R Observatory: Metrics for pcadapt version 4.4.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pcadapt

4.4.1

Fast Principal Component Analysis for Outlier Detection

2packages depend

18.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Florian PrivéFirst published 2015-09-0520 releasesCRAN page ↗GitHub ↗

Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis. Implements the method described in (Luu, 2016) DOI:10.1111/1755-0998.12592 and later revised in (Privé, 2020) DOI:10.1093/molbev/msaa053.

Install

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

install.packages("pcadapt", 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("bcm-uga/pcadapt")

Development version from bcm-uga/pcadapt. 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-pcadapt

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

# 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-pcadapt

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-pcadapt

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 4.6 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 177 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 21%
References docs: 0%

Downloads

18.7K

CRAN downloads in the past year

Rank #4,122 · ~51/day · ~1.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

51730 days

2K90 days

18.7K1 year

Compare downloads with other packages →

Also on474 r2u19 autocran3.3K conda_forge

Repository

GitHub ↗ bcm-uga/pcadapt

45Stars

11Forks

0Open issues

0Open PRs

0Releases

363Commits

9Contributors

363 commits · Last activity 2025-07-25 · 0% stars, 30d

Stars over time

2025-08-02 · 422026-07-07 · 45

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/bcm-uga/pcadapt on 2026-08-16.

Continuous integration (1)

GitHub Actions

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 (7)

bigutilsr data.table ggplot2 magrittr mmapcharr Rcpp RSpectra

LinkingTo (3)

mmapcharr Rcpp rmio

Suggests (5)

plotly shiny spelling testthat vcfR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

bigsnpr tidypopgen

Code & Tests

People & History

People (5)

Maintainer (1)

Florian Privé

Author, Maintainer · added in 4.0.0

Authors (3)

Florian Privé

Author, Maintainer · added in 4.0.0

Michael Blum

Author

Keurcien Luu

Author

Contributors (2)

Eric Bazin

Contributor · added in 4.0.0

Nicolas Duforet-Frebourg

Contributor · added in 3.0

Listed in earlier versions (1)

Michael G.B. Blum

no longer listed · 2.0 to 3.0.3

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
4.4.1Latest
2025-07-25 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
4.4.0
2024-09-24 · diff ↗
R
R 4.4.0 released · 2024-04-24
4.3.5
2023-08-29 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
4.3.3
2020-05-05 · diff ↗
R
R 4.0.0 released · 2020-04-24
4.3.1
2020-02-28 · diff ↗
unarchivedReturned to CRAN
2020-02-28
archivedRemoved from CRAN
2020-02-19
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26
4.1.0
2019-02-27 · diff ↗

Show 24 earlier events

4.0.3
2018-07-03 · diff ↗
unarchivedReturned to CRAN
2018-07-03
R
R 3.5.0 released · 2018-04-23
archivedRemoved from CRAN
2018-04-14
there are out-of-memory writes
4.0.1
2018-04-13 · diff ↗
unarchivedReturned to CRAN
2018-04-13
archivedRemoved from CRAN
2018-04-06
compiled code made illegal writes
4.0.0
2018-04-05 · diff ↗
unarchivedReturned to CRAN
2018-04-05
archivedRemoved from CRAN
2018-02-21
policy violation Misrepresentation of authorship of contents of 'src_Lapack' and 'src_convert' directories
R
R 3.4.0 released · 2017-04-21
3.0.4
2017-01-02 · diff ↗
3.0.3
2016-11-03 · diff ↗
3.0.2
2016-06-21 · diff ↗
3.0.1
2016-06-14 · diff ↗
R
R 3.3.0 released · 2016-05-03
3.0
2016-04-15 · diff ↗
2.2
2016-02-13 · diff ↗
2.1.1
2016-01-05 · diff ↗
2.1
2015-12-18 · diff ↗
2.0.1
2015-11-09 · diff ↗
2.0
2015-11-04 · diff ↗
1.0
2015-09-05
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-09-05
Total releases: 20 / 11 yrs
License: GPL (>= 2) OSI
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Anomaly Detection

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pcadapt")

Format

Privé, F., Bazin, E., Blum, M., Duforet-Frebourg, N., & Luu, K. (2025). pcadapt: Fast Principal Component Analysis for Outlier Detection (Version 4.4.1) [Computer software]. https://doi.org/10.32614/CRAN.package.pcadapt

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 pcadapt version 4.4.1 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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