Partially Observable Stochastic Processes (cont.)

• Reading a bit more about pomp. Looks like SCM and PMCMC offer nicely Bayesian inference tools using the same framework (rprocess and dmeasure), making a nice platform for implementing multiple methods. Almost feels like having the likelihood equation in hand again.
• A bit more skeptical about nonlinear forecasting and probe matching, as they feel even more heuristic or arbitrary. I suppose that’s just the price of having only rmeasure instead of dmeasure available though. Perhaps worth a closer look.
• Time to implement some saddle-node models and see what we can get…
• Also need to spend a bit more time working through examples on Vasilis’s earlywarings package.
• About ready to submit Prosecutor’s Fallacy paper. Repeating runs, some touch up on presentation still needed.

Evolution stuff

• treebase manuscript re-organization. – done
• treebase mansuscript simplify / clarify language – done
• treebase select examples, move technical examples to appendix – done
• treebase finalize new function list. – done
• More writing on Wrightscape manuscript. Reply to Peter.
• rfishbase new version to CRAN?

Treebase miscellaneous exploration examples?

• (histogram of species in treebase?)
• gene tree diversification rates vs species tree?
• gene tree of taxon of interest

Logistics

• ESA 2012 flight booked. Registration paid. need housing…
• Sent query for CSGF 2012 flights
• Need to book Evolution flight. Registration paid, housing paid.
• file reimbursements

Computing

• oooh: staticdocs