Fix emend. author bug in get_author_year() and update ref documentation

Strip emend. and everything after it so the ref column retains the
combination authority, not the emendation author. Update data.R and
mo_property.R docs to describe the correct semantics of the ref field.

https://claude.ai/code/session_01VH4Ju4Xq9aW1AHuoVbjGEo

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9057
+Version: 3.0.1.9058
 Date: 2026-05-02
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9057
+# AMR 3.0.1.9058
 
 Planned as v3.1.0, May 2026.
 
@@ -18,6 +18,7 @@ Planned as v3.1.0, May 2026.
 * `as.mic()`: values in scientific notation (e.g. `1e-3`) now handled correctly
 * `as.ab()`: codes containing "PH" or "TH" (e.g. `ETH`, `PHE`) no longer return `NA` when mixed with unrecognised input (#245)
 * Combined MIC/SIR input values (e.g. `"<= 0.002; S"` or `"S; 0.002"`) now parsed correctly (#252)
+* `get_author_year()` in the microorganism reproduction script now strips `emend.` and everything after it, so `ref` reflects the combination authority rather than the emendation author (e.g. *Rhodococcus equi* now returns "Goodfellow et al., 1977" instead of "Nouioui et al., 2018")
 * BRMO classification now includes bacterial complexes (#275)
 * Translation fixes for Italian CoNS/CoPS names (#256), Dutch antimicrobials, and `sir_df()` foreign-language output (#272)
 

R/data.R

@@ -109,7 +109,7 @@
 #' - `status` \cr Status of the taxon, either `r vector_or(microorganisms$status, documentation = TRUE)`
 #' - `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, `species`, `subspecies`\cr Taxonomic rank of the microorganism. Note that for fungi, *phylum* is equal to their taxonomic *division*. Also, for fungi, *subkingdom* and *subdivision* were left out since they do not occur in the bacterial taxonomy.
 #' - `rank`\cr Text of the taxonomic rank of the microorganism, such as `"species"` or `"genus"`
-#' - `ref`\cr Author(s) and year of related scientific publication. This contains only the *first surname* and year of the *latest* authors, e.g. "Wallis *et al.* 2006 *emend.* Smith and Jones 2018" becomes "Smith *et al.*, 2018". This field is directly retrieved from the source specified in the column `source`. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.
+#' - `ref`\cr Abbreviated authority citation for the nomenclatural act that established the current name combination, following ICNP conventions. For species described in their current genus (sp. nov.), this is the original description author(s) and year. For species transferred to a different genus (comb. nov.), this is the reclassification author(s) and year. Emendations are excluded. For synonyms, this is the authority under which the synonym was originally published. Data sourced primarily from LPSN, supplemented by GBIF where LPSN coverage is absent.
 #' - `oxygen_tolerance` \cr Oxygen tolerance, either `r vector_or(microorganisms$oxygen_tolerance, documentation = TRUE)`. These data were retrieved from BacDive (see *Source*). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently `r round(length(microorganisms$oxygen_tolerance[which(!is.na(microorganisms$oxygen_tolerance))]) / nrow(microorganisms[which(microorganisms$kingdom == "Bacteria"), ]) * 100, 1)`% of all `r format_included_data_number(nrow(microorganisms[which(microorganisms$kingdom == "Bacteria"), ]))` bacteria in the data set contain an oxygen tolerance.
 #' - `source`\cr Either `r vector_or(microorganisms$source, documentation = TRUE)` (see *Source*)
 #' - `lpsn`\cr Identifier ('Record number') of `r TAXONOMY_VERSION$LPSN$name`. This will be the first/highest LPSN identifier to keep one identifier per row. For example, *Acetobacter ascendens* has LPSN Record number 7864 and 11011. Only the first is available in the `microorganisms` data set. ***This is a unique identifier***, though available for only `r format_included_data_number(sum(!is.na(microorganisms$lpsn)))` records.

R/mo_property.R

@@ -42,6 +42,8 @@
 #' - `mo_ref("Enterobacter aerogenes")` will return `"Tindall et al., 2017"` (with a note about the renaming)
 #' - `mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Hormaeche et al., 1960"` (with a once-per-session warning that the name is outdated)
 #'
+#' [mo_ref()] returns the abbreviated authority of the nomenclatural act that created the queried name combination. When `keep_synonyms = FALSE` (default), this is the authority of the currently accepted name. When `keep_synonyms = TRUE`, this is the authority under which the queried (possibly outdated) name was published. Emendations (changes to the species description without a name change) are not reflected; only the combination or original description authority is returned.
+#'
 #' The short name ([mo_shortname()]) returns the first character of the genus and the full species, such as `"E. coli"`, for species and subspecies. Exceptions are abbreviations of staphylococci (such as *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning to the full name will be done using [as.mo()] internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will be considered *Escherichia coli*. As a result, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`.
 #'
 #' Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results.

data-raw/_reproduction_scripts/reproduction_of_microorganisms.R

@@ -122,8 +122,8 @@ get_author_year <- function(ref) {
   authors <- gsub("[A-Z-][a-z-]?[.]", "", authors, ignore.case = FALSE)
   # remove trailing and leading spaces
   authors <- trimws(authors)
-  # keep only the part after last 'emend.' to get the latest authors
-  authors <- gsub(".*emend[.] ?", "", authors)
+  # strip emend. and everything after it to retain the combination authority
+  authors <- gsub(" ?emend[.]?.*", "", authors)
   # only keep first author and replace all others by 'et al'
   authors <- gsub("(,| and| et| &| ex| emend\\.?) .*", " et al.", authors)
   # et al. always with ending dot