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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.
| Version: | 0.1.8 |
| Depends: | R (≥ 3.2.2) |
| Imports: | SiZer (≥ 0.1-4), stats, grDevices |
| Published: | 2024-06-17 |
| DOI: | 10.32614/CRAN.package.OptM |
| Author: | Robert Fitak [aut, cre] |
| Maintainer: | Robert Fitak <rfitak9 at gmail.com> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | no |
| Citation: | OptM citation info |
| Materials: | README |
| CRAN checks: | OptM results |
| Reference manual: | OptM.pdf |
| Package source: | OptM_0.1.8.tar.gz |
| Windows binaries: | r-devel: OptM_0.1.8.zip, r-release: OptM_0.1.8.zip, r-oldrel: OptM_0.1.8.zip |
| macOS binaries: | r-release (arm64): OptM_0.1.8.tgz, r-oldrel (arm64): OptM_0.1.8.tgz, r-release (x86_64): OptM_0.1.8.tgz, r-oldrel (x86_64): OptM_0.1.8.tgz |
| Old sources: | OptM archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.