R Observatory: Metrics for bigPLScox version 0.8.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bigPLScox

0.8.1Package record

Partial Least Squares for Cox Models with Big Matrices

0packages depend

2.9Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Frederic BertrandCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models for big data. Provides a Partial Least Squares (PLS) algorithm adapted to Cox proportional hazards models that works with 'bigmemory' matrices without loading the entire dataset in memory. Also implements a gradient-descent based solver for Cox proportional hazards models that works directly on 'bigmemory' matrices. Bertrand and Maumy (2023) https://hal.science/hal-05352069, and https://hal.science/hal-05352061 highlighted fitting and cross-validating PLS-based Cox models to censored big data.

Changes in 0.8.1

Fix links in the DESCRIPTION files.

From NEWS.md in the release

Install

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

install.packages("bigPLScox", 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("fbertran/bigPLScox")

Development version from fbertran/bigPLScox. 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-bigplscox

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

Health

CRAN checks

1ERROR12OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64

Package required but not available: ‘survcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 19.0 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR11 OK, 1 NOTE, 2 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.8.1

READMEYes · 1,165 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 0.8.1Citation fileYes · computed when R runs itWebsiteYes · pkgdown

Help pages: 52 (1 internal)includes a package overview page
Examples that run: 80%28 run in a plain check (4 of them under a condition) · 7 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 87%
Documented parameters: 83%
Return-value docs: 100%
Help pages citing references: 60%

Vignettes (3)

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #12,922 · ~8/day · ~245/mo

Releases R versions

Daily download trend is not available in this view yet.

28530 days

87390 days

2.9K1 year

Compare downloads with other packages →

Also on339 r2u

How downloads are counted

Repository

fbertran/bigplscox ↗Account: fbertran

1Stars

0Forks

0Open issues

0Open PRs

0Releases

45Commits

1Commit identities

45 commits · Last activity 2025-11-17 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2025-11-01 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/fbertran/bigplscox 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 (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-11-17

pkgdown site last built 2025-11-15, before release 0.8.1 (2025-11-18)

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing bigPLScox adds 114 packages (62 with compiled code, 100 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, TH.data 8.2 MB. 2 more not on CRAN are not measured.

Depends (1)

R >= 4.0.0

Imports (15)

bigmemory bigalgebra bigSurvSGD caret doParallel foreach kernlabmethodsRcpp risksetROC rms sgPLS survAUC survcompsurvival

LinkingTo (4)

BH Rcpp RcppArmadillo bigmemory

Suggests (7)

bench knitr plsRcox mvtnorm readr rmarkdown testthat

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 (2)

Frederic Bertrand

Maintainer since 0.6.0 (2025), Author

Myriam Maumy-Bertrand

Author

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.8.1Latest
record
2025-11-18 · current release · diff ↗ ·
added 3 exports
big_pls_cox_fast, big_pls_cox_transform, gd_diagnostics
0.6.0
record
2025-11-11
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-11-11
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 176 KB / 4 files
Download size: 711 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bigPLScox")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 bigPLScox version 0.8.1 [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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