R Observatory: Metrics for PopGenHelpR version 1.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PopGenHelpR

1.4.2Package record

Streamline Population Genomic and Genetic Analyses

0packages depend

6.4Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Keaka FarleighCRAN page ↗GitHub ↗Website ↗Issues ↗

Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.

Changes in 1.4.2

January 8th, 2025

-Updated documentation to ensure other packages are cited correctly.

From NEWS.md in the release

Install

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

install.packages("PopGenHelpR", 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("kfarleigh/PopGenHelpR")

Development version from kfarleigh/PopGenHelpR. 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-popgenhelpr

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-PopGenHelpR

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: 1.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-27

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-07-23
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 1.4.2

READMEYes · 196 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.4.2Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 15
Examples that run: 7%1 run in a plain check · 14 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 13%

Vignettes (1)

PopGenHelpR_vignette HTML

How these are measured

Downloads

6.4K

CRAN downloads in the past year

Rank #6,786 · ~18/day · ~537/mo

Releases R versions

Daily download trend is not available in this view yet.

40430 days

1.2K90 days

6.4K1 year

Compare downloads with other packages →

Also on88 r2u

How downloads are counted

Repository

kfarleigh/popgenhelpr ↗Account: kfarleigh

5Stars

1Forks

0Open issues

0Open PRs

0Releases

244Commits

3Commit identities

diversityfstheterozygosityinterpolationneispopulation-geneticspopulation-genomicsr

License file reads as GPL-3.0 · 244 commits · Last activity 2026-10-07 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2023-09-29 · 32026-07-07 · 5

How these are measured

PracticesBeta

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

Checks run against github.com/kfarleigh/popgenhelpr on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-07 · The repository has a site deploy workflow

pkgdown site last built 2026-10-07

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing PopGenHelpR adds 74 packages (45 with compiled code, 78 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (1)

R >= 2.10

Imports (15)

dplyr ggplot2 magrittrmethodsreshape2 rlang scatterpiestatsgeodata terra ggspatial spdep sfutilsvcfR

LinkingTo (0)

none

Suggests (3)

knitr 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 (4)

Keaka Farleigh

Christopher Blair

Author, Copyright holder, Contributor

Tereza Jezkova

Author, Copyright holder, Contributor

Mason Murphy

Author, Copyright holder, Contributor

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.4.2Latest
record
2026-01-08 · current release · diff ↗
1.4.1
record
2025-08-19 · diff ↗
1.4.0
record
2025-07-02 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.3.2
record
2024-08-02 · diff ↗
1.3.1
record
2024-07-26 · diff ↗ ·
removed 5 exports
Dif_Stats_Map, Dif_stats, Div_Stats_Map, Div_stats, Plot_ancestry
1.3.0
record
2024-05-09 · diff ↗ ·
added 9 exports
Ancestry_barchart, Differentiation, Heterozygosity, Network_map, PCA, Piechart_map, Plot_coordinates, Point_map, Private.alleles
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2023-08-16
1.2.1
record
2023-08-16 · diff ↗
archivedRemoved from CRAN
2023-07-18
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
1.0.0
record
2023-02-13
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-02-13
Total releases: 8 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 122 KB / 5 files
Download size: 1.9 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PopGenHelpR")

Format

Farleigh, K., Blair, C., Jezkova, T., & Murphy, M. (2026). PopGenHelpR: Streamline Population Genomic and Genetic Analyses (Version 1.4.2) [Computer software]. https://doi.org/10.32614/CRAN.package.PopGenHelpR

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 PopGenHelpR version 1.4.2 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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