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OptM
View on CRAN: Click
here
Download and install OptM package within the R console
Install from CRAN:
install.packages("OptM")
Install from Github:
library("remotes")
install_github("cran/OptM")
Install by package version:
library("remotes")
install_version("OptM", "0.1.8")
Attach the package and use:
library("OptM")
Maintained by
Robert Fitak
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-01-08
Latest Update: 2021-09-30
Description:
The popular population genetic software 'Treemix' by
'Pickrell and Pritchard' (2012)
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.
How to cite:
Robert Fitak (2019). OptM: Estimating the Optimal Number of Migration Edges from 'Treemix'. R package version 0.1.8, https://cran.r-project.org/web/packages/OptM. Accessed 16 Apr. 2025.
Previous versions and publish date:
Other packages that cited OptM R package
View OptM citation profile
Other R packages that OptM depends,
imports, suggests or enhances
Complete documentation for OptM
Functions, R codes and Examples using
the OptM R package
Some associated functions: optM . plot_optM .
Some associated R codes: optM.R . plot_optM.R . Full OptM package functions and examples
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