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OptM  

Estimating the Optimal Number of Migration Edges from 'Treemix'
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", "0.1.9")



Attach the package and use:
library("OptM")
Maintained by
Robert Fitak
[Scholar Profile | Author Map]
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 0.1.9, https://cran.r-project.org/web/packages/OptM. Accessed 03 Jun. 2025.
Previous versions and publish date:
0.1.1 (2019-01-08 17:40), 0.1.3 (2019-04-28 16:40), 0.1.5 (2021-07-27 16:40), 0.1.6 (2021-09-30 22:40), 0.1.8 (2024-06-17 05:50)
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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