R Observatory: Metrics for spOccupancy version 0.8.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

spOccupancy

0.8.2Package record

Single-Species, Multi-Species, and Integrated Spatial Occupancy Models

0packages depend

9.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

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

Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) doi:10.1080/01621459.2013.829001. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. 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. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) doi:10.1111/2041-210X.13110. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) doi:10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2 and Dorazio and Royle doi:10.1198/016214505000000015, respectively.

Changes in 0.8.2

Created a new function simFPOcc() that simulates data for the false-positive occupancy model of Chambert et al. (2018).
Fixed multiple bugs in prediction code that led to wrong predictions with specific combinations of non-spatial random effects (#58).
Fixed bug in prediction for NNGP = FALSE and an indexing problem with spMsPGOcc that could lead to scrambled output (#58).
Fixed a variety of small errors in prediction functions that led to function crashes (#58).
Fixed minor defects in multiple simulation functions (#59).

From NEWS.md in the release

Install

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

install.packages("spOccupancy", 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/spOccupancy")

Development version from ecoverseR/spOccupancy. 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-spoccupancy

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-spOccupancy

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-spOccupancy

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: 11.4 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
ERROR12 OK, 1 ERROR2026-06-07

Show 2 earlier changesHide 2 earlier changes

OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.8.2

READMEYes · 1,366 wordsVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · mentions 0.8.2Citation fileYes · cites a publicationWebsiteYes

Description cites a JSS article

Help pages: 120includes a package overview page
Examples that run: 100%63 run in a plain check
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 33%

How these are measured

Downloads

9.8K

CRAN downloads in the past year

Rank #3,214 · ~27/day · ~817/mo

Releases R versions

Daily download trend is not available in this view yet.

1.6K30 days

3.7K90 days

9.8K1 year

Compare downloads with other packages →

Also on600 r2u4 autocran57 c2d4u

How downloads are counted

Repository

ecoverser/spoccupancy ↗Organization: ecoverseR

77Stars

14Forks

4Open issues

0Open PRs

8Releases

260Commits

5Commit identities

License file reads as GPL-3.0 · 260 commits · Last activity 2026-10-07 · +1.3% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 86%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 8

Stars over time

2026-08-21 · 762026-10-16 · 77

Earlier repositories

github.com/biodiverse/spoccupancy · last recorded on 2026-08-16

How these are measured

PracticesBeta

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

Checks run against github.com/ecoverser/spoccupancy 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 (2)

README.Rmdpkgdown

Coverage (1)

Coverage reporting (Codecov)

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing spOccupancy adds 15 packages (8 with compiled code, 13 MB of source tarballs). Heaviest: lme4 4.3 MB, nloptr 2.1 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5.0

Imports (9)

statscoda abind RANN reformulas foreach doParallel spAbundancemethods

LinkingTo (0)

none

Suggests (1)

testthat

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 (3)

Jeffrey Doser

Author, Maintainer since 0.1.2 (2021)

Andrew Finley

Author

Marc Kery

Contributor · added in 0.5.1

Listed in earlier versions (1)

Marc Kéry

no longer listed · 0.4.0 to 0.5.0

Releases (21)

Pick two releases to compare their code metrics.

0.8.2Latest
record
2026-10-07 · current release · diff ↗ ·
added 1 export
simFPOcc
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.8.1
record
2024-12-14 · diff ↗
0.8.0
record
2024-12-14 · diff ↗ ·
added 4 exports
simTIntOcc, tIntPGOcc, stIntPGOcc, svcTIntPGOcc
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2024-04-19
0.7.6
record
2024-04-19 · diff ↗
archivedRemoved from CRAN
2024-04-12
issues were not corrected in time
0.7.3
record
2024-03-28 · diff ↗ ·
added 1 export
updateMCMC
0.7.2
record
2023-11-01 · diff ↗
0.7.1
record
2023-09-01 · diff ↗
0.7.0
record
2023-08-16 · diff ↗ ·
added 5 exports
svcMsPGOcc, stMsPGOcc, svcTMsPGOcc, simTMsOcc, tMsPGOcc
R
R 4.3.0 released · 2023-04-21
0.6.1
record
2023-03-11 · diff ↗
0.6.0
record
2023-03-03 · diff ↗ ·
added 3 exports
simIntMsOcc, intMsPGOcc, postHocLM

Show 13 earlier eventsHide 13 earlier events

0.5.2
record
2022-12-21 · diff ↗
0.5.1
record
2022-12-08 · diff ↗
0.5.0
record
2022-11-16 · diff ↗ ·
added 7 exports
simBinom, svcPGBinom, svcPGOcc, simTBinom, svcTPGBinom, svcTPGOcc, getSVCSamples
0.4.0
record
2022-07-13 · diff ↗ ·
added 3 exports
simTOcc, tPGOcc, stPGOcc
0.3.2
record
2022-05-22 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.1
record
2022-04-13 · diff ↗
0.3.0
record
2022-03-29 · diff ↗ ·
added 4 exports
lfMsPGOcc, sfMsPGOcc, lfJSDM, sfJSDM
0.2.1
record
2022-01-07 · diff ↗
0.2.0
record
2021-12-19 · diff ↗
0.1.3
record
2021-11-25 · diff ↗
0.1.2
record
2021-11-11
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-11-11
Total releases: 21 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 409 KB / 4 files
Download size: 1.2 MB

Appears in task views

Analysis of Ecological and Environmental Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("spOccupancy")

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 spOccupancy version 0.8.2 [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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