User:Daniel Mietchen/Notebook/Evolutionary MRI/2010/04/29

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 * style="background-color: #EEE"|[[Image:Magnetic resonance microscopy montage embryo fossil.png|128px]] Evolutionary MRI
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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Primate Phylogeny
Carl Boettiger 00:37, 30 April 2010 (EDT):
 * Simon sent me the tree data from their paper:
 * 1) primates pmid=19860891


 * This is the first calibrated ultrametric tree I've been able to couple to the primate data Daniel provided. I've preformed a quick ancestral state reconstruction on log brain weight (warmer colors are more massive).



R code to create figure

 * This is essentially just at the proof of concept level. A couple obvious steps:
 * 1) This uses a single tree from the posterior distribution of trees, which we'll eventually want to average over in the parameter estimation.  Meanwhile should use a consensus MLE tree instead.
 * 2) Trees are resolved to genus level, so traits should be genus averages (instead of subsamples).
 * 3) Ancestral state reconstruction under the Brownian Motion model is the most preliminary treatment, will certainly be interesting to consider the various multi-peak OU models and identify potential transitions between peaks, as well as power analysis for the model fits.
 * 4) Multidimensional trait inference should also be interesting
 * Possible bug? The Homo/Pan and Gorilla/Pan nodes would be expected to be in the Gorilla/Pan colour rather than the Homo colour.

Code and data on Github
New github repository for sharing code and data: sandbox git clone git://github.com/cboettig/sandbox.git git checkout 77af6613db294ca068cf
 * Grab this repository using git:
 * Revert to this edit's version of code and data using git:
 * Download the snapshot as an R package. More information on the downloads page of repository.

git checkout b1a90ad97b90d9cbeaa7
 * Carl Boettiger 16:17, 5 May 2010 (EDT):
 * Updated git version using R package is:


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