R Observatory: Metrics for clustTMB version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

clustTMB

0.1.0Package record

Spatio-Temporal Finite Mixture Model using 'TMB'

0packages depend

2.7Kdownloads / year

76.0%test coverage

11/13flavors OK

Overview

About

Maintained by Andrea M. HavronCRAN page ↗GitHub ↗Website ↗Issues ↗

Fits a spatio-temporal finite mixture model using 'TMB'. Covariate, spatial and temporal random effects can be incorporated into the gating formula using multinomial logistic regression, the expert formula using a generalized linear mixed model framework, or both.

Changes in 0.1.0

Initial CRAN submission.

From NEWS.md in the release

Install

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

install.packages("clustTMB", 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("Andrea-Havron/clustTMB")

Development version from Andrea-Havron/clustTMB. 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-clusttmb

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-clustTMB

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-clustTMB

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

2ERROR11OK

Check messages

ERRORre-building of vignette outputsr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

r-devel-linux-x86_64-fedora-clang

Error(s) in re-building vignettes:
--- re-building ‘CovarianceStructure.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘CovarianceStructure.Rmd’

--- re-building ‘SpatialExMeuseData.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 28 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
SUMMARY: processing the following file failed:
  ‘SpatialExMeuseData.Rmd’

Error: Vignette re-building failed.
Execution halted

r-devel-linux-x86_64-fedora-gcc

Error(s) in re-building vignettes:
--- re-building ‘CovarianceStructure.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘CovarianceStructure.Rmd’

Warning: elapsed-time limit of 1 hours reached for sub-process
--- re-building ‘SpatialExMeuseData.Rmd’ using rmarkdown
SUMMARY: processing the following file failed:
  ‘SpatialExMeuseData.Rmd’

Error: Vignette re-building failed.
Execution halted

CRAN check page ↗

Slowest check: 97.6 min · r-devel-linux-x86_64-fedora-clang

Status changes

ERROR11 OK, 2 ERRORNow
ERROR10 OK, 2 NOTE, 2 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 163 wordsVignettesYes · 2 · dynamicNEWSYes · 67% structured · mentions 0.1.0Citation fileYes · software entry onlyWebsiteYes · pkgdown

Help pages: 18 (3 internal)
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 90%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #17,208 · ~7/day · ~223/mo

Releases R versions

Daily download trend is not available in this view yet.

27330 days

73390 days

2.7K1 year

Compare downloads with other packages →

Also on368 r2u13 autocran

How downloads are counted

Repository

andrea-havron/clusttmb ↗Account: Andrea-Havron

5Stars

2Forks

6Open issues

2Open PRs

0Releases

370Commits

6Commit identities

370 commits · Last activity 2024-10-09

Responsiveness

How these are sampled

PRs merged (all time): 71%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-11 · 42026-07-07 · 5

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/andrea-havron/clusttmb on 2026-10-11.

Continuous integration (1)

GitHub Actions

Governance and community (1)

Contributing guide

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2024-10-09

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

36 external dependencies (excludes base and recommended)

Installing clustTMB adds 48 packages (33 with compiled code, 61 MB of source tarballs). Heaviest: BH 14 MB, sf 9.3 MB, sp 4.3 MB.

Depends (1)

R >= 4.0.0

Imports (12)

clusterclustMixType fmesher lme4Matrixmclustmethodsreformulas MoEClust sfstatsTMB

LinkingTo (2)

RcppEigen TMB

Suggests (26)

bookdown covr cowplot dplyr FMsmsnReg GGally ggplot2 ggspatial giscoR inlabru kableExtra knitr magrittr MixSim mvnfast mvtnorm palmerpenguins rmarkdown sdmTMB sp spData splancs testthat tidyr tweedie wesanderson

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Andrea M. Havron

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.0Latest
record
2024-10-14 · current release
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-10-14
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Download size: 168 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("clustTMB")

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

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 clustTMB 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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