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

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Comparative Phylogenetics
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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Adaptive Dynamics

 * Adding demos directory for the simulations to create the figures in ../../05/03 and ../../05/04
 * Updating the contour plot figure as per suggestions by Rupert and Ulf:


 * 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.


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