R Observatory: Metrics for pooledpeaks version 1.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pooledpeaks

1.2.2Package record

Genetic Analysis of Pooled Samples

0packages depend

5.9Kdownloads / year

87.8%test coverage

13/13flavors OK

Overview

About

Maintained by Kathleen KuestersCRAN page ↗GitHub ↗Issues ↗

Analyzing genetic data obtained from pooled samples. This package can read in Fragment Analysis output files, process the data, and score peaks, as well as facilitate various analyses, including cluster analysis, calculation of genetic distances and diversity indices, as well as bootstrap resampling for statistical inference. Specifically tailored to handle genetic data efficiently, researchers can explore population structure, genetic differentiation, and genetic relatedness among samples. We updated some functions from Covarrubias-Pazaran et al. (2016) doi:10.1186/s12863-016-0365-6 to allow for the use of new file formats and referenced the following to write our genetic analysis functions: Long et al. (2022) doi:10.1038/s41598-022-04776-0, Jost (2008) doi:10.1111/j.1365-294x.2008.03887.x, Nei (1973) doi:10.1073/pnas.70.12.3321, Foulley et al. (2006) doi:10.1016/j.livprodsci.2005.10.021, Chao et al. (2008) doi:10.1111/j.1541-0420.2008.01010.x.

Install

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

install.packages("pooledpeaks", 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("kmkuesters/pooledpeaks")

Development version from kmkuesters/pooledpeaks. 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-pooledpeaks

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-pooledpeaks

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

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.2

READMEYes · 410 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.2.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 30 (1 internal)includes a package overview page
Examples that run: 100%25 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Introduction to Using the pooledpeaks Workflow HTML

How these are measured

Downloads

5.9K

CRAN downloads in the past year

Rank #10,446 · ~16/day · ~490/mo

Releases R versions

Daily download trend is not available in this view yet.

37330 days

99390 days

5.9K1 year

Compare downloads with other packages →

Also on75 r2u

How downloads are counted

Repository

kmkuesters/pooledpeaks ↗Account: kmkuesters

1Stars

1Forks

0Open issues

0Open PRs

4Releases

79Commits

2Commit identities

License file reads as GPL-3.0 · 79 commits · Last activity 2025-05-09

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 130
Median days to close, 50 most recently updated closed PRs: 5

Stars over time

2025-05-06 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/kmkuesters/pooledpeaks on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing pooledpeaks adds 29 packages (20 with compiled code, 25 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, Fragman 1.6 MB.

Depends (0)

none

Imports (12)

ape dplyr Fragmangraphicsmagrittr pdftools qpdf rlangstatstibble tidyrutils

LinkingTo (0)

none

Suggests (4)

knitr plyr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (6)

Author

Author

Contributor

Contributor

Contributor

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.2Latest
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2025-05-09 · current release · diff ↗
1.2.1
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2025-05-01 · diff ↗
1.2.0
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2025-04-21 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.1
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2025-03-14 · diff ↗
1.1.0
record
2025-02-01 · diff ↗
1.0.7
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2024-11-20 · diff ↗
1.0.6
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2024-09-12 · diff ↗
1.0.5
record
2024-09-03
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-03
Total releases: 8 / 2 yrs
License: GPL (>= 3) OSI
Download size: 2.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pooledpeaks")

Format

Kuesters, K., Blank, W., Blanton, J., Blanton, R., Kovach, J., & Long, J. (2025). pooledpeaks: Genetic Analysis of Pooled Samples (Version 1.2.2) [Computer software]. https://doi.org/10.32614/CRAN.package.pooledpeaks

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 pooledpeaks version 1.2.2 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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