User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/10/03
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Likelihood Ratio Paper
Higher resolution power plot for Anoles tree
Figure (below right) shows power for increasing alpha in the Anoles tree. The vertical line shows the estimated value of alpha for the body-size data -- unlikely that a tree of this size can detect selection that is this weak even if it were present. Consequently, this fit should not be taken as evidence that BM is a better fit than the OU, but rather that the data is insufficient to inform this analysis.
The Geiger model fits
Thinking of extending bootstrap methods to work for geiger tests, i.e. can one justify the lambda transform?
Model likelihoods for Anoles under various tree transformations
> bm$Trait1$lnl  -53.66927 > ou$Trait1$lnl  -53.66268 > lambda$Trait1$lnl  -53.66927 > kappa$Trait1$lnl  -53.66927 > delta$Trait1$lnl  -53.49763 > eb$Trait1$lnl  -53.64517
Back to Writing
Reorganizing the manuscript structure ... again. (draft not shown). Mapping out the outline here:
Are phylogenies Informative?
Examples from Anoles
... hmm, how is it dark already? better find my bike lights and continue this later.
Adaptive Dynamics: Comparing contour plots
Meanwhile, some adaptive dynamics simulations have completed at least. Should remember to save png as higher resolution, but the bottom line seems to show substantial differences between analytic approximation and numerical simulation:
Comparing results, simulation on the left, Analytic on the right.