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add add_custom_antimicrobials()
This commit is contained in:
parent
4fe90092c7
commit
82e3198315
@ -1,5 +1,5 @@
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Package: AMR
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Package: AMR
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Version: 1.8.2.9009
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Version: 1.8.2.9010
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Date: 2022-10-10
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Date: 2022-10-10
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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@ -181,6 +181,7 @@ export(ab_selector)
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export(ab_synonyms)
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export(ab_synonyms)
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export(ab_tradenames)
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export(ab_tradenames)
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export(ab_url)
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export(ab_url)
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export(add_custom_antimicrobials)
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export(administrable_iv)
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export(administrable_iv)
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export(administrable_per_os)
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export(administrable_per_os)
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export(age)
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export(age)
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@ -212,6 +213,7 @@ export(cephalosporins_2nd)
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export(cephalosporins_3rd)
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export(cephalosporins_3rd)
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export(cephalosporins_4th)
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export(cephalosporins_4th)
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export(cephalosporins_5th)
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export(cephalosporins_5th)
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export(clear_custom_antimicrobials)
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export(count_I)
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export(count_I)
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export(count_IR)
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export(count_IR)
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export(count_R)
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export(count_R)
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3
NEWS.md
3
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.2.9009
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# AMR 1.8.2.9010
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@ -20,6 +20,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
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* 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.
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* 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.
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* 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.
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* 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.
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* Function `mo_current()` to get the currently valid taxonomic name of a microorganism
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* Function `mo_current()` to get the currently valid taxonomic name of a microorganism
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* Function `add_custom_antimicrobials()` to add custom antimicrobial codes and names to the `AMR` package
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* 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.
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* 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.
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* All data sets in this package are now exported as `tibble`, instead of base R `data.frame`s. Older R versions are still supported.
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* All data sets in this package are now exported as `tibble`, instead of base R `data.frame`s. Older R versions are still supported.
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* 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.
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* 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.
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20
R/ab.R
20
R/ab.R
@ -48,6 +48,8 @@
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#' Use the [`ab_*`][ab_property()] functions to get properties based on the returned antibiotic ID, see *Examples*.
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#' Use the [`ab_*`][ab_property()] functions to get properties based on the returned antibiotic ID, see *Examples*.
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#'
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#'
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#' 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.
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#' 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.
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#'
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#' You can add your own manual codes to be considered by [as.ab()] and all [`ab_*`][ab_property()] functions, see [add_custom_antimicrobials()].
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#' @section Source:
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#' @section Source:
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#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
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#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
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#'
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#'
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@ -218,7 +220,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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AB_lookup$generalised_loinc,
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AB_lookup$generalised_loinc,
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function(s) x[i] %in% s
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function(s) x[i] %in% s
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))
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))
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found <- AMR::antibiotics$ab[loinc_found == TRUE]
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found <- AB_lookup$ab[loinc_found == TRUE]
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if (length(found) > 0) {
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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next
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@ -229,7 +231,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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AB_lookup$generalised_synonyms,
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AB_lookup$generalised_synonyms,
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function(s) x[i] %in% s
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function(s) x[i] %in% s
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))
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))
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found <- AMR::antibiotics$ab[synonym_found == TRUE]
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found <- AB_lookup$ab[synonym_found == TRUE]
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if (length(found) > 0) {
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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next
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@ -241,7 +243,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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# require at least 2 characters for abbreviations
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# require at least 2 characters for abbreviations
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function(s) x[i] %in% s && nchar(x[i]) >= 2
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function(s) x[i] %in% s && nchar(x[i]) >= 2
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))
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))
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found <- AMR::antibiotics$ab[abbr_found == TRUE]
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found <- AB_lookup$ab[abbr_found == TRUE]
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if (length(found) > 0) {
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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next
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@ -288,13 +290,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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}
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}
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# try if name starts with it
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# try if name starts with it
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found <- AMR::antibiotics[which(AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
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found <- AB_lookup[which(AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
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if (length(found) > 0) {
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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next
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}
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}
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# try if name ends with it
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# try if name ends with it
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found <- AMR::antibiotics[which(AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
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found <- AB_lookup[which(AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
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if (nchar(x[i]) >= 4 && length(found) > 0) {
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if (nchar(x[i]) >= 4 && length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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next
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@ -305,7 +307,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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AB_lookup$generalised_synonyms,
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AB_lookup$generalised_synonyms,
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function(s) any(s %like% paste0("^", x_spelling))
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function(s) any(s %like% paste0("^", x_spelling))
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))
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))
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found <- AMR::antibiotics$ab[synonym_found == TRUE]
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found <- AB_lookup$ab[synonym_found == TRUE]
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if (length(found) > 0) {
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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next
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@ -583,7 +585,7 @@ as.data.frame.ab <- function(x, ...) {
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"[<-.ab" <- function(i, j, ..., value) {
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"[<-.ab" <- function(i, j, ..., value) {
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y <- NextMethod()
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y <- NextMethod()
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attributes(y) <- attributes(i)
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attributes(y) <- attributes(i)
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return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
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return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
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}
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}
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#' @method [[<- ab
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#' @method [[<- ab
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#' @export
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#' @export
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@ -591,7 +593,7 @@ as.data.frame.ab <- function(x, ...) {
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"[[<-.ab" <- function(i, j, ..., value) {
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"[[<-.ab" <- function(i, j, ..., value) {
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y <- NextMethod()
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y <- NextMethod()
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attributes(y) <- attributes(i)
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attributes(y) <- attributes(i)
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return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
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return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
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}
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}
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#' @method c ab
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#' @method c ab
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#' @export
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#' @export
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@ -600,7 +602,7 @@ c.ab <- function(...) {
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x <- list(...)[[1L]]
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x <- list(...)[[1L]]
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y <- NextMethod()
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y <- NextMethod()
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attributes(y) <- attributes(x)
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attributes(y) <- attributes(x)
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return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
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return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
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}
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}
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#' @method unique ab
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#' @method unique ab
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98
R/add_custom_antimicrobials.R
Normal file
98
R/add_custom_antimicrobials.R
Normal file
@ -0,0 +1,98 @@
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# ==================================================================== #
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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 #
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# https://github.com/msberends/AMR #
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# #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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#' Add Manual Antimicrobials to This Package
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#'
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#' With [add_custom_antimicrobials()] you can add your own manual antimicrobial codes to the `AMR` package.
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#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
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#' @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:
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#'
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#' ```r
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#' library(AMR)
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#' add_custom_antimicrobials(
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#' data.frame(ab = "TEST",
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#' name = "Test Antibiotic",
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#' group = "Test Group")
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#' )
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#' ```
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#'
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#' Use [clear_custom_antimicrobials()] to clear the previously added antimicrobials.
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#' @rdname add_custom_antimicrobials
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#' @export
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#' @examples
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#' \donttest{
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#'
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#' # returns NA and throws a warning:
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#' as.ab("test")
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#'
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#' # now a manual entry - it will be considered by as.ab() and
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#' # all ab_*() functions
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#' add_custom_antimicrobials(
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#' data.frame(ab = "TEST",
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#' name = "Test Antibiotic",
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#' group = "Test Group")
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#' )
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#'
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#' "test" is now a new antibiotic:
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#' as.ab("test")
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#' ab_name("test")
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#' ab_group("test")
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#' }
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add_custom_antimicrobials <- function(x) {
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meet_criteria(x, allow_class = "data.frame")
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stop_ifnot(all(c("ab", "name") %in% colnames(x)),
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"`x` must contain columns \"ab\" and \"name\".")
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stop_if(any(x$ab %in% AB_lookup$ab),
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"Antimicrobial code(s) ", vector_and(x$ab[x$ab %in% AB_lookup$ab]), " already exist in the internal `antibiotics` data set.")
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x <- x[, colnames(AB_lookup)[colnames(AB_lookup) %in% colnames(x)], drop = FALSE]
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x$generalised_name <- generalise_antibiotic_name(x$name)
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x$generalised_all <- as.list(x$generalised_name)
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bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = FALSE)
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if (!is.null(bind_rows)) {
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new_df <- bind_rows(AB_lookup, x)
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} else {
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new_df <- rbind(AB_lookup, x, stringsAsFactors = FALSE)
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}
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assignInNamespace(x = "AB_lookup",
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value = new_df,
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ns = asNamespace("AMR"))
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message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to internal `antibiotics` data set.")
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}
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#' @rdname add_custom_antimicrobials
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#' @export
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clear_custom_antimicrobials <- function() {
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assignInNamespace(x = "AB_lookup",
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value = create_AB_lookup(),
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ns = asNamespace("AMR"))
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message_("Manual antimicrobials cleared.")
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}
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43
inst/tinytest/test-add_custom_antimicrobials.R
Normal file
43
inst/tinytest/test-add_custom_antimicrobials.R
Normal file
@ -0,0 +1,43 @@
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# ==================================================================== #
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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 #
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# https://github.com/msberends/AMR #
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# #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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|
# #
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# Developed at the University of Groningen, the Netherlands, in #
|
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|
# collaboration with non-profit organisations Certe Medical #
|
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|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
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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 #
|
||||||
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||||
|
# the Free Software Foundation. #
|
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|
# 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. #
|
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|
# #
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|
# Visit our website for the full manual and a complete tutorial about #
|
||||||
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
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# ==================================================================== #
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expect_warning(as.ab("test"))
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expect_identical(as.character(suppressWarnings(as.ab("test"))), NA_character_)
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suppressMessages(
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add_custom_antimicrobials(
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data.frame(ab = "TEST",
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name = "Test Antibiotic",
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group = "Test Group")
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)
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)
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|
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expect_identical(as.character(as.ab("test")), "TEST")
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expect_identical(ab_name("test"), "Test Antibiotic")
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expect_identical(ab_group("test"), "Test Group")
|
50
man/add_custom_antimicrobials.Rd
Normal file
50
man/add_custom_antimicrobials.Rd
Normal file
@ -0,0 +1,50 @@
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|||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/add_custom_antimicrobials.R
|
||||||
|
\name{add_custom_antimicrobials}
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|
\alias{add_custom_antimicrobials}
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\alias{clear_custom_antimicrobials}
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\title{Add Manual Antimicrobials to This Package}
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|
\usage{
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add_custom_antimicrobials(x)
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|
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|
clear_custom_antimicrobials()
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|
}
|
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|
\arguments{
|
||||||
|
\item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"}
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|
}
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|
\description{
|
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|
With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own manual antimicrobial codes to the \code{AMR} package.
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||||||
|
}
|
||||||
|
\details{
|
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|
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)
|
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|
add_custom_antimicrobials(
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||||||
|
data.frame(ab = "TEST",
|
||||||
|
name = "Test Antibiotic",
|
||||||
|
group = "Test Group")
|
||||||
|
)
|
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|
}\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")
|
||||||
|
}
|
||||||
|
}
|
@ -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}.
|
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.
|
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}{
|
\section{Source}{
|
||||||
|
|
||||||
|
Loading…
Reference in New Issue
Block a user