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:
OptM_0.1.9.tar.gz
OptM_0.1.9.zip(r-4.7)OptM_0.1.9.zip(r-4.6)OptM_0.1.9.zip(r-4.5)
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✨
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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:63b4a98564. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 123 | ||
| source / vignettes | OK | 152 | ||
| linux-release-x86_64 | OK | 124 | ||
| macos-release-arm64 | OK | 135 | ||
| macos-oldrel-arm64 | OK | 136 | ||
| windows-devel | OK | 82 | ||
| windows-release | OK | 124 | ||
| windows-oldrel | OK | 108 | ||
| wasm-release | OK | 108 |
Dependencies:bootclicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesSiZerstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| optM function | optM |
| plot_optM function | plot_optM |
