Estimate Kinship and FST under Arbitrary Population Structure

Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2016) .

News

2017-09-11 - popkin 1.0.0.9000

Public release!

2017-11-21 - popkin 1.0.1.9000

Fix a bug in which genotypes input to popkin via a function (rather than a regular matrix or a BEDMatrix object) caused popkin to die. Now popkin behaves as expected. New test unit cases were added to test function inputs (previously this case was untested).

2017-11-24 - popkin 1.0.2.9000

Added option to set colors for the lines that separate subpopulations.

2018-01-08 - popkin 1.0.3

Minor non-code changes for first CRAN submission.

2018-01-13 - popkin 1.0.4

All doc examples are now run (all used to be "dontrun").
Other minor non-code changes for first CRAN submission.

2018-01-26 - popkin 1.0.5

Updated vignette code to work when suggested package "lfa" is not available (needed for CRAN tests). This change is not visible in rendered vignette included in package.

Reference manual

install.packages("popkin")

1.0.5 by Alejandro Ochoa, a year ago

https://github.com/StoreyLab/popkin/

Report a bug at https://github.com/StoreyLab/popkin/issues

Browse source code at https://github.com/cran/popkin

Authors: Alejandro Ochoa [aut, cre] , John D. Storey [aut]

Documentation: PDF Manual

GPL-3 license

Imports Rcpp, RColorBrewer, graphics

Suggests BEDMatrix, testthat, knitr, rmarkdown, lfa

Linking to Rcpp, RcppEigen

Suggested by bnpsd.

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