add mo_current()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9007
+Version: 1.8.2.9008
-Date: 2022-10-06
+Date: 2022-10-10
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by

NAMESPACE

@@ -267,6 +267,7 @@ export(mean_amr_distance)
 export(mo_authors)
 export(mo_class)
 export(mo_cleaning_regex)
+export(mo_current)
 export(mo_domain)
 export(mo_failures)
 export(mo_family)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9007
+# AMR 1.8.2.9008
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 
@@ -19,6 +19,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
   * Sequential coercion is now extremely fast as results are stored to the package environment, although coercion of unknown values must be run once per session. Previous results can be reset/removed with the new `mo_reset_session()` function.
 * 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
 * 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.

R/mo.R

@@ -1094,14 +1094,19 @@ load_mo_uncertainties <- function(metadata) {
   AMR_env$mo_uncertainties <- metadata$uncertainties
 }
 
-synonym_mo_to_accepted_mo <- function(x) {
+synonym_mo_to_accepted_mo <- function(x, fill_in_accepted = FALSE) {
   x_gbif <- AMR::microorganisms$gbif_renamed_to[match(x, AMR::microorganisms$mo)]
   x_lpsn <- AMR::microorganisms$lpsn_renamed_to[match(x, AMR::microorganisms$mo)]
   x_gbif[!x_gbif %in% AMR::microorganisms$gbif] <- NA
   x_lpsn[!x_lpsn %in% AMR::microorganisms$lpsn] <- NA
 
-  ifelse(is.na(x_lpsn),
+  out <- ifelse(is.na(x_lpsn),
     AMR::microorganisms$mo[match(x_gbif, AMR::microorganisms$gbif)],
     AMR::microorganisms$mo[match(x_lpsn, AMR::microorganisms$lpsn)]
   )
+  if (isTRUE(fill_in_accepted)) {
+    x_accepted <- which(AMR::microorganisms$status[match(x, AMR::microorganisms$mo)] == "accepted")
+    out[x_accepted] <- x[x_accepted]
+  }
+  out
 }

R/mo_property.R

@@ -56,13 +56,15 @@
 #' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
 #'
 #' SNOMED codes - [mo_snomed()] - are from the version of `r documentation_date(TAXONOMY_VERSION$SNOMED$accessed_date)`. See *Source* and the [microorganisms] data set for more info.
+#' 
+#' Old taxonomic names (so-called 'synonyms') can be retrieved with [mo_synonyms()], the current taxonomic name can be retrieved with [mo_current()]. Both functions return full names.
 #' @inheritSection mo_matching_score Matching Score for Microorganisms
 #' @inheritSection as.mo Source
 #' @rdname mo_property
 #' @name mo_property
 #' @return
 #' - An [integer] in case of [mo_year()]
-#' - A [list] in case of [mo_taxonomy()] and [mo_info()]
+#' - A [list] in case of [mo_taxonomy()], [mo_synonyms()] and [mo_info()]
 #' - A named [character] in case of [mo_url()]
 #' - A [numeric] in case of [mo_snomed()]
 #' - A [character] in all other cases
@@ -672,7 +674,7 @@ mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
   })
 
   if (length(syns) > 1) {
-    names(syns) <- mo_name(x)
+    names(syns) <- mo_name(x, language = language)
     result <- syns
   } else {
     result <- unlist(syns)
@@ -682,6 +684,16 @@ mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
   result
 }
 
+#' @rdname mo_property
+#' @export
+mo_current <- function(x, language = get_AMR_locale(), ...) {
+  meet_criteria(x, allow_NA = TRUE)
+  language <- validate_language(language)
+  x.mo <- suppressWarnings(as.mo(x, keep_synonyms = TRUE, ...))
+  out <- synonym_mo_to_accepted_mo(x.mo, fill_in_accepted = TRUE)
+  mo_name(out, language = language)
+}
+
 #' @rdname mo_property
 #' @export
 mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {

inst/tinytest/test-mo_property.R

@@ -113,6 +113,11 @@ expect_identical(
   mo_gbif("Escherichia coli")
 )
 
+expect_true("Escherichia blattae" %in% mo_synonyms("Shimwellia blattae"))
+expect_true(is.list(mo_synonyms(rep("Shimwellia blattae", 2))))
+expect_identical(mo_current(c("Escherichia blattae", "Escherichia coli")),
+                 c("Shimwellia blattae", "Escherichia coli"))
+
 expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
 expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
 

man/mo_property.Rd

@@ -30,6 +30,7 @@
 \alias{mo_rank}
 \alias{mo_taxonomy}
 \alias{mo_synonyms}
+\alias{mo_current}
 \alias{mo_info}
 \alias{mo_url}
 \title{Get Properties of a Microorganism}
@@ -231,6 +232,8 @@ mo_synonyms(
   ...
 )
 
+mo_current(x, language = get_AMR_locale(), ...)
+
 mo_info(
   x,
   language = get_AMR_locale(),
@@ -272,7 +275,7 @@ mo_property(
 \value{
 \itemize{
 \item An \link{integer} in case of \code{\link[=mo_year]{mo_year()}}
-\item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}} and \code{\link[=mo_info]{mo_info()}}
+\item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}}, \code{\link[=mo_synonyms]{mo_synonyms()}} and \code{\link[=mo_info]{mo_info()}}
 \item A named \link{character} in case of \code{\link[=mo_url]{mo_url()}}
 \item A \link{numeric} in case of \code{\link[=mo_snomed]{mo_snomed()}}
 \item A \link{character} in all other cases
@@ -304,6 +307,8 @@ All output \link[=translate]{will be translated} where possible.
 The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
 
 SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the version of 1 July, 2021. See \emph{Source} and the \link{microorganisms} data set for more info.
+
+Old taxonomic names (so-called 'synonyms') can be retrieved with \code{\link[=mo_synonyms]{mo_synonyms()}}, the current taxonomic name can be retrieved with \code{\link[=mo_current]{mo_current()}}. Both functions return full names.
 }
 \section{Matching Score for Microorganisms}{