OptM: Estimating the Optimal Number of Migration Edges from 'Treemix'

The popular population genetic software 'Treemix' by 'Pickrell and Pritchard' (2002) <DOI:10.1371/journal.pgen.1002967> estimates the number of migration edges on a population tree. However, it can be difficult to determine the number of migration edges to include. Previously, it was customary to stop adding migration edges when 99.8% of variation in the data was explained, but 'OptM' automates this process using an ad hoc statistic based on the second-order rate of change in the log likelihood. 'OptM' also has added functionality for various threshold modeling to compare with the ad hoc statistic.

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Package details

AuthorRobert Fitak [aut, cre]
MaintainerRobert Fitak <[email protected]>
LicenseGPL (>= 2)
Package repositoryView on CRAN
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OptM documentation built on Jan. 8, 2019, 5:05 p.m.