calcFst

Calculates Weir and Cockerham's Fst for frequency data

misc

Provides a mixture model for clustering individuals (or sampling groups) into stocks based on their genetic profile. Here, sampling groups are individuals that are sure to come from the same stock (e.g. breeding adults or larvae). The mixture (log-)likelihood is maximised using the EM-algorithm after finding good starting values via a K-means clustering of the genetic data. Details can be found in: Foster, S. D.; Feutry, P.; Grewe, P. M.; Berry, O.; Hui, F. K. C. & Davies (2020) <doi:10.1111/1755-0998.12920>.

Scott Foster

stockR

Identifying Stocks in Genetic Data

Scott D. Foster

calcFst function

You can put normal text in Arguments, too, like this. Remember to indent all arguments, as below.
<dl>
<dt> data</dt>
<dd>a nMarker by nAnimal matrix of allele frequencies. That is for animal i and codominant marker j data[j,i] is the number of copies of the SNP allele (0, 1, or 2).</dd><dt> grps</dt>
<dd>a numeric vector giving the populations of the nAnimals</dd></dl>

Arguments

Arnaud Estoup for original code in Turbo Pascal. Translation in Fortran and interface with R by Gilles Guillot (for Geneland package). Scott Foster for latest wrapper for stockR package.

Authors

Author

Calculate Fst statistics for frequency data — calcFst

You can put normal text in Arguments, too, like this. Remember to indent all arguments, as below.
<dl>
<dt> data</dt>
<dd>a nMarker by nAnimal matrix of allele frequencies. That is for animal i and codominant marker j data[j,i] is the number of copies of the SNP allele (0, 1, or 2).</dd>

<dt> grps</dt>
<dd>a numeric vector giving the populations of the nAnimals</dd>

</dl>

calcFst: Calculate Fst statistics for frequency data

Description

Usage

Value

Arguments

Authors

Author

Details

Examples