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dr. M.S. (Matthijs) BerendsandClaude Opus 5.5
d683b9e7c6
- data-raw/microorganisms_files/: registry of all MO codes of every release since v2.0.0 (78,992 codes, built from the git tags), approved renames, and README with the rules; decision by Matthijs S. Berends: MO codes from before v2.0.0 are not supported - as.mo(): codes of earlier releases are translated deterministically via the internal MO_RETIRED_CODES (generated from the registry); unknown codes are no longer guessed (previously F_TRCHP, Trichophyton in v3.0.1, became Talaromyces chlamydosporus) - synonym_mo_to_accepted_mo(): a missing target of one source no longer overwrites a valid target of another source (e.g. Chaetomium abuense), and no 'renamed to itself' - taxonomy build: codes are reused and reserved from the registry instead of the development data (fixes 40 codes reused in the 2026 development data), also for phylum to family; synonym cycles are broken; dangling 'renamed to' identifiers are removed; the build stops on any broken integrity rule before saving - run_microorganisms_build.R: runs the build in chunks at its checkpoints in one R process, with progress logging and resuming from any checkpoint; prompt updated accordingly - tests: shared integrity rules (helper-microorganisms.R) used by build and testthat, registry tests over all codes, sentinel organisms, regression tests; current defects of the data on main are listed in microorganisms_known_defects.csv until the next rebuild Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
114 lines
5.3 KiB
R
114 lines
5.3 KiB
R
# ==================================================================== #
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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 CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in the Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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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://amr-for-r.org #
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# ==================================================================== #
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# This script (re)creates data-raw/microorganisms_files/mo_code_registry.csv: the registry of all MO codes
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# that were ever part of a released version of the AMR package, since v2.0.0. See the README.md in this
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# folder for the rules.
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#
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# Run it from the root of the repository, after every new release (once its git tag exists):
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# source("data-raw/microorganisms_files/build_mo_code_registry.R")
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# It always rebuilds the whole registry from the git tags, so it is reproducible and can be run at any time.
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# Development versions (the main branch) are never part of the registry.
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library(dplyr)
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devtools::load_all(".", quiet = TRUE) # for %like_case%
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registry_file <- "data-raw/microorganisms_files/mo_code_registry.csv"
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# Decision by Matthijs S. Berends, 3 October 2026: MO codes from releases before v2.0.0 (12 March 2023)
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# are not supported.
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first_supported_release <- "2.0.0"
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# all release tags (vX.Y.Z, so no development versions) since the first supported release
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tags <- system2("git", "tag", stdout = TRUE)
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tags <- tags[tags %like_case% "^v[0-9]+[.][0-9]+[.][0-9]+$"]
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tags <- tags[numeric_version(sub("^v", "", tags)) >= numeric_version(first_supported_release)]
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tags <- tags[order(numeric_version(sub("^v", "", tags)))]
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message("Releases: ", toString(tags))
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read_release <- function(tag) {
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tmp <- tempfile(fileext = ".rda")
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on.exit(unlink(tmp))
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status <- system2("git", c("show", paste0(tag, ":data/microorganisms.rda")), stdout = tmp)
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if (!identical(status, 0L)) {
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stop("Could not read data/microorganisms.rda of ", tag, call. = FALSE)
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}
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env <- new.env()
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load(tmp, envir = env)
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mo <- as.data.frame(env$microorganisms, stringsAsFactors = FALSE)
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# until v3.0.1, `kingdom` contained what is now called `domain`
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if (!"domain" %in% colnames(mo)) {
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mo$domain <- mo$kingdom
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mo$domain[mo$domain == "(unknown kingdom)"] <- "(unknown domain)"
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}
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data.frame(
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release = tag,
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mo = as.character(mo$mo),
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fullname = mo$fullname,
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rank = mo$rank,
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domain = mo$domain,
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genus = mo$genus,
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species = mo$species,
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subspecies = mo$subspecies,
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stringsAsFactors = FALSE
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)
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}
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all_releases <- bind_rows(lapply(tags, read_release)) %>%
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mutate(release_order = match(release, tags))
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# one row per MO code; the name, rank and taxonomy are taken from the most recent release that contained the code
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registry <- all_releases %>%
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group_by(mo) %>%
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arrange(desc(release_order), .by_group = TRUE) %>%
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summarise(
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# other names the code had in older releases (e.g. a corrected subspecies name), for transparency
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# (must come first, since `fullname` is overwritten below)
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previous_names = paste(setdiff(unique(fullname), first(fullname)), collapse = "; "),
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fullname = first(fullname),
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rank = first(rank),
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domain = first(domain),
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genus = first(genus),
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species = first(species),
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subspecies = first(subspecies),
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first_release = tags[min(release_order)],
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last_release = tags[max(release_order)],
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.groups = "drop"
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) %>%
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relocate(previous_names, .after = everything()) %>%
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arrange(mo)
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message(
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nrow(registry), " MO codes, of which ", sum(registry$previous_names != ""),
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" had another name in an older release (check these when the registry changes)"
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)
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write.csv(registry, registry_file, row.names = FALSE, na = "")
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message("Saved to ", registry_file)
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