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From Jim:
I’m getting the hang of the oti query methods, trying to build a proper study list for the curation tool, to replace this hard-coded list:
http://dev.opentreeoflife.org/curator
The Qu…
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@rvosa Is the validator tool on the nexml website, http://www.nexml.org/nexml/phylows/validator, doing more checks than the standard XML schema validation? If so, perhaps we could wrap this as an R f…
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The NeXML extractor has to be extended to extract charset data.
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@rvosa CRAN tells me that RNeXML was failing several of the automated tests last night due to www.nexml.org timing out. The tests are hitting the validator on the site there.
I can rewrite the val…
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We'll want to support coercion into phylobase trees (phylo4, etc).
On one hand, since these trees are S4 objects, are more carefully defined than ape::phylo trees, richer, and more extensible, we c…
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I thought I was told that we were abandoning "canvas" for "figure," but I note that the default.nexss and testtree.nexss files still use "canvas". We need to finalize a decision for consistency movin…
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this will copy information into fields that ot uses for metadata.
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In this example I wonder if it makes sense to return by default the taxa labels as a column in the data.frame, perhaps the first column. Not a huge deal to move row names to a column, but a bit easier…
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If I understand the schema correctly, nexml permits multiple otus blocks, though I haven't seen this used.
In writing a function to add characters data to an existing `nexml` object, we run into th…
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Anyone have suggestions for the manuscript title?
Currently we have: "RNeXML: Parsing and Serializing the Next Generation of Phyloinformatic Data in R", but that's not really all that informative f…