R Observatory: Metrics for GGMncv version 2.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GGMncv

2.1.2Package record

Gaussian Graphical Models with Nonconvex Regularization

0packages depend

2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Philippe RastCRAN page ↗GitHub ↗Issues ↗

Estimate Gaussian graphical models with nonconvex penalties, including methods described by Williams (2020) doi:10.31234/osf.io/ad57p. Penalties include atan (Wang and Zhu, 2016) doi:10.1155/2016/6495417, seamless L0 (Dicker, Huang and Lin, 2013) doi:10.5705/ss.2011.074, exponential (Wang, Fan and Zhu, 2018) doi:10.1007/s10463-016-0588-3, smooth integration of counting and absolute deviation (Lv and Fan, 2009) doi:10.1214/09-AOS683, logarithm (Mazumder, Friedman and Hastie, 2011) doi:10.1198/jasa.2011.tm09738, Lq, smoothly clipped absolute deviation (Fan and Li, 2001) doi:10.1198/016214501753382273, and minimax concave penalty (Zhang, 2010) doi:10.1214/09-AOS729. The package also provides extensions for variable inclusion probabilities, multiple regression coefficients, and statistical inference (Janková and van de Geer, 2015) doi:10.1214/15-EJS1031.

Install

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

install.packages("GGMncv", 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("rast-lab/GGMncv")

Development version from rast-lab/GGMncv. 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-ggmncv

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-GGMncv

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-GGMncv

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: 4.4 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK6 OK2026-05-05

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.2

READMEYes · 3,148 wordsVignettesYes · 5 · dynamicNEWSYes · 67% structured · does not mention 2.1.2Citation fileNo

Help pages: 30includes a package overview page
Examples that run: 48%11 run in a plain check · 12 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 57% with a bibliography file

Vignettes (5)

Custom Network Comparison Tests HTML
High Dimensional Data: Must Read!! HTML
NCT: CPU Time HTML
NCT: Null Distributions HTML
Positive Manifold (Sign Restriction) HTML

How these are measured

Downloads

2K

CRAN downloads in the past year

Rank #10,509 · ~5/day · ~163/mo

Releases R versions

Daily download trend is not available in this view yet.

39830 days

96690 days

2K1 year

Compare downloads with other packages →

Also on377 r2u8 autocran

How downloads are counted

Repository

rast-lab/ggmncv ↗Organization: rast-lab

2Stars

0Forks

0Open issues

0Open PRs

0Releases

236Commits

2Commit identities

License file reads as GPL-2.0 · 236 commits · Last activity 2026-04-29 · 0% stars, 30d · The default branch showed an older version (2.1.1.9000) than CRAN on 2026-10-11

Responsiveness

not measured

Stars over time

2026-05-05 · 12026-07-07 · 2

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/rast-lab/ggmncv on 2026-10-11.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (2)

README.Rmdpkgdown

CRAN release process (1)

cran-comments.md

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing GGMncv adds 51 packages (23 with compiled code, 43 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, patchwork 3.2 MB.

Depends (1)

R >= 4.0.0

Imports (16)

Rcpp Rdpack reshape GGally (>= 1.4.0)ggplot2 glassoFast network (>= 1.15)numDeriv mathjaxr MASS (>= 7.3-51.5)methodsparallelpbapply snastatsutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (9)

car corpcor corrplot dplyr NetworkToolbox NetworkComparisonTest nlshrink rmarkdown knitr

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)

Philippe Rast

Maintainer since 2.1.2 (2026) · added in 2.1.2

Donald Williams

Author

Previously maintained by Donald Williams (1.0.0 to 2.1.1).

Releases (6)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-05-04
2.1.2Latest
record
2026-05-04 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-06-12
issues were not corrected despite reminders
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
2.1.1
record
2021-12-15 · diff ↗
2.1.0
record
2021-12-14 · diff ↗ ·
removed 1 export
ggm_compare

added 10 exports
compare_edges, confirm_edges, gen_net, get_graph, kl_mvn, ledoit_wolf, mle_known_graph, nct, score_binary, significance_test
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2020-11-16
2.0.0
record
2020-11-16 · diff ↗ ·
removed 1 export
GGMncv

added 4 exports
boot_eip, ggmncv, penalty_derivative, penalty_function
archivedRemoved from CRAN
2020-10-20
problems were not corrected in time
1.1.0
record
2020-07-11 · diff ↗ ·
added 3 exports
desparsify, ggm_compare, inference
1.0.0
record
2020-07-06

Show 1 earlier eventHide 1 earlier event

R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-06
Total releases: 6 / 6 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.0.0
Bundled data: 140 KB / 3 files
Download size: 1.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GGMncv")

Format

Rast, P., & Williams, D. (2026). GGMncv: Gaussian Graphical Models with Nonconvex Regularization (Version 2.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.GGMncv

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 GGMncv version 2.1.2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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