User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/08/05

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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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Batch Data

 * Some of the nexus files don't seem to read into R. Opening and saving the file in figtree solves this.

Labrid traits
--Carl Boettiger 00:52, 11 August 2010 (EDT) Note: labels on parameter bootstrap distributions have reversed wrasses and parrotfish. I've updated the software so that the plotting function takes care of the labeling automatically (when these were made it had to be added manually, while the automation of the data conversions and the painting by clade reversed the label assignments). See ../10.



Based on nboot = 100

Various muscle mass traits do not seem to converge.

Carnivora Traits


No preference for any model. OU.1 fit has non-zero, though small alpha, which cannot be distinguished significantly from the Brownian motion model. No evidence for either of the regimes models. (Might compare ws2 to ou1 though)

Brownian motion:

OU.1:

The coding of marine and freshwater separate, as well as a terrestrial regime does not converge under the wrightscape simplex method using the hansen initial conditions, but does just fine using the standard 1,1 initial conditions. Running now.

Mammalia
The huge mammalia data set takes a while even fitting the hansen model on the painting. bm loglik returns INF, ou1 returns loglik of -3727. the multiple regime model simplex routine fails to converge using the seed from ou2. Note the dramatic differences in the log body size optima found by the regime model. Certainly these differences must accomplish most of the difference in likelihood of this model.


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