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

The popular population genetic software 'Treemix' by 'Pickrell and Pritchard' (2012) <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.

Version: 0.1.3
Depends: R (≥ 3.2.2)
Imports: SiZer (≥ 0.1-4), stats, splines, grDevices, boot (≥ 1.3-20)
Published: 2019-04-28
Author: Robert Fitak [aut, cre]
Maintainer: Robert Fitak <rfitak9 at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
Citation: OptM citation info
Materials: README
CRAN checks: OptM results

Downloads:

Reference manual: OptM.pdf
Package source: OptM_0.1.3.tar.gz
Windows binaries: r-devel: OptM_0.1.3.zip, r-devel-gcc8: OptM_0.1.3.zip, r-release: OptM_0.1.3.zip, r-oldrel: OptM_0.1.3.zip
OS X binaries: r-release: OptM_0.1.3.tgz, r-oldrel: OptM_0.1.3.tgz
Old sources: OptM archive

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