R Observatory: Metrics for PopPsiSeqR version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PopPsiSeqR

1.0.2

Process and Visualize Evolve & Resequence Experiments

0packages depend

2.1Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Charles SoederFirst published 2025-08-202 releasesCRAN page ↗GitHub ↗

Handle data from evolve and resequence experiments. Measured allele frequencies (e.g., from variants called from high-throughput sequencing data) are compared using an update of the PsiSeq algorithm (Earley, Eric and Corbin Jones (2011) doi:10.1534/genetics.111.129445). Functions for saving and loading important files are also included, as well as functions for basic data visualization.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("PopPsiSeqR", 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("csoeder/PopPsiSeq")

Development version from csoeder/PopPsiSeq. 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-poppsiseqr

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

Health

CRAN checks

2ERROR11OK

Failing flavors

ERROR r-oldrel-macos-arm64
ERROR r-oldrel-macos-x86_64

Slowest check: 4.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.39

not tracked

Coverage

86%

Documentation · exports

13

Dependencies · direct

Check history

ERROR2026-03-10
9 OK · 0 NOTE · 0 WARNING · 5 ERROR · 0 FAILURE

Documentation

READMEYes · 218 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.1K

CRAN downloads in the past year

Rank #12,796 · ~6/day · ~179/mo

Releases R versions

Daily download trend is not available in this view yet.

13830 days

78990 days

2.1K1 year

Compare downloads with other packages →

Also on121 r2u

Repository

GitHub ↗ csoeder/poppsiseqr

1Stars

0Forks

1Open issues

0Open PRs

0Releases

10Commits

3Contributors

10 commits · Last activity 2025-12-03 · 0% stars, 30d

Stars over time

2026-01-12 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/csoeder/poppsiseqr on 2026-08-09.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (13)

rtracklayer GenomicRanges ggplot2 dplyr S4Vectors magrittr ggbio withrutilspatchwork tidyr rlang devtools

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Charles Soeder

Author, Maintainer, Copyright holder

Authors (1)

Charles Soeder

Author, Maintainer, Copyright holder

Copyright holders (1)

Charles Soeder

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.2Latest
2026-01-12 · current release · diff ↗
unarchivedReturned to CRAN
2026-01-12
archivedRemoved from CRAN
2025-10-02
check issues were not corrected in time
1.0.0
2025-08-20
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-08-20
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PopPsiSeqR")

Format

Soeder, C. (2026). PopPsiSeqR: Process and Visualize Evolve & Resequence Experiments (Version 1.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.PopPsiSeqR

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 PopPsiSeqR version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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