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PennChopMicrobiomeProgram / whatbacteria Public

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Add support for taxonomic synonyms and update taxonomic names#1

Merged

kylebittinger merged 17 commits into

mainPennChopMicrobiomeProgram/whatbacteria:mainfrom

add-synonymsPennChopMicrobiomeProgram/whatbacteria:add-synonymsCopy head branch name to clipboard

Apr 2, 2026

Conversation Commits17 (17)Checks Files changed

Merged

Add support for taxonomic synonyms and update taxonomic names#1
kylebittinger merged 17 commits into
mainfrom
add-synonyms

Commits

Commits on Apr 1, 2026

Add data-raw to .Rbuildignore
kylebittinger
committed
Add CSV tables and script to generate synonyms table
kylebittinger
committed
R version bump
kylebittinger
committed
Add taxon_synonyms data to package
kylebittinger
committed

Commits on Apr 2, 2026

Document data object
kylebittinger
committed
Fix line endings in what.R and test-match.R
kylebittinger
committed
Add internal functions to begin matching taxa with synonyms
kylebittinger
committed
Remove print statement in resolve_taxa
kylebittinger
committed
Add function to match taxa with pre-split lineage vectors
kylebittinger
committed
Add new match_annotation function with synonyms
kylebittinger
committed
Replace match_annotation function with one including synonyms
kylebittinger
committed
Update docs
kylebittinger
committed
Add Rmarkdown version of README
kylebittinger
committed
Update taxon tables with new names
kylebittinger
committed
Update README with synonyms
kylebittinger
committed
Document synonym parameters and make qualified references to package data
kylebittinger
committed
Update version, author, minimum R version in DESCRIPTION
kylebittinger
committed

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