Post date: Feb 02, 2015 9:16:14 PM
I have fixed a few minor bugs with the cross-validation procedure. Simple trial runs still suggest that it will be minimally informative, primarily because when allele frequencies are similar in both populations knowing the ancestry isn't important and when they are not even a single locus has enough information on ancestry. Still, I am running it again to see if there is any information to be gained from CV, or if not to show that it is worthless and make a general recommendation about choosing a scale parameter. Here is one of the 30 runs (3 conditions by 10 reps):
cd /local/scratch/
popanc -o outcvF_r9f0.3gen_demog_gens10.hdf5 -m 4000 -b 2000 -t 4 -f 1 -w 0 -v 1 -c 0.1,0.5,1,5,10 /labs/evolution/projects/popanc_sims/sims/genoP0F_r9f0.3gen_demog_gens10.txt /labs/evolution/projects/popanc_sims/sims/genoP1F_r9f0.3gen_demog_gens10.txt /labs/evolution/projects/popanc_sims/sims/genoAdmxF_r9f0.3gen_demog_gens10.txt > /labs/evolution/projects/popanc_sims/mcmc.cv/cvF_r9f0.3gen_demog_gens10
scp outcvF_r9f0.3gen_demog_gens10.hdf5 /labs/evolution/projects/popanc_sims/mcmc.cv/