R Observatory: Metrics for randPedPCA version 1.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

randPedPCA

1.1.3Package record

Fast PCA for Large Pedigrees

0packages depend

2.2Kdownloads / year

70.3%test coverage

13/13flavors OK

Overview

About

Maintained by Hannes BecherCRAN page ↗

Carry out principal component analysis (PCA) of very large pedigrees such as found in breeding populations! This package exploits sparse matrices and randomised linear algebra to deliver a gazillion-times speed-up compared to naive singular value decoposition (SVD) (and eigen decomposition).

Install

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

install.packages("randPedPCA", 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-randpedpca

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-randPedPCA

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-randPedPCA

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

13OK

CRAN check page ↗

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-08
ERROR12 OK, 1 ERROR2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.3

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 17
Examples that run: 100%4 run in a plain check
Exported functions with examples: 44%
Documented parameters: 93%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

pedigree-pca HTML

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #20,368 · ~6/day · ~182/mo

Releases R versions

Daily download trend is not available in this view yet.

27130 days

64990 days

2.2K1 year

Compare downloads with other packages →

Also on75 r2u7 autocran

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing randPedPCA adds 6 packages (6 with compiled code, 6.8 MB of source tarballs). Heaviest: spam 3.1 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB.

Depends (6)

R >= 3.5spamMatrixmethodspedigreeTools RSpectra

Imports (0)

none

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat rgl

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)

Hannes Becher

Maintainer since 1.0.0 (2025)

Ros Craddock

Author

Gregor Gorjanc

Author

Hanbin Lee

Author

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.3Latest
record
2025-07-22 · current release · diff ↗
1.1.2
record
2025-06-16 · diff ↗
1.0.1
record
2025-04-24 · diff ↗
1.0.0
record
2025-04-24
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-04-24
Total releases: 4 / 1 yrs
License: GPL (>= 2) OSI · relicensed from MIT + file LICENSE in 1.1.3
Minimum R: ≥ 3.5
Bundled data: 462 KB / 6 files
Download size: 2.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("randPedPCA")

Format

Becher, H., Craddock, R., Gorjanc, G., & Lee, H. (2025). randPedPCA: Fast PCA for Large Pedigrees (Version 1.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.randPedPCA

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 randPedPCA version 1.1.3 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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