Joseph W. Brown

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icon company Royal Ontario Museum icon location Sector ZZ9 Plural Z Alpha

Results 134 comments of Joseph W. Brown

Why can't I retrieve the subtree for Lycopodiidae

When I query the taxonomy [things get even weirder](https://tree.opentreeoflife.org/taxonomy/browse?id=5602224).

Why can't I retrieve the subtree for Lycopodiidae

@rossmounce Ok it seems that the tree and taxonomy are unfortunately currently out of sync. Trying to find ETA on fix.

Why can't I retrieve the subtree for Lycopodiidae

Pinging @kcranston on ETA.

Why can't I retrieve the subtree for Lycopodiidae

Regardless, this is clearly an upstream OT problem, not a rotl problem.

create functions to interact with collections endpoint

This is a good idea. Both querying and creating novel collections.

create function to check that the taxa listed by tnrs_match_names are in the TOL

If those taxa are not in the tree, it is because they are not monophyletic in the tree. OT used to return something like "invalid_ids" or "valid_but_not_in_tree" (not those names...

create function to check that the taxa listed by tnrs_match_names are in the TOL

Sounds good for now. I imagine OT will fix this, but no time soon.

create function to check that the taxa listed by tnrs_match_names are in the TOL

Hi @paternogbc. This is an [Open Tree issue](https://github.com/OpenTreeOfLife/germinator/wiki/Synthetic-tree-API-v3#induced_subtree), not a `rotl` issue. As mentioned above and on the linked page, if _any_ `ott_id` is not matched, an error is returned....

create function to check that the taxa listed by tnrs_match_names are in the TOL

@fmichonneau Individual ott_ids can be queried using [node_info](https://github.com/OpenTreeOfLife/germinator/wiki/Synthetic-tree-API-v3#node_info). This could be very slow and tedious, but doable. However, it looks like this [may be fixed soon](https://github.com/OpenTreeOfLife/treemachine/issues/226). Probably better to have...

GHA failing for mac (armadillo)

Hrm. The [log](https://github.com/FePhyFoFum/phyx/actions/runs/9582112251/job/26420376130) does not indicate any issue with installing armadillo (or its dependencies): ``` ==> Installing armadillo ==> Pouring armadillo--12.8.4.arm64_sonoma.bottle.tar.gz ``` However, on `configure` it cannot find armadillo (or...