Duplicate taxon names from OToL causes error about rotl HOT 5 CLOSED

Thanks for the bug report @bomeara, I'll leave it to @fmichonneau to work out what rncl should do. Just thought I'd let you know of a possible work-around, in case this is a rate-limiting step for you at the moment.

You can use the 'internal' api-mapping functions to get a character representation of the tree, and ape to read that tree (note, for the example at least I had to remove the spaces from taxon names):

tr <- rotl:::.get_study_tree(study_id="pg_710", 
                             tree_id="tree1277", 
                             tip_label='ot:otttaxonname',  #triple 't', double ''n"
                             format="newick")
parsed_tr <- ape::read.tree(text=gsub(" ", "_", tr)
parsed_tr

Phylogenetic tree with 108 tips and 107 internal nodes.

Tip labels:
    'Helianthus_annuus', 'Canarina_canariensis', 'Jasione_montana', 'Legousia_hybrida', 'Campanula_asperuloides', 'Campanula_latifolia', ...

Rooted; includes branch lengths

Hope that's some help to you, and that we can find a less hack way for this to work in the long run :)

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Beautiful, @dwinter, thank you. This will work nicely for now (datelife update to pull from OpenTree).

Minor note for those using the example: there's a missing right parens on this line
parsed_tr <- ape::read.tree(text=gsub(" ", "_", tr))

Relevant XKCD

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Thanks for bringing this up.

The issue is that NCL follows the strict definition of the NEXUS file format that doesn't allow duplicated taxon names. I don't think there is an easy way to fix this in the C++ code.

I think the best option would be to add a suffix, I'll try to implement this in a couple of weeks when I'm back home.

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Hi @bomeara,

I implemented a fix for this. With get_study_tree duplicated labels will be disambiguated by adding a suffix _1, _2, _3, etc. before being parsed by NCL.

If you have a chance to give it a try, please let me know how it works for you.

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Yes, this seems to work. Thanks!

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