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dr. M.S. (Matthijs) BerendsandClaude Opus 5.5
ca5fa333ca
Review of reproduction_of_microorganisms.R against the 2026 intermediates: - genus homonyms: overrides, LPSN/MycoBank first, status within LPSN/MycoBank, move misplaced protists, remove true homonyms (Necator, Capillaria, Graphium) - keep clinically relevant names that are not validly published (Tropheryma) - one set of relevant genera for all filters; 30 genera added to MO_RELEVANT_GENERA - MycoBank classification parsed from all columns; empty values never overwrite - GBIF synonyms in another genus get the lineage of their own genus - prevalence no longer copied from genus; current names inherit from synonyms - inferred records follow the relevance filters (no more unrelated lichens) - ASCII names before deduplication (12 duplicate full names in 2026) - MO codes: robust code parsing, reserved old codes, single allocator, domain column used directly (2026 rename would now fail) - name clean-up applied to taxonomy before MO codes, BacDive rows filled - unattended running: review() instead of View(), CSV export of reviews, LPSN cache and retries, stops when raw source files are missing - reproduction_of_microorganisms_CLAUDE.md: prompt for an unattended run with findings report and checklist for human review in the PR Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
35 lines
482 B
Plaintext
Executable File
35 lines
482 B
Plaintext
Executable File
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.RData
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tests/testthat/Rplots.pdf
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inst/doc
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index.html
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README.html
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*.dll
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vignettes/*.R
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.DS_Store
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.Rprofile
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packrat/lib*/
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packrat/src/
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data-raw/taxa.txt
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data-raw/taxon.tab
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data-raw/CLSI*.pdf
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data-raw/DSMZ_bactnames.xlsx
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data-raw/country_analysis_url_token.R
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data-raw/country_analysis2.R
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data-raw/taxonomy.csv
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data-raw/lpsn_scrape_cache.rds
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data-raw/WHONET/*
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