R Observatory: Metrics for bnpsd version 1.3.13

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bnpsd

1.3.13

Simulate Genotypes from the BN-PSD Admixture Model

4packages depend

4.5Kdownloads / year

85.6%test coverage

11/13checks pass

Overview

About

Maintained by Alejandro OchoaFirst published 2018-01-166 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("bnpsd", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("StoreyLab/bnpsd")

Development version from StoreyLab/bnpsd. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bnpsd

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-bnpsd

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-bnpsd

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.85

85.6%

Coverage · measured lines

100%

Documentation · exports

3

Dependencies · direct

Check history

NOTE2026-05-24
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-23
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 235 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

4.5K

CRAN downloads in the past year

Rank #11,252 · ~12/day · ~379/mo

Releases R versions

Daily download trend is not available in this view yet.

22730 days

86690 days

4.5K1 year

Compare downloads with other packages →

Also on105 r2u33 autocran

Repository

GitHub ↗ storeylab/bnpsd

9Stars

0Forks

0Open issues

0Open PRs

6Releases

104Commits

1Contributors

License GPL-3.0 · 104 commits · Last activity 2023-07-21 · 0% stars, 30d

Stars over time

2022-03-14 · 82026-07-15 · 9

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/storeylab/bnpsd on 2026-08-16.

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

statsape nnls

LinkingTo (0)

none

Suggests (5)

popkin testthat knitr rmarkdown RColorBrewer

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

ggmix popkin simfam simtrait

Code & Tests

People & History

People (2)

Maintainer (1)

Alejandro Ochoa

Author, Maintainer

Authors (2)

Alejandro Ochoa

Author, Maintainer

John D. Storey

Author

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.3.13Latest
2021-08-25 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2.3
2021-02-12 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2.1
2020-01-10 · diff ↗
1.1.1
2019-05-15 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0.4
2019-02-12 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.1
2018-01-16
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-01-16
Total releases: 6 / 8 yrs
License: GPL (>= 3) OSI
Download size: 348 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bnpsd")

Format

Ochoa, A., & Storey, J. D. (2021). bnpsd: Simulate Genotypes from the BN-PSD Admixture Model (Version 1.3.13) [Computer software]. https://doi.org/10.32614/CRAN.package.bnpsd

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for bnpsd version 1.3.13 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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