R Observatory: Metrics for spAbundance version 0.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

spAbundance

0.2.1Package record

Univariate and Multivariate Spatial Modeling of Species Abundance

1packages depend

8.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jeffrey DoserCRAN page ↗GitHub ↗Website ↗Issues ↗

Fits single-species (univariate) and multi-species (multivariate) non-spatial and spatial abundance models in a Bayesian framework using Markov Chain Monte Carlo (MCMC). Spatial models are fit using Nearest Neighbor Gaussian Processes (NNGPs). Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) doi:10.1080/01621459.2015.1044091 and Finley, Datta, and Banerjee (2022) doi:10.18637/jss.v103.i05. Fits single-species and multi-species spatial and non-spatial versions of generalized linear mixed models (Gaussian, Poisson, Negative Binomial), N-mixture models (Royle 2004 doi:10.1111/j.0006-341X.2004.00142.x) and hierarchical distance sampling models (Royle, Dawson, Bates (2004) doi:10.1890/03-3127). Multi-species spatial models are fit using a spatial factor modeling approach with NNGPs for computational efficiency.

Changes in 0.2.1

Fixed a C++ memory issue in predict.spAbund() that could result in crashes under certain situations.

From NEWS.md in the release

Install

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

install.packages("spAbundance", 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("biodiverse/spAbundance")

Development version from biodiverse/spAbundance. 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-spabundance

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-spAbundance

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-spAbundance

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: 7.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
WARNING12 OK, 1 WARNING2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.1

READMEYes · 1,109 wordsVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · mentions 0.2.1Citation fileYes · cites a publicationWebsiteYes

Description cites a JSS article

Help pages: 82
Examples that run: 100%43 run in a plain check
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 27%

How these are measured

Downloads

8.5K

CRAN downloads in the past year

Rank #3,606 · ~23/day · ~712/mo

Releases R versions

Daily download trend is not available in this view yet.

1K30 days

2.8K90 days

8.5K1 year

Compare downloads with other packages →

Also on428 r2u3 autocran

How downloads are counted

Repository

ecoverseR/spAbundance ↗Organization: ecoverseR

Moved from biodiverse/spabundance.

20Stars

2Forks

1Open issues

0Open PRs

0Releases

105Commits

1Commit identities

License file reads as GPL-3.0 · 105 commits · Last activity 2026-06-29 · Default branch at 0.2.2, ahead of CRAN 0.2.1 (checked 2026-10-22)

Responsiveness

not measured

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/biodiverse/spabundance on 2026-10-22.

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 (1)

README.Rmd

Coverage (1)

Coverage reporting (Codecov)

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing spAbundance adds 14 packages (7 with compiled code, 12 MB of source tarballs). Heaviest: lme4 4.3 MB, nloptr 2.1 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5.0

Imports (8)

statscoda abind RANN lme4 foreach doParallelmethods

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

spOccupancy

How these are counted

Code & Tests

Datasets

People & History

People (2)

Jeffrey Doser

Author, Maintainer since 0.1.0 (2023)

Andrew Finley

Author

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.2.1Latest
record
2024-10-06 · current release · diff ↗
0.2.0
record
2024-09-26 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.3
record
2024-04-08 · diff ↗
0.1.1
record
2024-03-22 · diff ↗
0.1.0
record
2023-10-20
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-10-20
Total releases: 5 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 62 KB / 6 files
Download size: 624 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("spAbundance")

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

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 spAbundance version 0.2.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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