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AMR/data-raw/microorganisms_files/README.md
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dr. M.S. (Matthijs) BerendsandClaude Opus 5.5 83a4853936 (v3.0.1.9097) Never remove released taxa; link orthographic variants; registry line in NEWS 
- taxonomy build: released taxa (since v2.0.0) that are missing are restored from their
  last release with their old code and last known status, and are exempt from later
  removals (decision by Matthijs S. Berends)
- exceptions are retired on purpose in data-raw/microorganisms_files/mo_code_retirements.csv
  with a reason: other organisms with the same genus name (e.g. the Graphium butterflies,
  wrongly in the Fungi until v3.0.1) and taxa whose genus is now only known in another
  domain; as.mo() translates these codes to NA with that reason
- synonyms without a current name are linked to an accepted name in the same genus that
  only differs by a Latin gender ending (e.g. Candida glabratus -> Nakaseomyces glabratus)
- placeholders such as "(unknown class)" never become records; codes of manually added
  records are matched by domain and name
- integrity rule released_taxon_missing; known defects of the data on main updated

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-03 14:15:08 +02:00

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MO code registry

MO codes (such as B_ESCHR_COLI) are stored by users in their own data, sometimes for years. A code must therefore always mean the same taxon, in every future version of the AMR package. This folder contains the registry that guarantees this.

Files

File Contents
mo_code_registry.csv Every MO code that was ever part of a released version of the AMR package since v2.0.0, with the taxon it denotes (name, rank, domain, genus, species, subspecies), the first and last release it was in, and older names of the same code (e.g. a corrected spelling).
build_mo_code_registry.R Recreates mo_code_registry.csv from the git tags of all releases. Run it after every new release.
mo_code_renames.csv The only allowed exceptions: registered codes that get another name, because it is the same taxon (e.g. a corrected spelling or a renamed species group). Every row needs approved_by and approved_date.
mo_code_retirements.csv Registered codes that are retired on purpose, because their taxon was another organism (e.g. the Graphium butterflies, which were wrongly in the Fungi until v3.0.1). Written by the taxonomy build, with the reason; as.mo() translates these codes to NA with that reason. Every new row must be reviewed in the git diff.

Rules

  1. Only releases count. Development versions (the main branch) are never part of the registry. Codes that only existed in a development version carry no weight and may be reassigned.
  2. Codes from before v2.0.0 are not supported. Decision by Matthijs S. Berends, 3 October 2026: MO codes from releases before v2.0.0 (12 March 2023) are not supported. Every code in all releases since v2.0.0 has always meant the same taxon (checked on 3 October 2026), so the registry starts without conflicts.
  3. A registered code is never given to another taxon. The taxonomy build (data-raw/_reproduction_scripts/reproduction_of_microorganisms.R) reuses the code of every taxon in the registry (most recent release first), never gives a registered code to a new taxon, and stops if a registered code would get another name than in the registry, unless that is listed and approved in mo_code_renames.csv.
  4. A released taxon is never removed. Decision by Matthijs S. Berends, 3 October 2026. If a released taxon is missing in a new build (e.g. not validly published or not clinically relevant anymore), the build restores it from its last release, with its old code and last known status. The only exception are retired codes (see mo_code_retirements.csv).
  5. A registered code that is no longer in the data still works. as.mo() translates it to the current code of the same taxon (by its name, so also if the taxon moved to another domain), using an internal lookup table (MO_RETIRED_CODES) that is created from the registry in data-raw/_pre_commit_checks.R. If the taxon is no longer in the data at all, the result is NA with a warning. The package never guesses.
  6. Tests enforce all of this. tests/testthat/test-data-microorganisms.R checks the current data against the registry and the renames, and checks that every registered code resolves to its own taxon.

After a release

  1. Make sure the git tag of the release exists (e.g. v3.1.0).
  2. Run source("data-raw/microorganisms_files/build_mo_code_registry.R") from the root of the repository.
  3. Review the changes to mo_code_registry.csv (git diff): only new codes may be added, and existing codes may only get a later last_release. Commit the result.
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