R Observatory: Metrics for gllvm version 2.0.15

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

gllvm

2.0.15Package record

Generalized Linear Latent Variable Models

1packages dependsuggested by 1

11.4Kdownloads / year

33.4%test coverage

13/13flavors OK

Overview

About

Maintained by Jenni NikuCRAN page ↗GitHub ↗Website ↗Issues ↗

Analysis of multivariate data using generalized linear latent variable models (gllvm). Estimation is performed using either the Laplace method, variational approximations, or extended variational approximations, implemented via TMB (Kristensen et al. (2016), doi:10.18637/jss.v070.i05).

Changes in 2.0.15

CRAN update version 2.0.15, see also news for 2.0.14
Ordinal with cloglog link implemented
Parametrization of ordered beta cutoffs changed to cumulative parametrization

Bugfixes

Bug related to NaNs in SigmaB and starting values fixed

From NEWS.md in the release

Install

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

install.packages("gllvm", 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("JenniNiku/gllvm")

Development version from JenniNiku/gllvm. 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-gllvm

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-gllvm

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-gllvm

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: 18.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-09
ERROR12 OK, 1 ERROR2026-06-24
OK13 OK2026-06-09

Show 7 earlier changesHide 7 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-12
WARNING12 OK, 1 WARNING2026-05-11
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-24
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-23
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.15

READMEYes · 592 wordsVignettesYes · 10 · dynamicNEWSYes · 67% structured · mentions 2.0.15Citation fileYes · cites a publicationWebsiteYes · pkgdown

Description cites a JSS article

Help pages: 41
Examples that run: 28%8 run in a plain check · 6 only when donttest examples are enabled (R CMD check --as-cran) · 15 never run
Exported functions with examples: 72%
Documented parameters: 57%
Return-value docs: 41%
Help pages citing references: 34%

Vignettes (10)

How these are measured

Downloads

11.4K

CRAN downloads in the past year

Rank #3,339 · ~31/day · ~950/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

3.3K90 days

11.4K1 year

Compare downloads with other packages →

Also on555 r2u4 autocran79 c2d4u

How downloads are counted

Repository

jenniniku/gllvm ↗Account: JenniNiku

63Stars

24Forks

15Open issues

0Open PRs

6Releases

2,147Commits

12Commit identities

2,147 commits · Last activity 2026-10-20 · 0% stars, 30d · Discussions: 80 posts

Responsiveness

How these are sampled

PRs merged (all time): 86%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 6

Stars over time

2025-09-03 · 602026-09-05 · 63

How these are measured

PracticesBeta

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

Checks run against github.com/jenniniku/gllvm on 2026-10-18.

Docs source (1)

GitHub Pages site last deployed 2026-09-14

Reproducibility and dev environment (1)

data-raw/

Research and citation (1)

CITATION.cff

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing gllvm adds 7 packages (5 with compiled code, 6.5 MB of source tarballs). Heaviest: nloptr 2.1 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB.

Depends (2)

R >= 3.5.0TMB

Imports (7)

MASSMatrixfishModmgcvalabama nloptrmethods

LinkingTo (3)

TMB Rcpp RcppEigen

Suggests (9)

knitr rmarkdown testthat gclus corrplotlatticemvabund apeparallel

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

ResistantProcrustes

Suggests, most downloaded first

ecostats

How these are counted

Code & Tests

Datasets

People & History

People (8)

Jenni Niku

Author, Maintainer since 0.1.0 (2017)

Author

Author

Author

Author · added in 1.4.0

Sara Taskinen

Author

David I. Warton

Author

Bert van der Veen

Author · added in 1.2.3

Releases (24)

Pick two releases to compare their code metrics.

2.0.15Latest
record
2026-09-11 · current release · diff ↗
2.0.13
record
2026-07-09 · diff ↗
2.0.11
record
2026-06-22 · diff ↗ ·
added 1 export
ranef
2.0.10
record
2026-05-10 · diff ↗ ·
added 6 exports
glmmVA, predictPairwise, predictPairwise.gllvm, predictSR, predictSR.gllvm, residuals.predictSR.gllvm
R
R 4.6.0 released · 2026-04-24
2.0.5
record
2025-07-13 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.0.2
record
2025-04-08 · diff ↗ ·
added 1 export
update.gllvm
2.0.1
record
2025-04-01 · diff ↗ ·
added 2 exports
goodnessOfFit, print.VP.gllvm
2.0
record
2024-11-26 · diff ↗ ·
added 13 exports
VP, getEnvironCor, getEnvironCor.gllvm, getEnvironCov, getEnvironCov.gllvm, getLoadings, getLoadings.gllvm, phyloplot, phyloplot.gllvm, plotVP, plotVarPartitioning, varPartitioning, varPartitioning.gllvm
R
R 4.4.0 released · 2024-04-24
1.4.3
record
2023-09-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.4.1
record
2023-01-07 · diff ↗
1.4.0
record
2022-12-17 · diff ↗ ·
removed 3 exports
nobs, predict, vcov

added 2 exports
confint.gllvm, logLik.gllvm
R
R 4.2.0 released · 2022-04-22

Show 18 earlier eventsHide 18 earlier events

1.3.1
record
2021-07-28 · diff ↗ ·
removed 2 exports
gradient.length, gradient.length.gllvm

added 1 export
print.summary.gllvm
R
R 4.1.0 released · 2021-05-18
1.3.0
record
2021-04-30 · diff ↗ ·
added 12 exports
AICc, AICc.gllvm, gradient.length, gradient.length.gllvm, nobs, nobs.gllvm, optima, optima.gllvm, tolerances, tolerances.gllvm, vcov, vcov.gllvm
1.2.3
record
2020-12-11 · diff ↗ ·
added 2 exports
se, se.gllvm
1.2.2
record
2020-05-11 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2.1
record
2020-01-23 · diff ↗
1.2.0
record
2019-12-20 · diff ↗ ·
added 2 exports
randomCoefplot, randomCoefplot.gllvm
1.1.7
record
2019-09-17 · diff ↗
1.1.6
record
2019-08-23 · diff ↗ ·
added 6 exports
getLV, getLV.gllvm, predictLVs, predictLVs.gllvm, simulate, simulate.gllvm
R
R 3.6.0 released · 2019-04-26
1.1.3
record
2019-04-16 · diff ↗ ·
added 6 exports
getPredictErr, getPredictErr.gllvm, getResidualCov, getResidualCov.gllvm, predict, predict.gllvm
1.1.2
record
2019-01-02 · diff ↗
1.1.0
record
2018-11-14 · diff ↗
1.0
record
2018-07-30 · diff ↗ ·
added 3 exports
coefplot, getResidualCor, ordiplot
R
R 3.5.0 released · 2018-04-23
0.1.0
record
2017-12-20
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-12-20
Total releases: 24 / 9 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 178 KB / 6 files
Download size: 3.0 MB

Appears in task views

Analysis of Ecological and Environmental Data Mixed, Multilevel, and Hierarchical Models in R

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("gllvm")

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

The repository also keeps a CITATION.cff.

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 gllvm version 2.0.15 [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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