Package: OptM 0.1.8

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.

Authors:Robert Fitak [aut, cre]

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OptM.pdf |OptM.html✨
OptM/json (API)

# Install 'OptM' in R:
install.packages('OptM', repos = c('https://rfitak.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.01 score 2 stars 51 scripts 345 downloads 2 mentions 2 exports 38 dependencies

Last updated 5 months agofrom:c96207971c. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-winOKNov 15 2024
R-4.5-linuxOKNov 15 2024
R-4.4-winOKNov 15 2024
R-4.4-macOKNov 15 2024
R-4.3-winOKNov 15 2024
R-4.3-macOKNov 15 2024

Exports:optMplot_optM

Dependencies:bootclicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrlangscalesSiZerstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr