population dispersals: method to estimate allele frequencies in a region considering geographical locations of sampling sites, the nonequal number of samples in locations, and, most crucially, possible ways of dispersals within a region. It utilizes hierarchical Bayesian Modeling, compositional nature of frequencies and the Wright-Fisher model of drift.
Initial data contais two parts:
(1) covariance matrix between samples based on the hypothetical dispersals within a region: data/cov_mx
(2) allele frequencies in locations within regions data\samples
To demonstrate the test, please run:
estim_routes.pyto get estimates of allele frequenciesget_stat.pyto get statisticks for mcmc
To run popdisp methods, you need Python 3.4 or later. A list of required Python packages that the popdisp depends on, are in requirements.txt.
Anna Igolkina developed the popdisp package, e-mail.
The popdisp package is open-sourced software licensed under the MIT license.