R Observatory: Metrics for pcadapt version 4.4.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pcadapt

4.4.1Package record

Fast Principal Component Analysis for Outlier Detection

0packages dependsuggested by 2

12.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Florian PrivéCRAN page ↗GitHub ↗Issues ↗

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. 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-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). 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: 4.6 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-02
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.4.1

READMEYes · 177 wordsVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · does not mention 4.4.1Citation fileYes · cites a publication

Help pages: 19 (12 internal)
Examples that run: 25%1 run in a plain check · 3 hold no code
Exported functions with examples: 21%
Documented parameters: 99%
Return-value docs: 21%
Help pages citing references: 0%

How these are measured

Downloads

12.6K

CRAN downloads in the past year

Rank #4,043 · ~35/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

72730 days

2.2K90 days

12.6K1 year

Compare downloads with other packages →

Also on510 r2u4 autocran3.2K conda_forge

How downloads are counted

Repository

bcm-uga/pcadapt ↗Organization: bcm-uga

47Stars

12Forks

3Open issues

8Open PRs

0Releases

368Commits

10Commit identities

368 commits · Last activity 2026-09-08 · +2.2% stars, 30d · Default branch at 4.4.2, ahead of CRAN 4.4.1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 32
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-02 · 422026-10-20 · 47

How these are measured

PracticesBeta

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

Checks run against github.com/bcm-uga/pcadapt on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (1)

GitHub Pages site last deployed 2026-09-08

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 pcadapt adds 40 packages (22 with compiled code, 43 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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

0direct

0indirect

Suggested by 2

Suggests, most downloaded first

bigsnpr tidypopgen

How these are counted

Code & Tests

Datasets

People & History

People (5)

Florian Privé

Author, Maintainer since 4.3.1 (2020) · added in 4.0.0

Michael Blum

Author

Keurcien Luu

Author

Eric Bazin

Contributor · added in 4.0.0

Nicolas Duforet-Frebourg

Contributor · added in 3.0

Previously maintained by Michael Blum (4.0.0 to 4.1.0) and Keurcien Luu (1.0 to 3.0.4).

Listed in earlier versions (1)

Michael G.B. Blum

no longer listed · 2.0 to 3.0.3

Releases (20)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
4.4.1Latest
record
2025-07-25 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
4.4.0
record
2024-09-24 · diff ↗
R
R 4.4.0 released · 2024-04-24
4.3.5
record
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
record
2020-05-05 · diff ↗
R
R 4.0.0 released · 2020-04-24
unarchivedReturned to CRAN
2020-02-28
4.3.1
record
2020-02-28 · diff ↗
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
record
2019-02-27 · diff ↗

Show 24 earlier eventsHide 24 earlier events

unarchivedReturned to CRAN
2018-07-03
4.0.3
record
2018-07-03 · diff ↗
R
R 3.5.0 released · 2018-04-23
archivedRemoved from CRAN
2018-04-14
there are out-of-memory writes
unarchivedReturned to CRAN
2018-04-13
4.0.1
record
2018-04-13 · diff ↗
archivedRemoved from CRAN
2018-04-06
compiled code made illegal writes
unarchivedReturned to CRAN
2018-04-05
4.0.0
record
2018-04-05 · diff ↗ ·
removed 13 exports
compute.pval, convert.line, corpca, cover.to.pool, create.pcadapt, create.pcadapt.pool, get.pool.matrix, manhattan.plotting, neutral.plotting, pvalqq.plotting, sample.geno, score.plotting, scree.plotting

added 8 exports
bed2matrix, hist_plot, manhattan_plot, qq_plot, run.pcadapt, score_plot, scree_plot, writeBed
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
record
2017-01-02 · diff ↗ ·
added 3 exports
cover.to.pool, get.pool.matrix, sample.geno
3.0.3
record
2016-11-03 · diff ↗ ·
added 3 exports
convert.line, create.pcadapt.pool, vcf2pcadapt
3.0.2
record
2016-06-21 · diff ↗
3.0.1
record
2016-06-14 · diff ↗ ·
removed 1 export
read4pcadapt

added 3 exports
get.pc, get.pop.names, read.pcadapt
R
R 3.3.0 released · 2016-05-03
3.0
record
2016-04-15 · diff ↗ ·
removed 11 exports
computeStats, fstCalc, fstGeno, getPopColors, manhattanPlot, neutralDistribution, pval, pvalqqPlot, read.genotype, scoresPlot, screePlot

added 8 exports
compute.pval, create.pcadapt, get.score.color, manhattan.plotting, neutral.plotting, pvalqq.plotting, score.plotting, scree.plotting
2.2
record
2016-02-13 · diff ↗
2.1.1
record
2016-01-05 · diff ↗
2.1
record
2015-12-18 · diff ↗
2.0.1
record
2015-11-09 · diff ↗
2.0
record
2015-11-04 · diff ↗ ·
removed 7 exports
fdrCalc, fdrControl, fdrList, kurtosis, outlier, sdevEstimation, sdevList

added 3 exports
computeStats, fstCalc, fstGeno
1.0
record
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

Appears in task views

Anomaly Detection

Cite

Cite this package

Run in R for the authors' entry:

citation("pcadapt")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/molbev/msaa053.

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 v2026-10-22. 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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