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

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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