R Observatory: Metrics for PCAmatchR version 0.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PCAmatchR

0.3.3Package record

Match Cases to Controls Based on Genotype Principal Components

0packages depend

3Kdownloads / year

81.0%test coverage

11/13flavors OK

Overview

About

Maintained by Derek W. BrownCRAN page ↗GitHub ↗Issues ↗Declared funder: NCI

Matches cases to controls based on genotype principal components (PC). In order to produce better results, matches are based on the weighted distance of PCs where the weights are equal to the % variance explained by that PC. A weighted Mahalanobis distance metric (Kidd et al. (1987) DOI:10.1016/0031-3203(87)90066-5) is used to determine matches.

Changes in 0.3.3

Change maintainer email address
Add mandatory ‘Maintainer’ field to Description file
Increment version number
Update RoxygenNote version in description file to 7.2.2

From NEWS.md in the release

Install

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

install.packages("PCAmatchR", 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("machiela-lab/PCAmatchR")

Development version from machiela-lab/PCAmatchR. 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-pcamatchr

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-PCAmatchR

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-PCAmatchR

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Derek W. Brown <derek9@gwmail.gwu.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 1.2 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.3

READMEYes · 311 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.3.3Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 5
Examples that run: 80%4 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #16,720 · ~8/day · ~252/mo

Releases R versions

Daily download trend is not available in this view yet.

26230 days

75090 days

3K1 year

Compare downloads with other packages →

Also on71 r2u2 autocran

How downloads are counted

Repository

machiela-lab/pcamatchr ↗Organization: machiela-lab

8Stars

6Forks

2Open issues

0Open PRs

4Releases

181Commits

4Commit identities

181 commits · Last activity 2022-11-29

Responsiveness

not measured

Stars over time

2024-11-04 · 72026-07-07 · 8

How these are measured

PracticesBeta

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

Checks run against github.com/machiela-lab/pcamatchr on 2026-10-18.

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing PCAmatchR adds no packages beyond those that come with R.

Depends (1)

R >= 3.5.0

Imports (0)

none

LinkingTo (0)

none

Suggests (5)

optmatch testthat knitr rmarkdown R.rsp

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)

Derek W. Brown

Author, Maintainer since 0.1.6 (2020)

Mitchel J. Machiela

Author

Timothy A. Myers

Contributor

NCI

Copyright holder, Funder

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.3.3Latest
record
2022-12-01 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.2
record
2022-03-02 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.3.0
record
2021-01-10 · diff ↗
0.2.1
record
2020-08-04 · diff ↗
0.1.6
record
2020-04-24
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-04-24
Total releases: 5 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 376 KB / 3 files
Download size: 836 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("PCAmatchR")

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

It points to 10.1093/bioinformatics/btaa784.

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 PCAmatchR version 0.3.3 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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