pcadapt: Fast Principal Component Analysis for Outlier Detection

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>.

Version:	4.4.1
Imports:	bigutilsr (≥ 0.3), data.table, ggplot2 (≥ 3.4), magrittr, mmapcharr (≥ 0.3), Rcpp (≥ 0.12.8), RSpectra
LinkingTo:	mmapcharr, Rcpp, rmio
Suggests:	plotly, shiny, spelling, testthat, vcfR
Published:	2025-07-25
DOI:	10.32614/CRAN.package.pcadapt
Author:	Keurcien Luu [aut], Michael Blum [aut], Florian Privé [aut, cre], Eric Bazin [ctb], Nicolas Duforet-Frebourg [ctb]
Maintainer:	Florian Privé <florian.prive.21 at gmail.com>
BugReports:	https://github.com/bcm-uga/pcadapt/issues
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL:	https://github.com/bcm-uga/pcadapt
NeedsCompilation:	yes
Language:	en-US
Citation:	pcadapt citation info
Materials:	README, NEWS
In views:	AnomalyDetection
CRAN checks:	pcadapt results

Documentation:

Reference manual:

pcadapt.html , pcadapt.pdf

Downloads:

Package source:	pcadapt_4.4.1.tar.gz
Windows binaries:	r-devel: pcadapt_4.4.1.zip, r-release: pcadapt_4.4.1.zip, r-oldrel: pcadapt_4.4.1.zip
macOS binaries:	r-release (arm64): pcadapt_4.4.1.tgz, r-oldrel (arm64): pcadapt_4.4.1.tgz, r-release (x86_64): pcadapt_4.4.1.tgz, r-oldrel (x86_64): pcadapt_4.4.1.tgz
Old sources:	pcadapt archive

Reverse dependencies:

Reverse suggests:

bigsnpr

Linking:

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