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Update functions to include infrataxa - #268

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ehwenk merged 10 commits into
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Update-functions-to-include-infrataxa
Mar 24, 2026
Merged

Update functions to include infrataxa#268
ehwenk merged 10 commits into
masterfrom
Update-functions-to-include-infrataxa

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@ehwenk

@ehwenk ehwenk commented Mar 23, 2026

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  • Updates to the three diversity functions to include a parameter that lets you also include infrataxa (subspecies, varieties, forms)
  • Added the columns family and taxon_id to created_species_state_origin_matrix
  • Added tests for all 3 functions

ehwenk added 3 commits January 7, 2026 11:46
Per request of several users, update `create_species_state_origin_matrix` and `native_anywhere_in_australia` to include a parameter that includes infrataxa.

Right now the original "species only" variant of the function is the default, but maybe the parameter `include_infrataxa` should instead default to TRUE.

Also, these two functions label the column with taxon names as "species". Would it be better to use either "taxon_name" or "accepted_name"?
remove `(` at start of genus names. Relevant for some hybrids of hybrid names
- added tests
- updated documentation
- additional small changes
@ehwenk
ehwenk requested a review from wcornwell March 23, 2026 05:00
@wcornwell

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i think i can fix this one, should i try?

@dfalster

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Go for it @wcornwell !

@dfalster

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There's another PR about to merged into master so perhaps wait until that has been merged in before updating this branch from master

@dfalster
dfalster self-requested a review March 24, 2026 08:43

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Seems promising !

@ehwenk
ehwenk merged commit fcff246 into master Mar 24, 2026
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@ehwenk
ehwenk deleted the Update-functions-to-include-infrataxa branch March 24, 2026 09:31
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3 participants