hierfstat: General information on the hierfstat package
In hierfstat: Estimation and Tests of Hierarchical F-Statistics
hierfstat R Documentation
General information on the hierfstat package
Description
This package contains functions to estimate hierarchical F-statistics for any number of hierarchical levels using the method described in Yang (1998). It also contains functions allowing to test the significance of population differentiation at any given level using the likelihood ratio G-statistic, showed previoulsly to be the most powerful statistic to test for differnetiation (Goudet et al., 1996) . The difficulty in a hierarchical design is to identify which units should be permutted. Functions samp.within and samp.between give permutations of a sequence that allows reordering of the observations in the original data frame. An exemple of application is given in the help page for function g.stats.glob.
Hierfstat includes now all the capabilities of Fstat, and many others. A new serie of functions implementing the statistics described in Weir and Goudet (2017) and Goudet et al. (2018) (beta.dosage, fs.dosage) have been written to deal with large genomic data sets and take as input a matrix of allelic dosages, the number of alternate alleles an individual carries at a locus.
Several functions have been written to simulate genetic data, or to import them from existing sofwares such as quantiNemo or Hudson's ms
Hierfstat links easily with the gaston, SNPRelate and adegenet packages, among others.
Author(s)
Jerome Goudet jerome.goudet@unil.ch
References
Goudet J. (2005) Hierfstat, a package for R to compute and test variance components and F-statistics. Molecular Ecology Notes. 5:184-186
Goudet J., Raymond, M., DeMeeus, T. and Rousset F. (1996) Testing differentiation in diploid populations. Genetics. 144: 1933-1940
Weir B.S. and Goudet J. (2017) A Unified Characterization of Population Structure and Relatedness. Genetics. 206: 2085-2103
Goudet J., Kay T. and Weir B.S. (2018) How to estimate kinship. Molecular Ecology. 27: 4121:4135
Weir, B.S. (1996) Genetic Data Analysis II. Sinauer Associates.
Yang, R.C. (1998) Estimating hierarchical F-statistics. Evolution 52(4):950-956
hierfstat documentation built on May 6, 2022, 1:05 a.m.
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| hierfstat | R Documentation |
General information on the hierfstat package
Description
This package contains functions to estimate hierarchical F-statistics for any number of hierarchical levels using the method described in Yang (1998). It also contains functions allowing to test the significance of population differentiation at any given level using the likelihood ratio G-statistic, showed previoulsly to be the most powerful statistic to test for differnetiation (Goudet et al., 1996) . The difficulty in a hierarchical design is to identify which units should be permutted. Functions samp.within and samp.between give permutations of a sequence that allows reordering of the observations in the original data frame. An exemple of application is given in the help page for function g.stats.glob.
Hierfstat includes now all the capabilities of Fstat, and many others. A new serie of functions implementing the statistics described in Weir and Goudet (2017) and Goudet et al. (2018) (beta.dosage, fs.dosage) have been written to deal with large genomic data sets and take as input a matrix of allelic dosages, the number of alternate alleles an individual carries at a locus.
Several functions have been written to simulate genetic data, or to import them from existing sofwares such as quantiNemo or Hudson's ms
Hierfstat links easily with the gaston, SNPRelate and adegenet packages, among others.
Author(s)
Jerome Goudet jerome.goudet@unil.ch
References
Goudet J. (2005) Hierfstat, a package for R to compute and test variance components and F-statistics. Molecular Ecology Notes. 5:184-186
Goudet J., Raymond, M., DeMeeus, T. and Rousset F. (1996) Testing differentiation in diploid populations. Genetics. 144: 1933-1940
Weir B.S. and Goudet J. (2017) A Unified Characterization of Population Structure and Relatedness. Genetics. 206: 2085-2103
Goudet J., Kay T. and Weir B.S. (2018) How to estimate kinship. Molecular Ecology. 27: 4121:4135
Weir, B.S. (1996) Genetic Data Analysis II. Sinauer Associates.
Yang, R.C. (1998) Estimating hierarchical F-statistics. Evolution 52(4):950-956
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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