tnrs_match_names and tol_induced_subtree only pull 250 species about rotl HOT 5 CLOSED

OT does have a limit on the number of tips, but this is 25K or 100K (depending on the format). I just successfully got an induced tree of 357 hummingbirds. So maybe something went wrong when you concatenated the ids?

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Huh, the function 'tol_induced_subtree' seems to be working now (though I need to move through ott ids that aren't found).

Any idea why the function 'tnrs_match_names' doesn't work? I don't mind taking some extra steps to make a larger dataframe, but it would be nice to have the function run in one go.

Thanks for the help!

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Yeah, that is a hard limit for the TNRS fuzzy matching. I'm afraid I am not aware of how to get around it (i.e., by turning off the fuzzy match).

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@akahrl Did you change anything in your script to get the 'top_induced_subtree' function to work? I am running up against the same issue where I call the 'tnrs_match_names' function in batches and the resultant data frame is the appropriate length, but the induced tree built off of it still only contains the first 250 species.

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So sorry for the super late reply (parental leave). As josephwb pointed out, there is a limit to the TNRS fuzzy matching. I changed my code to this:

taxa <- tnrs_match_names(unique(data[1:4176, 1]), context="Animals", do_approximate_matching=FALSE)

And it solved the problem.

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