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
- Ralph P and Coop G (2010). “Parallel Adaptation: One or Many Waves of Advance of an Advantageous Allele?” Genetics, 186. ISSN 0016-6731, https://dx.doi.org/10.1534/genetics.110.119594.