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I have come across several examples where specimens are linked as vouchers to publications, but these publications do not show up in the related projects that collected or used the specimen. Shouldn't…
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## Phylo code review - 20th April 2014
### General notes
Overall very good, and a great start for the Bio.jl phylo module. Here I have attempted to map out what would be required to get to a version …
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**Where:** [Biodiv 224, UBC](https://www.google.ca/maps/place/Beaty+Biodiversity+Museum,+Vancouver,+BC+V6T+1Z4/@49.2634569,-123.2500362,17z/data=!4m2!3m1!1s0x548672c9f84be123:0x1c431143106eb830)
**Whe…
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Overall, I think this package is a fantastic resource. This is a greatly needed tool
in biodiversity sciences and you have done a excellent job with the package, the
manuscript, and the supplementary …
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Tree "paintings" indicating different evolutionary regimes/modes along different parts of a phylogeny are a particularly common use case for comparative phylogenetics in R.
The current 'standard' s…
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I'm intrigued by @rvosa's suggestion of showing how RNeXML can be used to document both the character data and phylogenetic data used in comparative phylogenetics, which accounts for many of the R pac…
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First, I tried the following setup in RVM:
Ruby 1.9.3p362 (2012-12-25 revision 38607) [x86_64-linux]
with the following locally installed gems:
activesupport (3.1.9)
addressable (2.3.2)
builder (3.…
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Might imagine a user would want to extract character data that comes in nexus format (used by http://www.morphobank.org/, for instance) into NeXML.
Unfortunately, though ape provides `read.nexus.dat…
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NeXML, like nexus, can contain a lot of character matrix (e.g. sequence) data. Current approach, like the `read.nexus` functions, simply ignores this.
We will want to be able to read and manipulat…