User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/05/05

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Comparative Phylogenetics
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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Primates

 * Primates project now has a Github repository. Updates are  embedded from here.


 * Experimenting with distributing code and data effectively. Pluses and minuses of three options:
 * 1) zipped file with R code and data.  Requires setting working directory, harder to update.  Subsequent uploads must include all the data, rather than incremental.
 * 2) Directly grab repository over github. Simple to update and access, stores only incremental changes.  Requires knowledge of git
 * 3) R package: Nicely integrates data, code, and documentation.  Requires installing R packages.


 * Learning the R packaging system for data. You can have .R files in the data/ directory of a package.  The call to the data function runs those files from that directory, making it unnecessary to specify the path to the data and allowing the use of complicated functions, see the example from the ape package:


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