Tuesday, simulations & appendix

Today mostly working over code sets for examples in appendix, and increasing replicates.  Somehow more trouble than it should be, see commit history for today.

ibm_sim.R – simulate from individual-based dynamics containing a saddle-node bifurcation (fully hysteresis model).

ibm_analysis.R – run figure1, 2, 3 analysis (correlation test, bootstrap of test, likelihood test) on each data.

ibm_likelihood.R – shouldn’t be needed, all code is in deut_examples.R.  Running now due to earlier parallel instance errors during montecarlotest.  Running now at 2000 replicates on zero at nice 19, and with 80 replicates at nice 10.

deut_likelihood.R – shouldn’t be needed, all code is in deut_examples.R, which I reran today with 2000 replicates. Running this now due to earlier parallel instance errors during montecarlotest. (on one, at nice 19)

Deuterium from Glaciation I & II with 2000 replicates, along with CaCO3 data in appendix.R, calls saved data from above to regenerate plots.

Misc

  • Organizing for Felsenstein’s visit

  • Wainwright lab meeting: discussion of launching new website, lab blog

  • CPB Seminar: Yaniv presenting meiotic drive work, Peter presenting spatial wave in multiple mutations work (Ralph & Coop, Genetics 2010(Ralph & Coop, 2010)).

Need code updates:

  • socialR localized save.  Also save code call?

  • Still need to track filenames of code, not just commit numbers.

References