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add add_custom_antimicrobials()

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dr. M.S. (Matthijs) Berends 2022-10-10 20:20:39 +02:00
parent 4fe90092c7
commit 82e3198315
8 changed files with 209 additions and 11 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.8.2.9009
Version: 1.8.2.9010
Date: 2022-10-10
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NAMESPACE
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@ -181,6 +181,7 @@ export(ab_selector)
export(ab_synonyms)
export(ab_tradenames)
export(ab_url)
export(add_custom_antimicrobials)
export(administrable_iv)
export(administrable_per_os)
export(age)
@ -212,6 +213,7 @@ export(cephalosporins_2nd)
export(cephalosporins_3rd)
export(cephalosporins_4th)
export(cephalosporins_5th)
export(clear_custom_antimicrobials)
export(count_I)
export(count_IR)
export(count_R)

3
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9009
# AMR 1.8.2.9010
This version will eventually become v2.0! We're happy to reach a new major milestone soon!
@ -20,6 +20,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
* Function `mean_amr_distance()` to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.
* Function `rsi_interpretation_history()` to view the history of previous runs of `as.rsi()`. This returns a 'logbook' with the selected guideline, reference table and specific interpretation of each row in a data set on which `as.rsi()` was run.
* Function `mo_current()` to get the currently valid taxonomic name of a microorganism
* Function `add_custom_antimicrobials()` to add custom antimicrobial codes and names to the `AMR` package
* Support for `data.frame`-enhancing R packages, more specifically: `data.table::data.table`, `janitor::tabyl`, `tibble::tibble`, and `tsibble::tsibble`. AMR package functions that have a data set as output (such as `rsi_df()` and `bug_drug_combinations()`), will now return the same data type as the input.
* All data sets in this package are now exported as `tibble`, instead of base R `data.frame`s. Older R versions are still supported.
* Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The `AMR` package is now available in 16 languages.

20
R/ab.R
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@ -48,6 +48,8 @@
#' Use the [`ab_*`][ab_property()] functions to get properties based on the returned antibiotic ID, see *Examples*.
#'
#' Note: the [as.ab()] and [`ab_*`][ab_property()] functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
#'
#' You can add your own manual codes to be considered by [as.ab()] and all [`ab_*`][ab_property()] functions, see [add_custom_antimicrobials()].
#' @section Source:
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
#'
@ -218,7 +220,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
AB_lookup$generalised_loinc,
function(s) x[i] %in% s
))
found <- AMR::antibiotics$ab[loinc_found == TRUE]
found <- AB_lookup$ab[loinc_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -229,7 +231,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
AB_lookup$generalised_synonyms,
function(s) x[i] %in% s
))
found <- AMR::antibiotics$ab[synonym_found == TRUE]
found <- AB_lookup$ab[synonym_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -241,7 +243,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# require at least 2 characters for abbreviations
function(s) x[i] %in% s && nchar(x[i]) >= 2
))
found <- AMR::antibiotics$ab[abbr_found == TRUE]
found <- AB_lookup$ab[abbr_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -288,13 +290,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
# try if name starts with it
found <- AMR::antibiotics[which(AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
found <- AB_lookup[which(AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# try if name ends with it
found <- AMR::antibiotics[which(AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
found <- AB_lookup[which(AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
if (nchar(x[i]) >= 4 && length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -305,7 +307,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
AB_lookup$generalised_synonyms,
function(s) any(s %like% paste0("^", x_spelling))
))
found <- AMR::antibiotics$ab[synonym_found == TRUE]
found <- AB_lookup$ab[synonym_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -583,7 +585,7 @@ as.data.frame.ab <- function(x, ...) {
"[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(i)
return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
}
#' @method [[<- ab
#' @export
@ -591,7 +593,7 @@ as.data.frame.ab <- function(x, ...) {
"[[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(i)
return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
}
#' @method c ab
#' @export
@ -600,7 +602,7 @@ c.ab <- function(...) {
x <- list(...)[[1L]]
y <- NextMethod()
attributes(y) <- attributes(x)
return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
}
#' @method unique ab

98
R/add_custom_antimicrobials.R Normal file
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@ -0,0 +1,98 @@
# ==================================================================== #
# TITLE #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# 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. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Add Manual Antimicrobials to This Package
#'
#' With [add_custom_antimicrobials()] you can add your own manual antimicrobial codes to the `AMR` package.
#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
#' @details Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your `.Rprofile` file to circumvent this, for example:
#'
#' ```r
#' library(AMR)
#' add_custom_antimicrobials(
#' data.frame(ab = "TEST",
#' name = "Test Antibiotic",
#' group = "Test Group")
#' )
#' ```
#'
#' Use [clear_custom_antimicrobials()] to clear the previously added antimicrobials.
#' @rdname add_custom_antimicrobials
#' @export
#' @examples
#' \donttest{
#'
#' # returns NA and throws a warning:
#' as.ab("test")
#'
#' # now a manual entry - it will be considered by as.ab() and
#' # all ab_*() functions
#' add_custom_antimicrobials(
#' data.frame(ab = "TEST",
#' name = "Test Antibiotic",
#' group = "Test Group")
#' )
#'
#' "test" is now a new antibiotic:
#' as.ab("test")
#' ab_name("test")
#' ab_group("test")
#' }
add_custom_antimicrobials <- function(x) {
meet_criteria(x, allow_class = "data.frame")
stop_ifnot(all(c("ab", "name") %in% colnames(x)),
"`x` must contain columns \"ab\" and \"name\".")
stop_if(any(x$ab %in% AB_lookup$ab),
"Antimicrobial code(s) ", vector_and(x$ab[x$ab %in% AB_lookup$ab]), " already exist in the internal `antibiotics` data set.")
x <- x[, colnames(AB_lookup)[colnames(AB_lookup) %in% colnames(x)], drop = FALSE]
x$generalised_name <- generalise_antibiotic_name(x$name)
x$generalised_all <- as.list(x$generalised_name)
bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = FALSE)
if (!is.null(bind_rows)) {
new_df <- bind_rows(AB_lookup, x)
} else {
new_df <- rbind(AB_lookup, x, stringsAsFactors = FALSE)
}
assignInNamespace(x = "AB_lookup",
value = new_df,
ns = asNamespace("AMR"))
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to internal `antibiotics` data set.")
}
#' @rdname add_custom_antimicrobials
#' @export
clear_custom_antimicrobials <- function() {
assignInNamespace(x = "AB_lookup",
value = create_AB_lookup(),
ns = asNamespace("AMR"))
message_("Manual antimicrobials cleared.")
}

43
inst/tinytest/test-add_custom_antimicrobials.R Normal file
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@ -0,0 +1,43 @@
# ==================================================================== #
# TITLE #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# 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. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_warning(as.ab("test"))
expect_identical(as.character(suppressWarnings(as.ab("test"))), NA_character_)
suppressMessages(
add_custom_antimicrobials(
data.frame(ab = "TEST",
name = "Test Antibiotic",
group = "Test Group")
)
)
expect_identical(as.character(as.ab("test")), "TEST")
expect_identical(ab_name("test"), "Test Antibiotic")
expect_identical(ab_group("test"), "Test Group")

50
man/add_custom_antimicrobials.Rd Normal file
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@ -0,0 +1,50 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/add_custom_antimicrobials.R
\name{add_custom_antimicrobials}
\alias{add_custom_antimicrobials}
\alias{clear_custom_antimicrobials}
\title{Add Manual Antimicrobials to This Package}
\usage{
add_custom_antimicrobials(x)
clear_custom_antimicrobials()
}
\arguments{
\item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"}
}
\description{
With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own manual antimicrobial codes to the \code{AMR} package.
}
\details{
Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your \code{.Rprofile} file to circumvent this, for example:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{library(AMR)
add_custom_antimicrobials(
data.frame(ab = "TEST",
name = "Test Antibiotic",
group = "Test Group")
)
}\if{html}{\out{</div>}}
Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to clear the previously added antimicrobials.
}
\examples{
\donttest{
# returns NA and throws a warning:
as.ab("test")
# now a manual entry - it will be considered by as.ab() and
# all ab_*() functions
add_custom_antimicrobials(
data.frame(ab = "TEST",
name = "Test Antibiotic",
group = "Test Group")
)
"test" is now a new antibiotic:
as.ab("test")
ab_name("test")
ab_group("test")
}
}

2
man/as.ab.Rd
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@ -39,6 +39,8 @@ All these properties will be searched for the user input. The \code{\link[=as.ab
Use the \code{\link[=ab_property]{ab_*}} functions to get properties based on the returned antibiotic ID, see \emph{Examples}.
Note: the \code{\link[=as.ab]{as.ab()}} and \code{\link[=ab_property]{ab_*}} functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
You can add your own manual codes to be considered by \code{\link[=as.ab]{as.ab()}} and all \code{\link[=ab_property]{ab_*}} functions, see \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
}
\section{Source}{