Analysis
Summarizing recently completed runs:
- Reviewing last night’s runs. Some mcmcs complete:
Labrid prot.y alpha
and some crashed mcmc’s on Zero launched Tuesday night. (gape.y, close, open don’t seem to want to run)
the sigma-theta Vs alpha-theta on parrotfish (size-corrected) protrusion (over intramandibular innovation), which looks indistinguishable:
sigma-theta vs alpha-theta, parrotfish prot.y
alpha v sigma also indistinguishable on this data, see yesterday.
Closing, alpha vs sigma, parrotfish (intramandibular, 200 reps)
Alpha
Sigma
Comparison
Would like nicer with more replicates, but clearly distinguishable, as were yesterday’s when theta could also vary. Note: Green is intramdibular, blue is other. If trait can’t vary across phylogeny, then there’s only a green distribution for both.
Runs launched today
Would really like a full labrid tree, Pharyngeal innovation, alpha-v-sigma MLE. Running on zero at nice 0 (10:59am).
an alpha-sigma mcmc of labrid tree would also be nice. Trying on eleven (nice 10) now. (~11:15a)
Would be nice to compare directly against Brownie/pure diversification. running on parrotfish close ratio at (nice 1) on one (2:48pm).
Would also be nice on labrids protrusion. running on zero, nice 5 (2:55pm)
Code Updates
Added plotting facility for MLE bootstrap distributions. Needs to be added to the calls for the MLE examples.
Presentation
Add tree for the examples
Distribution walkthrough
distinguish between MCMC and bootstraps clearly.
Describe software package availability
Motivate better the need for other models
Checking in on Warningsignals
- caco3 run was terminated, deut run never restarted after lapply failed. running deut_analysis.R now (n19) on zero (3:00pm).
Misc
Filed TreeBASE bug in logicals
Excellent set of slides and commentary by Rod Page on the state of phylogeny visualization.