R Observatory: Metrics for pedgene version 4.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pedgene

4.1Package record

Gene-Level Variant Association Tests for Pedigree Data

0packages depend

4.9Kdownloads / year

–test coverage

10/13flavors OK

Overview

About

Maintained by Jason SinnwellCRAN page ↗

Gene-level variant association tests with disease status for pedigree data: kernel and burden association statistics.

Changes in 4.1

remove depencency on kinship2, replace with bioconductor Pedixplorer
index rows of ped/geno by famid_id to match kinship dimnames, which makes robust to lc_collate char-sorting settings

From inst/NEWS.Rd in the release

Install

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

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

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

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-pedgene

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-pedgene

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-pedgene

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

3ERROR10OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package required but not available: ‘Pedixplorer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

ERRORwhether package can be installedr-release-windows-x86_64

Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.6/pedgene.Rcheck/00install.out' for details.

CRAN check page ↗

Slowest check: 5.7 min · r-oldrel-windows-x86_64

Status changes

ERROR10 OK, 3 ERRORNow
ERROR10 OK, 4 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.1

READMEYes · 69 wordsVignettesYes · 1 · dynamicNEWSYes · mentions 4.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 5
Examples that run: 100%2 run in a plain check
Exported functions with examples: 33%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 20%

Vignettes (1)

pedgene_manual PDF

How these are measured

Downloads

4.9K

CRAN downloads in the past year

Rank #10,174 · ~13/day · ~405/mo

Releases R versions

Daily download trend is not available in this view yet.

35330 days

1K90 days

4.9K1 year

Compare downloads with other packages →

Also on76 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing pedgene adds 8 packages (5 with compiled code, 6.2 MB of source tarballs). Heaviest: survey 2.3 MB, Rcpp 1.8 MB, RcppArmadillo 1.0 MB. 1 more not on CRAN is not measured.

Depends (6)

R >= 4.4.0statsMatrixCompQuadForm survey Pedixplorer

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

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 (3)

Jason Sinnwell

Author, Maintainer since 1.3 (2013)

Schaid Daniel

Author · added in 2.7

Visconti Alessia

Contributor · added in 3.1

Previously maintained by Dan Schaid (1.1 to 1.2).

Listed in earlier versions (1)

Dan Schaid

no longer listed · 1.1 to 2.1

Releases (14)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
4.1Latest
record
2025-09-08 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
3.9
record
2024-04-10 · diff ↗
3.8
record
2024-03-05 · diff ↗
R
R 4.3.0 released · 2023-04-21
3.6
record
2022-10-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
3.3
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2020-02-19 · diff ↗
3.2
record
2019-05-23 · diff ↗
3.1
record
2019-05-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23

Show 12 earlier eventsHide 12 earlier events

R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
2.9
record
2015-10-10 · diff ↗
2.7
record
2015-08-03 · diff ↗
R
R 3.2.0 released · 2015-04-16
2.1
record
2014-06-24 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.4
record
2014-03-20 · diff ↗
1.3
record
2013-12-03 · diff ↗
1.2
record
2013-11-18 · diff ↗
1.1
record
2013-11-08
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-11-08
Total releases: 14 / 13 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.4.0
Bundled data: 1.1 KB / 4 files
Download size: 248 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pedgene")

Format

Sinnwell, J., Alessia, V., & Daniel, S. (2025). pedgene: Gene-Level Variant Association Tests for Pedigree Data (Version 4.1) [Computer software]. https://doi.org/10.32614/CRAN.package.pedgene

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 pedgene version 4.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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