CRAN/E | OptM

OptM

Estimating the Optimal Number of Migration Edges from 'Treemix'

Installation

About

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.

Citation OptM citation info

Key Metrics

Version 0.1.6
R ≥ 3.2.2
Published 2021-09-30 910 days ago
Needs compilation? no
License GPL-2
License GPL-3
CRAN checks OptM results

Downloads

Yesterday 9 0%
Last 7 days 62 -30%
Last 30 days 272 +3%
Last 90 days 968 +28%
Last 365 days 3.356 -13%

Maintainer

Maintainer

Robert Fitak

rfitak9@gmail.com

Authors

Robert Fitak

aut / cre

Material

README
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

OptM archive

Depends

R ≥ 3.2.2

Imports

SiZer ≥ 0.1-4
stats
splines
grDevices
boot ≥ 1.3-20