R Observatory: Metrics for CJIVE version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CJIVE

0.1.0Package record

Canonical Joint and Individual Variation Explained (CJIVE)

0packages depend

2.7Kdownloads / year

2.3%test coverage

11/13flavors OK

Overview

About

Maintained by Raphiel MurdenCRAN page ↗

Joint and Individual Variation Explained (JIVE) is a method for decomposing multiple datasets obtained on the same subjects into shared structure, structure unique to each dataset, and noise. The two most common implementations are R.JIVE, an iterative approach, and AJIVE, which uses principal angle analysis. JIVE estimates subspaces but interpreting these subspaces can be challenging with AJIVE or R.JIVE. We expand upon insights into AJIVE as a canonical correlation analysis (CCA) of principal component scores. This reformulation, which we call CJIVE, 1) provides an ordering of joint components by the degree of correlation between corresponding canonical variables; 2) uses a computationally efficient permutation test for the number of joint components, which provides a p-value for each component; and 3) can be used to predict subject scores for out-of-sample observations. Please cite the following article when utilizing this package: Murden, R., Zhang, Z., Guo, Y., & Risk, B. (2022) doi:10.3389/fnins.2022.969510.

Install

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

install.packages("CJIVE", 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-cjive

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-CJIVE

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-CJIVE

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: ‘Raphiel Murden <rmurden@emory.edu>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 1.6 min · r-devel-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 0.1.0

READMEYes · 154 wordsVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 22
Examples that run: 100%5 run in a plain check
Exported functions with examples: 23%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #17,362 · ~7/day · ~225/mo

Releases R versions

Daily download trend is not available in this view yet.

30630 days

72990 days

2.7K1 year

Compare downloads with other packages →

Also on79 r2u14 autocran

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing CJIVE adds 35 packages (21 with compiled code, 45 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, gplots 4.6 MB.

Depends (0)

none

Imports (6)

rootSolve ggplot2 reshape2 fields gplots psych

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Raphiel Murden

Author, Maintainer since 0.1.0 (2023)

Benjamin Risk

Author

Releases (1)

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
0.1.0Latest
record
2023-01-20 · current release
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-20
Total releases: 1 / 3 yrs
License: MIT + file LICENSE OSI
Download size: 25 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("CJIVE")

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

It points to 10.3389/fnins.2022.969510.

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 CJIVE version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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