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.

Getting started

Package details

AuthorRobert Fitak [aut, cre]
MaintainerRobert Fitak <[email protected]>
LicenseGPL (>= 2)
Version0.1.1
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("OptM")

Try the OptM package in your browser

Any scripts or data that you put into this service are public.

OptM documentation built on Jan. 8, 2019, 5:05 p.m.