User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/03/14

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Working on a couple new ideas:

  • Multiple partitions
  • Community phylogenetics nulls
  • Diversification rates w/ stationary distributions

Tools exploration

  • Finding my forum a very useful tool for recording and organizing around idea. Nice complement to this notebook which helps me organize temporally instead.
  • Becoming convinced I should transition from svn to git. Created a git-hub account and have started learning the basic git commands. The Git community book and the website video tutorials have been very helpful.
  • Meanwhile, RabbitVCS is a very slick SVN manager integrated directly into the Nautilus browser. I've also added the svn commands to hotkeys through my vimrc script.
  • listened to an interesting talk by Willbanks on science commons and Generative Science'.'


Working on the multiple partitions question for discretization of continuous data.

  • Maximum likelihood implementation in R for an arbitrary but fixed number of peaks.
  • Writing the MCMC approach now to allow Bayesian partitioning.
    • Will be a good test case for the reversible jump process
    • Potentially a good test case to explore Dirchlet Process Prior

Project now has a code repository

  • Hosting through github.
  • Several advantages to the git system -- no central repository, easier branching / merging, faster.
  • github interface also seems to have several advantages relative to google code. In addition to supporting git, provides a more intuitive and visually appealing layout for the project.