R Observatory: Metrics for OmicsPLS version 2.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

OmicsPLS

2.1.0Package record

Data Integration with Two-Way Orthogonal Partial Least Squares

1packages depend

4.4Kdownloads / year

87.2%test coverage

13/13flavors OK

Overview

About

Maintained by Said el BouhaddaniCRAN page ↗

Performs the O2PLS data integration method for two datasets, yielding joint and data-specific parts for each dataset. The algorithm automatically switches to a memory-efficient approach to fit O2PLS to high dimensional data. It provides a rigorous and a faster alternative cross-validation method to select the number of components, as well as functions to report proportions of explained variation and to construct plots of the results. See the software article by el Bouhaddani et al (2018) doi:10.1186/s12859-018-2371-3, and Trygg and Wold (2003) doi:10.1002/cem.775. It also performs Sparse Group (Penalized) O2PLS, see Gu et al (2020) doi:10.1186/s12859-021-03958-3 and cross-validation for the degree of sparsity.

Install

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

install.packages("OmicsPLS", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-omicspls

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-OmicsPLS

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-OmicsPLS

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: 3.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-12

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-05-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.0

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 40 (13 internal)includes a package overview page
Examples that run: 100%14 run in a plain check
Exported functions with examples: 34%
Documented parameters: 100%
Return-value docs: 75%
Help pages citing references: 0%

Vignettes (1)

The OmicsPLS R Package HTML

How these are measured

Downloads

4.4K

CRAN downloads in the past year

Rank #6,462 · ~12/day · ~369/mo

Releases R versions

Daily download trend is not available in this view yet.

55730 days

1.3K90 days

4.4K1 year

Compare downloads with other packages →

Also on79 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing OmicsPLS adds 26 packages (13 with compiled code, 16 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

Depends (0)

none

Imports (9)

graphicsstatsdplyr ggplot2parallelmagrittr tibble softImpute withr

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown gplots

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

MMINP

How these are counted

Code & Tests

People & History

People (6)

Said el Bouhaddani

Author, Maintainer since 1.0.1 (2017)

Zander Gu

Author · added in 2.1.0

Jeanine Houwing-Duistermaat

Author

Geurt Jongbloed

Author

Szymon Kielbasa

Author

Hae-Won Uh

Author

Listed in earlier versions (1)

Zhujie Gu

no longer listed · 2.0.2

Releases (7)

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
2.1.0Latest
record
2025-04-01 · current release · diff ↗
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
2.0.2
record
2021-05-19 · diff ↗ ·
added 12 exports
crossval_sparsity, cv_lambda_checker, cv_lambda_checker_group, err_back, impute_matrix, lambda_checker, lambda_checker_group, norm_vec, orth_vec, so2m_group, thresh_n, thresh_n_gr
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.2.0
record
2019-07-24 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.1.0
record
2018-01-22 · diff ↗ ·
added 1 export
scores
1.0.3
record
2017-08-08 · diff ↗
1.0.2
record
2017-07-08 · diff ↗
1.0.1
record
2017-05-09

Show 1 earlier eventHide 1 earlier event

R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-09
Total releases: 7 / 9 yrs
License: GPL-3 OSI
Download size: 188 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("OmicsPLS")

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

It points to 10.1186/s12859-018-2371-3.

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 OmicsPLS version 2.1.0 [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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