Priors

These values are used to parametrize the assumed probability models. In most cases they have little effect on the results, and the user may not want to worry about them. The values of CORRA and CORRB matter somewhat when FREQSCORR=1. The value of ALPHA has quite an effect if INFERALPHA=0.

ALPHA (double) Dirichlet parameter ($\alpha$) for degree of admixture (this is the initial value if INFERALPHA==1).

CORRA, CORRB (double) See FREQSCORR. The prior for $f^{(l)}$ is taken to be Gamma with mean CORRA$*$CORRB, and variance CORRA$*$CORRB$^2$.

EPSILON (double) Dirichlet parameter for allele frequencies when FREQSCORR=0. A value of 1.0 (which produces a uniform distribution) seems to work fine.

UNIFPRIORALPHA (Boolean), ALPHAMAX (double) Assume a uniform prior for $\alpha$ which runs between 0 and ALPHAMAX. This model seems to work fine; the alternative model (when UNIFPRIORALPHA=0) is to take $\alpha$ as having a Gamma prior, with mean ALPHAPRIORA $\times$ ALPHAPRIORB, and variance ALPHAPRIORA $\times$ ALPHAPRIORB$^2$.

ALPHAPRIORA, ALPHAPRIORB (double) See UNIFPRIORALPHA.