Fstat.output: Computes F statistics on the output of an inference by MCMC...
In Geneland: Detection of Structure from Multilocus Genetic Data
Description
Usage
Arguments
Value
Author(s)
References
Description
Computes F statistics according to Weir and Cockerham's
estimators. Missing values are allowed but as of today, the NA code is only treated as an extra
allele which might bias the result. This function should not be used on haploid data.
Usage
1
Fstat.output(coordinates,genotypes,ploidy,burnin,path.mcmc)
Arguments
coordinates
Matrix with one line per individual and two columns
genotypes
Genotypes of individuals. A matrix with one line per
individual and 2 columns per locus
burnin
Integer: number of saved iterations to discard.
ploidy
Integer: 1 or 2 (default is 2).
Do not use for haploid data.
path.mcmc
Path to output files directory
Value
A list with components
Pairwise.Fis
A matrix of real numbers estimating the pairwise Fis
Pairwise.Fst
A matrix of real numbers estimating the pairwise Fst
Author(s)
Arnaud Estoup for original code in Turbo Pascal.
Translation in Fortran and interface with R by Gilles Guillot
References
Weir, B.S. and C.C. Cockerham,
Estimating F-statistics for the analysis of population structure,
Evolution, 1984,
vol. 38, 1358-1370.
Geneland documentation built on April 14, 2017, 2:31 p.m.
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Description Usage Arguments Value Author(s) References
Description
Computes F statistics according to Weir and Cockerham's estimators. Missing values are allowed but as of today, the NA code is only treated as an extra allele which might bias the result. This function should not be used on haploid data.
Usage
1 | Fstat.output(coordinates,genotypes,ploidy,burnin,path.mcmc)
|
Arguments
coordinates |
Matrix with one line per individual and two columns |
genotypes |
Genotypes of individuals. A matrix with one line per individual and 2 columns per locus |
burnin |
Integer: number of saved iterations to discard. |
ploidy |
Integer: 1 or 2 (default is 2). Do not use for haploid data. |
path.mcmc |
Path to output files directory |
Value
A list with components
Pairwise.Fis |
A matrix of real numbers estimating the pairwise Fis |
Pairwise.Fst |
A matrix of real numbers estimating the pairwise Fst |
Author(s)
Arnaud Estoup for original code in Turbo Pascal.
Translation in Fortran and interface with R by Gilles Guillot
References
Weir, B.S. and C.C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution, 1984, vol. 38, 1358-1370.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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