SpaceMix

SpaceMixSpaceMix is a method for inferring and visualizing spatial patterns of population genetic structure and admixture.  This statistical method that uses genome-wide polymorphism data to build “geogenetic maps,” in which the distances between samples reflect genetic, rather than geographic, distance.  In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances.  This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map.  The PDF of the paper can be found here.  A vignette walking through how to run SpaceMix is included in the R package (see below).
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To start using SpaceMix:
(1) Go to my github account, download the .tar.gz file and install in R using
> install.packages(“~/SpaceMix_X.tar.gz”,repos=NULL)
where “X” in the package name denotes the number of
the most current version.

OR

(2) install directly from github using
> require(devtools)
> install_github(“gbradburd/SpaceMix”,build_vignettes=TRUE)

You can then look at the vignette with
> vignette(“spacemix_vignette”)

and you can see all documented functions using
> ??SpaceMix