R Observatory: Metrics for ubms version 1.2.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ubms

1.2.9Package record

Bayesian Models for Data from Unmarked Animals using 'Stan'

0packages dependsuggested by 1

7.9Kdownloads / year

80.5%test coverage

8/13flavors OK

Overview

About

Maintained by Ken KellnerCRAN page ↗GitHub ↗Website ↗Issues ↗

Fit Bayesian hierarchical models of animal abundance and occurrence via the 'rstan' package, the R interface to the 'Stan' C++ library. Supported models include single-season occupancy, dynamic occupancy, and N-mixture abundance models. Covariates on model parameters are specified using a formula-based interface similar to package 'unmarked', while also allowing for estimation of random slope and intercept terms. References: Carpenter et al. (2017) doi:10.18637/jss.v076.i01; Fiske and Chandler (2011) doi:10.18637/jss.v043.i10.

Changes in 1.2.9

Updated compatibility with upcoming changes to loo_compare() output structure in the loo package (> 2.9.0), which now returns a data frame instead of a matrix and includes additional diagnostic columns.

From NEWS.md in the release

Install

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

install.packages("ubms", 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("ecoverseR/ubms")

Development version from ecoverseR/ubms. 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-ubms

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-ubms

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-ubms

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

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  ubms/tests/testthat/test_submodel.R (.Dim: 12, .Dimnames: 12)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.

CRAN check page ↗

Slowest check: 22.4 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTE2026-07-29
ERROR8 OK, 4 NOTE, 1 ERROR2026-07-27
NOTE11 OK, 2 NOTE2026-07-16
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08

Show 5 earlier changesHide 5 earlier changes

OK12 OK2026-04-25
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-23
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.9

README· In the repository, left out of the releaseVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 1.2.9Citation fileYes · cites a publicationWebsiteYes · pkgdown

Description cites a JSS article

Help pages: 43includes a package overview page
Examples that run: 22%2 run in a plain check · 7 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 64%
Documented parameters: 100%
Return-value docs: 93%
Help pages citing references: 26%

Vignettes (4)

How these are measured

Downloads

7.9K

CRAN downloads in the past year

Rank #4,935 · ~22/day · ~657/mo

Releases R versions

Daily download trend is not available in this view yet.

59030 days

1.7K90 days

7.9K1 year

Compare downloads with other packages →

Also on386 r2u4 autocran

How downloads are counted

Repository

ecoverser/ubms ↗Organization: ecoverseR

39Stars

11Forks

3Open issues

1Open PRs

8Releases

340Commits

6Commit identities

stanoccupancyhierarchical-modelsn-mixture-modeldistance-samplingr

License file reads as GPL-3.0 · 340 commits · Last activity 2026-04-22 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 11
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-04-03 · 372026-08-25 · 39

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/ecoverser/ubms on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (2)

pkgdown

GitHub Pages site last deployed 2025-08-25

Coverage (2)

Coverage reporting.covrignore

Reproducibility and dev environment (1)

Makefile

Show all practicesHide 1 practice

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing ubms adds 56 packages (27 with compiled code, 48 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, loo 2.7 MB.

Depends (2)

R >= 3.4.0unmarked

Imports (13)

ggplot2 gridExtra looMatrixmethodspbapply Rcpp reformulas rlang RSpectra rstan rstantoolsstats

LinkingTo (7)

BH Rcpp RcppArmadillo (>= 0.9.300.2.0)RcppEigen rstan StanHeaders RcppParallel

Suggests (5)

knitr raster rmarkdown terra testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

camtrapR

How these are counted

Code & Tests

People & History

People (1)

Ken Kellner

Maintainer since 1.0.1 (2021), Author

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.9Latest
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2026-04-22 · current release · diff ↗
1.2.8
record
2025-09-29 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.2.7
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2024-10-01 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.6
record
2023-09-11 · diff ↗
1.2.5
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2023-08-21 · diff ↗
1.2.4
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2023-05-25 · diff ↗
1.2.3
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2023-05-17 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.2
record
2022-11-10 · diff ↗ ·
added 2 exports
extract_log_lik, laplace
R
R 4.2.0 released · 2022-04-22
1.1.0
record
2021-11-30 · diff ↗ ·
added 8 exports
RSR, cauchy, gamma, logistic, normal, plot_spatial, student_t, uniform
R
R 4.1.0 released · 2021-05-18
1.0.2
record
2021-02-02 · diff ↗

Show 2 earlier eventsHide 2 earlier events

1.0.1
record
2021-01-19
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-19
Total releases: 11 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.4.0
Download size: 1.2 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("ubms")

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

It points to 10.1111/2041-210x.13777.

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 ubms version 1.2.9 [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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