R Observatory: Metrics for PMA version 1.2-4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PMA

1.2-4Package record

Penalized Multivariate Analysis

2packages dependsuggested by 3

20.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Balasubramanian NarasimhanCRAN page ↗GitHub ↗Issues ↗

Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis, described in Witten, Tibshirani and Hastie (2009) doi:10.1093/biostatistics/kxp008 and Witten and Tibshirani (2009) Extensions of sparse canonical correlation analysis, with applications to genomic data doi:10.2202/1544-6115.1470.

Install

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

install.packages("PMA", 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("bnaras/PMA")

Development version from bnaras/PMA. 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-pma

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

# 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-PMA

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: 2.8 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2-4

READMEYes · 13 wordsVignettesNoNEWSYes · 100% structured · does not mention 1.2-4Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 11 (1 internal)includes a package overview page
Examples that run: 33%3 run in a plain check · 1 never run · 5 hold no code
Exported functions with examples: 90%
Documented parameters: 99%
Return-value docs: 90%
Help pages citing references: 100% with a bibliography file

How these are measured

Downloads

20.9K

CRAN downloads in the past year

Rank #3,908 · ~57/day · ~1.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

82830 days

2.4K90 days

20.9K1 year

Compare downloads with other packages →

Also on534 r2u4 autocran3K conda_forge1K bioconda43 c2d4u

How downloads are counted

Repository

bnaras/pma ↗Account: bnaras

7Stars

3Forks

10Open issues

0Open PRs

0Releases

19Commits

1Commit identities

19 commits · Last activity 2024-02-06 · The default branch showed an older version (1.2-3) than CRAN on 2026-10-18

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-23 · 72026-07-07 · 7

How these are measured

PracticesBeta

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

Checks run against github.com/bnaras/pma 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)

README.Rmd

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

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

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

Depends (1)

R >= 2.10

Imports (1)

utils

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Suggested by 3

Depends, Imports or LinkingTo, most downloaded first

HMC prinvars

Suggests, most downloaded first

conos ccar3 epca

How these are counted

Code & Tests

People & History

People (4)

Balasubramanian Narasimhan

Maintainer since 1.2-3 (2024), Author · added in 1.0.8

Sam Gross

Author · added in 1.0.4

Rob Tibshirani

Author

Daniela Witten

Author

Previously maintained by Rob Tibshirani (1.0 to 1.2-2).

Releases (18)

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
1.2-4Latest
record
2024-09-03 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2-3
record
2024-02-07 · diff ↗
1.2-2
record
2023-07-20 · diff ↗ ·
added 1 export
download_breast_data
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
R
R 4.0.0 released · 2020-04-24
1.2.1
record
2020-02-03 · diff ↗
unarchivedReturned to CRAN
2020-01-16
1.2
record
2020-01-16 · diff ↗ ·
removed 15 exports
print.MultiCCA, print.MultiCCA.permute, print.SPC.cv, plot.SPC.cv, print.SPC, print.CCA, print.CCA.permute, print.PMDL1FL, print.PMDL1FL.cv, print.PMDL1L1, print.PMDL1L1.cv, plot.PMDL1L1.cv, plot.PMDL1FL.cv, plot.CCA.permute, plot.MultiCCA.permute
R
R 3.6.0 released · 2019-04-26
1.1
record
2019-02-05 · diff ↗ ·
removed 9 exports
cor.xl.LoadData, cor.xl.RunAnalysis, cor.xl.Plot1, cor.xl.Plot2, cor.xl.Plot3, cor.xl.Plot2a, cor.xl.Plot2b, cor.xl.Plot3a, cor.xl.Plot3b
R
R 3.5.0 released · 2018-04-23

Show 26 earlier eventsHide 26 earlier events

orphanedOrphaned by its maintainer
2018-04-20
check problems were not corrected despite multiple notifications Including C++ misuse of = for == and non-registration of S3 methods
1.0.11
record
2018-04-20 · diff ↗
1.0.10
record
2018-04-20 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
1.0.9
record
2013-03-25 · diff ↗ ·
removed 15 exports
print.multicca, print.multiccaperm, print.spccv, plot.spccv, print.spc, print.cca, print.ccaperm, print.pmdl1fl, print.pmdl1flcv, print.pmdl1l1, print.pmdl1l1cv, plot.pmdl1l1cv, plot.pmdl1flcv, plot.ccaperm, plot.multiccaperm

added 15 exports
print.MultiCCA, print.MultiCCA.permute, print.SPC.cv, plot.SPC.cv, print.SPC, print.CCA, print.CCA.permute, print.PMDL1FL, print.PMDL1FL.cv, print.PMDL1L1, print.PMDL1L1.cv, plot.PMDL1L1.cv, plot.PMDL1FL.cv, plot.CCA.permute, plot.MultiCCA.permute
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
1.0.8
record
2011-08-11 · diff ↗
R
R 2.13.0 released · 2011-04-13
1.0.7.1
record
2011-02-06 · diff ↗
R
R 2.12.0 released · 2010-10-15
1.0.7
record
2010-05-16 · diff ↗
1.0.6
record
2010-04-22 · diff ↗
R
R 2.11.0 released · 2010-04-22
1.0.5
record
2009-12-06 · diff ↗
R
R 2.10.0 released · 2009-10-26
1.0.4
record
2009-10-23 · diff ↗ ·
removed 6 exports
print.ccal1fl, print.ccaperml1fl, print.ccaperml1l1, print.ccal1l1, plot.ccaperml1l1, plot.ccaperml1fl

added 17 exports
print.multicca, print.multiccaperm, MultiCCA, MultiCCA.permute, print.cca, print.ccaperm, plot.ccaperm, plot.multiccaperm, cor.xl.LoadData, cor.xl.RunAnalysis, cor.xl.Plot1, cor.xl.Plot2, cor.xl.Plot3, cor.xl.Plot2a, cor.xl.Plot2b, cor.xl.Plot3a, cor.xl.Plot3b
R
R 2.9.0 released · 2009-04-17
1.0.2
record
2009-04-15 · diff ↗
1.0.1
record
2009-02-16 · diff ↗
1.0
record
2009-02-12
R
R 2.8.0 released · 2008-10-20

Package metadata

First published: 2009-02-12
Total releases: 18 / 17 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Download size: 76 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PMA")

Format

Narasimhan, B., Gross, S., Tibshirani, R., & Witten, D. (2024). PMA: Penalized Multivariate Analysis (Version 1.2-4) [Computer software]. https://doi.org/10.32614/CRAN.package.PMA

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 PMA version 1.2-4 [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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