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bnpsd
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Download and install bnpsd package within the R console
Install from CRAN:
install.packages("bnpsd")
Install from Github:
library("remotes")
install_github("cran/bnpsd")
Install by package version:
library("remotes")
install_version("bnpsd", "1.3.13")
Attach the package and use:
library("bnpsd")
Maintained by
Alejandro Ochoa
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-01-16
Latest Update: 2021-08-25
Description:
The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate subpopulations from which n individuals draw their alleles dictated by their individual-specific admixture proportions. The BN-PSD model additionally imposes the Balding-Nichols (BN) allele frequency model to the intermediate populations, which therefore evolved independently from a common ancestral population T with subpopulation-specific FST (Wright's fixation index) parameters. The BN-PSD model can be used to yield complex population structures. This simulation approach is now extended to subpopulations related by a tree. Method described in Ochoa and Storey (2021) .
How to cite:
Alejandro Ochoa (2018). bnpsd: Simulate Genotypes from the BN-PSD Admixture Model. R package version 1.3.13, https://cran.r-project.org/web/packages/bnpsd
Previous versions and publish date:
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Functions, R codes and Examples using
the bnpsd R package
Some associated functions: admix_prop_1d_circular . admix_prop_1d_linear . admix_prop_indep_subpops . bnpsd . coanc_admix . coanc_to_kinship . coanc_tree . draw_all_admix . draw_genotypes_admix . draw_p_anc . draw_p_subpops . draw_p_subpops_tree . fit_tree . fixed_loci . fst_admix . make_p_ind_admix . scale_tree . tree_additive . tree_reindex_tips . tree_reorder . undiff_af .
Some associated R codes: admix_prop_1d_circular.R . admix_prop_1d_linear.R . admix_prop_indep_subpops.R . bias_coeff_admix.R . bias_coeff_admix_fit.R . bnpsd.R . coanc_admix.R . coanc_to_kinship.R . coanc_tree.R . compare_names.R . draw_all_admix.R . draw_genotypes_admix.R . draw_p_anc.R . draw_p_subpops.R . draw_p_subpops_tree.R . fit_tree.R . fixed_loci.R . fst_admix.R . make_p_ind_admix.R . names_coanc.R . rescale_coanc_subpops.R . scale_tree.R . tree_additive.R . tree_reindex_tips.R . tree_reorder.R . undiff_af.R . validate_coanc_tree.R . Full bnpsd package functions and examples
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