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I find that I cannot parse the following XML files in data/treebase, mostly because they appear to be empty?
```
S1001.xml
S10071.xml
S10316.xml
S10503.xml
S11762.xml
S11811.xml
S12156.xml
S1224.xm…
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Now that we can do the basics (substantial testing #15 aside, ) it might be good to reach out to r-sig-phylo and the nexml-discuss mailing lists for input, critique and feature requests? What exactly…
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nexml can contain a single `` node inside the `` node, multiple `` nodes in a single `` node, or even multiple `` nodes. The first two cases map naturally onto a "phylo" object and a "multiPhylo" obj…
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@mtholder has written code which will validate NexSON and produce errors (a JSON blob that maps to XML that violates the NeXML schema) and warnings (files that are not ideal with respect to
OpenTree's…
leto updated
10 years ago
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It should be possible to use different tree inference programs / algorithms. For ex: we now use examl, must be able to also use *BEAST. The upshot is that we might want to make the sequence selection …
rvosa updated
10 years ago
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If we extract a list of character matrices for the same OTU set, it might make sense to combine them into the same `data.frame` (would have to be a `data.frame` and not a matrix, since some columns mi…
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Warn or error on special cases (e.g. some valid nexml trees probably cannot be completely valid phylo objects. For instance, `network` with horizontal transfer events.
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rooted trees can become unrooted in converting from ape to nexml and back. make sure to handle this more carefully!
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Not sure if this idea makes sense, so looking for feedback.
It seems like it would be possible to provide utilities (or preferably interfaces to existing utilities) that convert between EML and oth…
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Crazy idea: when reading into a phylo, should we create a new RNeXML environment, store the full nexml tree in there, and add a new slot to the phylo object storing an unevaluated `get("", envir=RNeXM…