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:
OptM_0.1.8.tar.gz
OptM_0.1.8.zip(r-4.5)OptM_0.1.8.zip(r-4.4)OptM_0.1.8.zip(r-4.3)
OptM_0.1.8.tgz(r-4.4-any)OptM_0.1.8.tgz(r-4.3-any)
OptM_0.1.8.tar.gz(r-4.5-noble)OptM_0.1.8.tar.gz(r-4.4-noble)
OptM_0.1.8.tgz(r-4.4-emscripten)OptM_0.1.8.tgz(r-4.3-emscripten)
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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 months agofrom:c96207971c. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 16 2024 |
R-4.5-win | OK | Oct 16 2024 |
R-4.5-linux | OK | Oct 16 2024 |
R-4.4-win | OK | Oct 16 2024 |
R-4.4-mac | OK | Oct 16 2024 |
R-4.3-win | OK | Oct 16 2024 |
R-4.3-mac | OK | Oct 16 2024 |
Dependencies:bootclicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrlangscalesSiZerstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
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optM function | optM |
plot_optM function | plot_optM |