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.
| Version: |
0.1.6 |
| Depends: |
R (≥ 3.2.2) |
| Imports: |
SiZer (≥ 0.1-4), stats, splines, grDevices, boot (≥ 1.3-20) |
| Published: |
2021-09-30 |
| 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 |
Documentation:
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