = FALSE))
|
|
vapply(
|
|
FUN.VALUE = logical(1),
|
|
X = x_transposed,
|
|
FUN = function(y) scope_fn(y %in% result, na.rm = na.rm),
|
|
USE.NAMES = FALSE
|
|
)
|
|
}
|
|
|
|
#' @method all ab_selector
|
|
#' @export
|
|
#' @noRd
|
|
all.ab_selector <- function(..., na.rm = FALSE) {
|
|
all_any_ab_selector("all", ..., na.rm = na.rm)
|
|
}
|
|
|
|
#' @method any ab_selector
|
|
#' @export
|
|
#' @noRd
|
|
any.ab_selector <- function(..., na.rm = FALSE) {
|
|
all_any_ab_selector("any", ..., na.rm = na.rm)
|
|
}
|
|
|
|
|
|
#' @method all ab_selector_any_all
|
|
#' @export
|
|
#' @noRd
|
|
all.ab_selector_any_all <- function(..., na.rm = FALSE) {
|
|
# this is all() on a logical vector from `==.ab_selector` or `!=.ab_selector`
|
|
# e.g., example_isolates %>% filter(all(carbapenems() == "R"))
|
|
# so just return the vector as is, only correcting for na.rm
|
|
out <- unclass(c(...))
|
|
if (isTRUE(na.rm)) {
|
|
out <- out[!is.na(out)]
|
|
}
|
|
out
|
|
}
|
|
|
|
#' @method any ab_selector_any_all
|
|
#' @export
|
|
#' @noRd
|
|
any.ab_selector_any_all <- function(..., na.rm = FALSE) {
|
|
# this is any() on a logical vector from `==.ab_selector` or `!=.ab_selector`
|
|
# e.g., example_isolates %>% filter(any(carbapenems() == "R"))
|
|
# so just return the vector as is, only correcting for na.rm
|
|
out <- unclass(c(...))
|
|
if (isTRUE(na.rm)) {
|
|
out <- out[!is.na(out)]
|
|
}
|
|
out
|
|
}
|
|
|
|
#' @method == ab_selector
|
|
#' @export
|
|
#' @noRd
|
|
`==.ab_selector` <- function(e1, e2) {
|
|
calls <- as.character(match.call())
|
|
fn_name <- calls[2]
|
|
fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
|
|
if (is_any(fn_name)) {
|
|
type <- "any"
|
|
} else if (is_all(fn_name)) {
|
|
type <- "all"
|
|
} else {
|
|
type <- "all"
|
|
if (length(e1) > 1) {
|
|
message_(
|
|
"Assuming a filter on ", type, " ", length(e1), " ", gsub("[\\(\\)]", "", fn_name),
|
|
". Wrap around `all()` or `any()` to prevent this note."
|
|
)
|
|
}
|
|
}
|
|
structure(all_any_ab_selector(type = type, e1, e2),
|
|
class = c("ab_selector_any_all", "logical")
|
|
)
|
|
}
|
|
|
|
#' @method != ab_selector
|
|
#' @export
|
|
#' @noRd
|
|
`!=.ab_selector` <- function(e1, e2) {
|
|
calls <- as.character(match.call())
|
|
fn_name <- calls[2]
|
|
fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
|
|
if (is_any(fn_name)) {
|
|
type <- "any"
|
|
} else if (is_all(fn_name)) {
|
|
type <- "all"
|
|
} else {
|
|
type <- "all"
|
|
if (length(e1) > 1) {
|
|
message_(
|
|
"Assuming a filter on ", type, " ", length(e1), " ", gsub("[\\(\\)]", "", fn_name),
|
|
". Wrap around `all()` or `any()` to prevent this note."
|
|
)
|
|
}
|
|
}
|
|
# this is `!=`, so turn around the values
|
|
sir <- c("S", "SDD", "I", "R", "NI")
|
|
e2 <- sir[sir != e2]
|
|
structure(all_any_ab_selector(type = type, e1, e2),
|
|
class = c("ab_selector_any_all", "logical")
|
|
)
|
|
}
|
|
|
|
#' @method & ab_selector
|
|
#' @export
|
|
#' @noRd
|
|
`&.ab_selector` <- function(e1, e2) {
|
|
# this is only required for base R, since tidyselect has already implemented this
|
|
# e.g., for: example_isolates[, penicillins() & administrable_per_os()]
|
|
structure(intersect(unclass(e1), unclass(e2)),
|
|
class = c("ab_selector", "character")
|
|
)
|
|
}
|
|
#' @method | ab_selector
|
|
#' @export
|
|
#' @noRd
|
|
`|.ab_selector` <- function(e1, e2) {
|
|
# this is only required for base R, since tidyselect has already implemented this
|
|
# e.g., for: example_isolates[, penicillins() | administrable_per_os()]
|
|
structure(union(unclass(e1), unclass(e2)),
|
|
class = c("ab_selector", "character")
|
|
)
|
|
}
|
|
|
|
is_any <- function(el1) {
|
|
syscalls <- paste0(trimws2(deparse(sys.calls())), collapse = " ")
|
|
el1 <- gsub("(.*),.*", "\\1", el1)
|
|
syscalls %like% paste0("[^_a-zA-Z0-9]any\\(", "(c\\()?", el1)
|
|
}
|
|
is_all <- function(el1) {
|
|
syscalls <- paste0(trimws2(deparse(sys.calls())), collapse = " ")
|
|
el1 <- gsub("(.*),.*", "\\1", el1)
|
|
syscalls %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1)
|
|
}
|
|
|
|
find_ab_group <- function(ab_class_args) {
|
|
ab_class_args <- gsub("[^a-zA-Z0-9]", ".*", ab_class_args)
|
|
AMR_env$AB_lookup %pm>%
|
|
subset(group %like% ab_class_args |
|
|
atc_group1 %like% ab_class_args |
|
|
atc_group2 %like% ab_class_args) %pm>%
|
|
pm_pull(group) %pm>%
|
|
unique() %pm>%
|
|
tolower() %pm>%
|
|
sort() %pm>%
|
|
paste(collapse = "/")
|
|
}
|
|
|
|
find_ab_names <- function(ab_group, n = 3) {
|
|
ab_group <- gsub("[^a-zA-Z|0-9]", ".*", ab_group)
|
|
|
|
# try popular first, they have DDDs
|
|
drugs <- AMR_env$AB_lookup[which((!is.na(AMR_env$AB_lookup$iv_ddd) | !is.na(AMR_env$AB_lookup$oral_ddd)) &
|
|
AMR_env$AB_lookup$name %unlike% " " &
|
|
AMR_env$AB_lookup$group %like% ab_group &
|
|
AMR_env$AB_lookup$ab %unlike% "[0-9]$"), ]$name
|
|
if (length(drugs) < n) {
|
|
# now try it all
|
|
drugs <- AMR_env$AB_lookup[which((AMR_env$AB_lookup$group %like% ab_group |
|
|
AMR_env$AB_lookup$atc_group1 %like% ab_group |
|
|
AMR_env$AB_lookup$atc_group2 %like% ab_group) &
|
|
AMR_env$AB_lookup$ab %unlike% "[0-9]$"), ]$name
|
|
}
|
|
if (length(drugs) == 0) {
|
|
return("??")
|
|
}
|
|
vector_or(
|
|
ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
|
|
tolower = TRUE,
|
|
language = NULL
|
|
),
|
|
quotes = FALSE
|
|
)
|
|
}
|
|
|
|
message_agent_names <- function(function_name, agents, ab_group = NULL, examples = "", ab_class_args = NULL, call = NULL) {
|
|
if (message_not_thrown_before(function_name, sort(agents))) {
|
|
if (length(agents) == 0) {
|
|
if (is.null(ab_group)) {
|
|
message_("For `", function_name, "()` no antimicrobial drugs found", examples, ".")
|
|
} else if (ab_group == "administrable_per_os") {
|
|
message_("No orally administrable drugs found", examples, ".")
|
|
} else if (ab_group == "administrable_iv") {
|
|
message_("No IV administrable drugs found", examples, ".")
|
|
} else {
|
|
message_("No antimicrobial drugs of class '", ab_group, "' found", examples, ".")
|
|
}
|
|
} else {
|
|
agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
|
|
agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
|
|
need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
|
|
agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
|
|
message_(
|
|
"For `", function_name, "(",
|
|
ifelse(function_name == "ab_class",
|
|
paste0("\"", ab_class_args, "\""),
|
|
ifelse(!is.null(call),
|
|
paste0(deparse(call), collapse = " "),
|
|
""
|
|
)
|
|
),
|
|
")` using ",
|
|
ifelse(length(agents) == 1, "column ", "columns "),
|
|
vector_and(agents_formatted, quotes = FALSE, sort = FALSE)
|
|
)
|
|
}
|
|
}
|
|
}
|