wrightscape examples

[flickr-gallery mode=“search” tags=“phylogenetics” min_upload_date=“2012-01-03 7:00:37” max_upload_date=“2012-01-03 22:23:37”]

  • kt and open seem the best focal traits. Unclear what good null traits to use would be.

  • Unclear if anything is gained by indep thetas in this example.

  • Performance of alpha v theta?

Edited plotting of likelihood comparisons, just grouped by trait to get common axis. (Difficult to get intelligent zooming on facet_grid to ignore the outliers). Trying such as:

lims <- cast(dat, comparison ~ trait, function(x) quantile(x, c(.05,.95)))
coord_cartesian(ylim=c(min(lims), max(lims)), wise=TRUE)

but I need different ylims for each row when facet_grid has scales=“free_y”.

[flickr-gallery mode=“search” tags=“phylogenetics” min_upload_date=“2012-01-04 7:00:37” max_upload_date=“2012-01-04 13:23:37”]

Running likelihood ratio comparisons across all traits in following model comparisons:

  1. Brownie vs alphas

  2. Brownie vs thetas (ouch/hansen)

  3. thetas vs alphas

  4. sigmas vs alpha-thetas

  5. alphas vs alpha-thetas

  6. thetas vs alpha-thetas

on both two-shifts regime model and the intramandibular regime model.

[flickr-gallery mode=“search” tags=“phylogenetics” min_upload_date=“2012-01-06 7:30:37” max_upload_date=“2012-01-06 14:35:00”]

New model comparisons

  1. BM vs Brownie

  2. BM vs OU

  3. Brownie vs alphas

  4. Brownie vs thetas

  5. OU vs Brownie

  6. thetas vs alphas

Labrid data, intramandibular innovation (Summary Plot)

Individual images:

[flickr-gallery mode=“search” tags=“phylogenetics” min_upload_date=“2012-01-06 14:35:00” max_upload_date=“2012-01-06 16:00:37”]

Parrotfish only

Not really enough power in Parrotfish-only version:

[flickr-gallery mode=“search” tags=“phylogenetics” min_upload_date=“2012-01-06 16:05:00” max_upload_date=“2012-01-06 16:30:37”]

Full Labrids

Still running: two-shifts version