diff --git a/DESCRIPTION b/DESCRIPTION index 6d4baf3ce..d1aff1547 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 3.0.1.9149 +Version: 3.0.1.9150 Date: 2026-10-15 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 4456d696d..60392b15d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9149 +# AMR 3.0.1.9150 Planned as v3.1.0, mid October 2026. diff --git a/data-raw/taxonomy_review/2026-10/REPORT.md b/data-raw/taxonomy_review/2026-10/REPORT.md index 549a08bf8..3f4261374 100644 --- a/data-raw/taxonomy_review/2026-10/REPORT.md +++ b/data-raw/taxonomy_review/2026-10/REPORT.md @@ -405,3 +405,20 @@ simplex* and *Enterobius vermicularis* as accepted), while this build had them a `MO_RELEVANT_GENERA` now). Effect: 24 never released, not relevant COL records less. The data sets that are computed from this one are recreated in the right order by the new `run_after_microorganisms_build.R`, which the build runs at its end; `reproduction_of_intrinsic_resistant.R` uses `devtools::load_all()` instead of the installed package + +## 7. Open issues for the next update (15 October 2026) + +Found while correcting the WHONET codes in `microorganisms.codes` (v3.0.1.9149), left for the next taxonomy update: + +- [ ] **Bacterial GBIF records next to LPSN.** 8,638 bacterial records have `source = "GBIF"`, 7,445 of them accepted. + They are kept because LPSN has no record with their name, and they bring the GBIF synonymy along, which can create a + parallel taxon. Example: LPSN does not know *Faecalimonas nexile* (*Clostridium nexile* is *Faecalimonas nexilis*, + and *phoceensis* is in *Coprococcus* since 2025), but the GBIF records *Faecalimonas nexile* (synonym) and + *Faecalimonas phoceensis* (accepted), both already in v3.0.1, make `as.mo("Faecalimonas nexile")` return *F. + phoceensis*, next to LPSN's *Coprococcus phoceensis*. To do: determine how many bacterial GBIF records duplicate an + LPSN taxon, decide how they are linked or removed, and add a strict test. +- [ ] **Outdated names kept as separate accepted records**, e.g. *Arthroderma obtusum* and *Arthroderma racemosum* + next to *Nannizzia obtusa* and *Nannizzia racemosa*, and *Microsporum cookei* next to *Paraphyton cookei* (Dukik et al. + 2017). The WHONET pipeline shows them: an older WHONET name only refers to the same taxon as the current WHONET name if + `microorganisms` links them. +- [ ] **Lower-case serovar name**: *Salmonella panama* (`B_SLMNL_PANM`) instead of *Salmonella* Panama.