Package: OptM 0.1.9

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]

OptM_0.1.9.tar.gz
OptM_0.1.9.zip(r-4.7-any)OptM_0.1.9.zip(r-4.6-any)OptM_0.1.9.zip(r-4.5-any)
OptM_0.1.9.tgz(r-4.6-any)OptM_0.1.9.tgz(r-4.5-any)
OptM_0.1.9.tar.gz(r-4.7-any)OptM_0.1.9.tar.gz(r-4.6-any)
OptM_0.1.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
OptM/json (API)

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

On CRAN:

Conda:

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

3.31 score 2 stars 101 scripts 488 downloads 2 mentions 2 exports 31 dependencies

Last updated from:63b4a98564. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK102
source / vignettesOK192
linux-releaseOK105
macos-releaseOK125
macos-oldrelOK140
windows-develOK66
windows-releaseOK66
windows-oldrelOK69
wasm-releaseOK85

Exports:optMplot_optM

Dependencies:bootclicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesSiZerstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr