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:	0.1.9
Depends:	R (≥ 3.2.2)
Imports:	SiZer (≥ 0.1-4), stats, grDevices
Published:	2025-05-21
DOI:	10.32614/CRAN.package.OptM
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

Documentation:

Reference manual:

OptM.html , OptM.pdf

Downloads:

Package source:	OptM_0.1.9.tar.gz
Windows binaries:	r-devel: OptM_0.1.9.zip, r-release: OptM_0.1.9.zip, r-oldrel: OptM_0.1.9.zip
macOS binaries:	r-release (arm64): OptM_0.1.9.tgz, r-oldrel (arm64): OptM_0.1.9.tgz, r-release (x86_64): OptM_0.1.9.tgz, r-oldrel (x86_64): OptM_0.1.9.tgz
Old sources:	OptM archive

Linking:

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