User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/08/04

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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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Data Format functions

 * Spent much of the day trying to code an intelligent data-preprocessing function. Seems to mostly be working now, see github for details.  Testing on a variety of datasets.


 * Currently the function assumes paintings can be specified by common ancestors of a set of tips, assumes non-overlapping clades. Doesn't error-check for this either.


 * should also have more output processing functions, particularly to return a "phylo" object together with paintings (see earlier existing code in my Comparative-Phylogenetics repository).

Exploration on new data sets

 * Carnivora -- running with aquatic/terrestrial encoding and marine/freshwater/terrestrial encoding. Both set to run overnight.  Wrightscape's simplex method has some trouble with certain initial conditions on the three-regime model.
 * Mammalia -- body size, with regime by biome (aquatic, terrestrial, volant (bats). Huge data set, also running over night.
 * Cetacea -- body size by diet. my preprocessing function seems to have some trouble with the painting


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