User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/04/21

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Adaptive Dynamics

  • Wrapping up paper on waiting time to branching in adaptive dynamics.
  • Cleaning up code from summer. Now in a local git repository in adaptiveDynamics/code
  • Moved ensemble parallelization to higher level, so parallelization can be performed in R or C.
  • Adding documentation

Current status

  • Calculates the waiting time to complete phase 1, phase 2, and phase 3 successfully from individual-based simulation.
Phase 1
Completed when 2 branches exist over threshold
Phase 2
Completed when a third population has established over threshold exterior to a stable pair
Phase 3
Completed when two populations over threshold are separated in traitspace by more than finishline units


Thoughts On Notebook separation

  • Wrapping up the adaptive dynamics project from this summer at IIASA. Not really a comparative phylogenetics topic but it's evolution and I've got to write it down somewhere, there are advantages and disadvantages of maintaining separate notebooks for separate projects. Since this is something I've been thinking about lately will take a moment to write it down.
    • Advantages: Provides a clearer progression of a single body of work. Particularly when two projects are entirely unrelated, interleaving them would be very frustrating. A very good search/tag/aggregation system would alleviate this. I should start using categories
    • Disadvantages: Selecting the division level for notebook. At what level does a project become an independent idea? i.e. is the stochastic population dynamics in structured populations independent of the warning signals work? There's also content that isn't directly relevant to one notebook or another. I think if I didn't work in two separate labs (Hastings and Wainwright) everything would be one notebook.

backup and local editing

  • Experimenting with mvs commandline client to download and upload pages to the wiki, as described here.