diff --git a/DESCRIPTION b/DESCRIPTION index 339701ea..1ce9129c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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) diff --git a/NAMESPACE b/NAMESPACE index fa976b43..4e8bf5c9 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -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) diff --git a/NEWS.md b/NEWS.md index ac84d2f2..2fa7c633 100755 --- a/NEWS.md +++ b/NEWS.md @@ -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. diff --git a/R/ab.R b/R/ab.R index 777b2373..e719789c 100755 --- a/R/ab.R +++ b/R/ab.R @@ -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 diff --git a/R/add_custom_antimicrobials.R b/R/add_custom_antimicrobials.R new file mode 100644 index 00000000..1548ef7e --- /dev/null +++ b/R/add_custom_antimicrobials.R @@ -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.") +} diff --git a/inst/tinytest/test-add_custom_antimicrobials.R b/inst/tinytest/test-add_custom_antimicrobials.R new file mode 100644 index 00000000..1c080353 --- /dev/null +++ b/inst/tinytest/test-add_custom_antimicrobials.R @@ -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") diff --git a/man/add_custom_antimicrobials.Rd b/man/add_custom_antimicrobials.Rd new file mode 100644 index 00000000..de69e6d6 --- /dev/null +++ b/man/add_custom_antimicrobials.Rd @@ -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{
}}\preformatted{library(AMR) +add_custom_antimicrobials( + data.frame(ab = "TEST", + name = "Test Antibiotic", + group = "Test Group") +) +}\if{html}{\out{
}} + +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") +} +} diff --git a/man/as.ab.Rd b/man/as.ab.Rd index 138d19df..04faf07c 100644 --- a/man/as.ab.Rd +++ b/man/as.ab.Rd @@ -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}{