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) <10.1101>.10.1101>
2017-09-11 - popkin 184.108.40.20600
2017-11-21 - popkin 220.127.116.1100
- 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 18.104.22.16800
- 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
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.
2018-02-01 - popkin 22.214.171.12400
plotPopkin now allows NULL elements in input list x, makes empty plots with titles (good for placeholders or other non-existent data)
Clarified plotPopkin documentation (that marPad is added to xMar values if set)
README.md now contains instructions for installing from CRAN as well as from GitHub.
2018-07-30 - popkin 126.96.36.19900
- Internal function printLabs (used by plotPopkin) is now more flexible in where it places its labels (new args "side1" and "side2")
2018-08-08 - popkin 188.8.131.5200
- Added option for continuous colors, off by default. Default is still to use only the 17 colors given directly by RColorBrewer.
2018-09-05 - popkin 184.108.40.20600
- Changed some function parameter defaults from missing to NULL, added more validation tests (affects fst, inbr, plotPopkin).
2018-10-19 - popkin 220.127.116.1100
- Added neff function (estimates effective sample size given a kinship matrix and weights; can find optimal weights that are non-negative or sign-unconstrained, yielding maximum neff values)
2019-02-13 - popkin 18.104.22.16800
popkin function preserves the individual names if they are present in the input genotype matrix.
These names get copied to the rows and columns of the output kinship matrix.
Converted the vignette from PDF to HTML
2019-02-13 - popkin 1.1.2
- Minor non-code changes for second CRAN submission.