Package: bnpsd 1.3.14.9000

Alejandro Ochoa

bnpsd: Simulate Genotypes from the BN-PSD Admixture Model

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) <doi:10.1371/journal.pgen.1009241>.

Authors:Alejandro Ochoa [aut, cre], John D. Storey [aut]

bnpsd_1.3.14.9000.tar.gz
bnpsd_1.3.14.9000.zip(r-4.7)bnpsd_1.3.14.9000.zip(r-4.6)bnpsd_1.3.14.9000.zip(r-4.5)
bnpsd_1.3.14.9000.tgz(r-4.6-any)bnpsd_1.3.14.9000.tgz(r-4.5-any)
bnpsd_1.3.14.9000.tar.gz(r-4.7-any)bnpsd_1.3.14.9000.tar.gz(r-4.6-any)
bnpsd_1.3.14.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bnpsd/json (API)

# Install 'bnpsd' in R:

install.packages('bnpsd', repos = c('https://storeylab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/storeylab/bnpsd/issues

On CRAN:

5.56 score 8 stars 45 scripts 325 downloads 2 mentions 21 exports 6 dependencies

Last updated from:c101b07810. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	163
source / vignettes	OK	185
linux-release-x86_64	OK	126
macos-release-arm64	OK	139
macos-oldrel-arm64	OK	169
windows-devel	OK	83
windows-release	OK	76
windows-oldrel	OK	91
wasm-release	OK	102

Exports:admix_prop_1d_circular admix_prop_1d_linear admix_prop_indep_subpops coanc_admix coanc_to_kinship coanc_tree draw_all_admix draw_all_unstructured 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

Dependencies:ape digest lattice nlme nnls Rcpp

Simulate Admixed Populations with bnpsd

Rendered frombnpsd.Rmdusingknitr::rmarkdown

Last update: 2021-08-02
Started: 2017-08-13

Help page	Topics
Construct admixture proportion matrix for circular 1D geography	admix_prop_1d_circular
Construct admixture proportion matrix for 1D geography	admix_prop_1d_linear
Construct admixture proportion matrix for independent subpopulations	admix_prop_indep_subpops
A package for modeling and simulating an admixed population	bnpsd-package bnpsd
Construct the coancestry matrix of an admixture model	coanc_admix
Transform coancestry matrix to kinship matrix	coanc_to_kinship
Calculate coancestry matrix corresponding to a tree	coanc_tree
Simulate random allele frequencies and genotypes from the BN-PSD admixture model	draw_all_admix
Simulate random allele frequencies and genotypes from the unstructured model	draw_all_unstructured
Draw genotypes from the admixture model	draw_genotypes_admix
Draw random Uniform or Beta ancestral allele frequencies	draw_p_anc
Draw allele frequencies for independent subpopulations	draw_p_subpops
Draw allele frequencies for subpopulations related by a tree	draw_p_subpops_tree
Fit a tree structure to a coancestry matrix	fit_tree
Identify fixed loci	fixed_loci
Calculate FST for the admixed individuals	fst_admix
Construct individual-specific allele frequency matrix under the PSD admixture model	make_p_ind_admix
Scale a coancestry tree	scale_tree
Calculate additive edges for a coancestry tree, or viceversa	tree_additive
Reindex tree tips in order of appearance in edges	tree_reindex_tips
Reorder tree tips to best match a desired order	tree_reorder
Undifferentiate an allele distribution	undiff_af

Package: bnpsd 1.3.14.9000

bnpsd: Simulate Genotypes from the BN-PSD Admixture Model

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)