User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/08/11

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Adaptive Dynamics

Branching times, original figure
  1. use more points for the simulation, and don't put them on a regular grid, but maybe draw them from a uniform distribution, so as not to create spurious impressions of symmetry. You could then maybe also use the tripack package to draw colored Voronoi cells instead of same-sized symbols.
  2. color cells as grayscales from white (short) to dark (long survival) because the colors probably falsely suggest discrete jumps where there are probably none. Also, a legend that relates the colors to the numbers on the contour lines would be helpful for the viewer.
  3. make the contour lines (from analytics) more smooth, presumably by choosing more supporting points.
  4. choose axes to cover the same range and make plot quadratic, so that symmetries are easily revealed.

& more questions:

  1. Calculate the expected survival time, if we just assume that the dimorphic population moves away from the branching point on a trajectory given by the canonical equation, given a (demographically equilibrated) starting point at (or near) the branching point?
  2. How does this picture now change (if it does?) when the total number of individuals is in- or decreased and the relative magnitude of demographic fluctuations thus changed?

Some notebook commentary

Unfortunately I once again regret that I did not have a lab notebook last summer while doing most of this research. At least I have the version history, though in svn, and the biweekly reports.