R Observatory: Metrics for glmpca version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

glmpca

0.2.0Package record

Dimension Reduction of Non-Normally Distributed Data

2packages depend

13.2Kdownloads / year

42.0%test coverage

11/13flavors OK

Overview

About

Maintained by F. William TownesCRAN page ↗GitHub ↗Issues ↗

Implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices. Townes FW, Hicks SC, Aryee MJ, Irizarry RA (2019) doi:10.1186/s13059-019-1861-6. Townes FW (2019) arXiv:1907.02647.

Changes in 0.2.0

This release should be backwards-compatible even though some arguments are now deprecated.

Added

AvaGrad optimizer which is faster and more numerically stable than Fisher scoring.
Minibatch methods (memoized and stochastic gradients) to support large sparse Matrices
Automatic tuning of optimization hyperparameters (learning rate or penalty)
Negative binomial likelihood with feature-specific overdispersion parameters
print and predict methods for fitted glmpca object

Changed

more detailed documentation of main glmpca function
split off large blocks of code in the main glmpca function to separate functions
organize results as an S3 class instead of a list
moved arguments penalty and verbose into the ctl parameters list

Show all changes in 0.2.0Hide the rest of the changes in 0.2.0

deprecated family mult and bern, replaced with family binom
control parameter eps has now been renamed tol

From NEWS.md in the release

Install

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

install.packages("glmpca", 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("willtownes/glmpca")

Development version from willtownes/glmpca. 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-glmpca

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-glmpca

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-glmpca

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: ‘F. William Townes <will.townes@gmail.com>’

The Description field contains
  <arXiv:1907.02647>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘glmpca.Rd’:
    https://doi.org/10.1186/s13059-019-1861-6

CRAN check page ↗

Slowest check: 2.5 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 0.2.0

READMEYes · 90 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 2
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 85%
Return-value docs: 100%
Help pages citing references: 50%

Vignettes (1)

Applying GLM-PCA to Data HTML

How these are measured

Downloads

13.2K

CRAN downloads in the past year

Rank #3,459 · ~36/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

1K30 days

3.2K90 days

13.2K1 year

Compare downloads with other packages →

Also on261 r2u4 autocran2.5K conda_forge

How downloads are counted

Repository

willtownes/glmpca ↗Account: willtownes

98Stars

11Forks

19Open issues

0Open PRs

0Releases

68Commits

6Commit identities

License file reads as LGPL-3.0 · 68 commits · Last activity 2024-04-18 · +1% stars, 30d · Default branch at 0.2.0.9000, ahead of CRAN 0.2.0 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 17
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-24 · 952026-10-13 · 98

How these are measured

PracticesBeta

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

Checks run against github.com/willtownes/glmpca on 2026-10-22.

Continuous integration (1)

Travis CI (config file)

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

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

Depends (1)

R >= 3.5

Imports (4)

MASSmethodsstatsutils

LinkingTo (0)

none

Suggests (7)

covr ggplot2 knitr logisticPCA markdownMatrixtestthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Depends, Imports or LinkingTo, most downloaded first

pmartR scpoisson

How these are counted

Code & Tests

People & History

People (3)

F. William Townes

Kelly Street

Author

Jake Yeung

Contributor

Releases (2)

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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.2.0Latest
record
2020-07-18 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.0
record
2019-09-27
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-09-27
Total releases: 2 / 7 yrs
License: LGPL (>= 3) | file LICENSE OSI · relicensed from Artistic-2.0 in 0.2.0
Minimum R: ≥ 3.5
Download size: 163 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("glmpca")

Format

Townes, F. W., Street, K., & Yeung, J. (2020). glmpca: Dimension Reduction of Non-Normally Distributed Data (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.glmpca

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 glmpca version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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