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


  • 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