R Observatory: Metrics for hSDM version 1.4.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hSDM

1.4.4Package record

Hierarchical Bayesian Species Distribution Models

0packages depend

3.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Ghislain VieilledentCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: CIRAD

User-friendly and fast set of functions for estimating parameters of hierarchical Bayesian species distribution models (Latimer and others 2006 doi:10.1890/04-0609). Such models allow interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results.

Changes in 1.4.4

Minor changes to correct an error while checking on CRAN.

From NEWS.md in the release

Install

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

install.packages("hSDM", 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("ghislainv/hSDM")

Development version from ghislainv/hSDM. 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-hsdm

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-hSDM

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-hSDM

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: 5.8 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-10
WARNING12 OK, 1 WARNING2026-05-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.4

READMEYes · 331 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.4.4Citation fileNoWebsiteYes · pkgdown

Help pages: 25includes a package overview page
Examples that run: 6%1 run in a plain check · 16 never run
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 84%

Vignettes (2)

Introduction to hSDM
Publications HTML

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #12,553 · ~10/day · ~298/mo

Releases R versions

Daily download trend is not available in this view yet.

38730 days

89390 days

3.6K1 year

Compare downloads with other packages →

Also on350 r2u8 autocran

How downloads are counted

Repository

ghislainv/hsdm ↗Account: ghislainv

10Stars

1Forks

10Open issues

0Open PRs

5Releases

140Commits

2Commit identities

140 commits · Last activity 2023-09-06

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 311
Median days to close, 50 most recently updated closed PRs: not measured

How these are measured

PracticesBeta

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

Checks run against github.com/ghislainv/hsdm on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (2)

Code of conductContributing guide

Docs source (3)

pkgdown

GitHub Pages site last deployed 2023-09-06 · The repository has a site deploy workflow

pkgdown site last built 2023-09-06

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing hSDM adds 1 package (0 with compiled code, 73 KB of source tarballs). Heaviest: coda 73 KB.

Depends (0)

none

Imports (1)

coda

LinkingTo (0)

none

Suggests (5)

knitr raster sp rmarkdown bookdown

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 (12)

Ghislain Vieilledent

Author, Maintainer since 1.0 (2012)

Matthieu Autier

Contributor · added in 1.4.1

Alan E. Gelfand

Contributor

Jérôme Guélat

Contributor · added in 1.4

Marc Kéry

Contributor · added in 1.4

Andrew M. Latimer

Contributor

Cory Merow

Contributor

Frédéric Mortier

Contributor · added in 1.4

John A. Silander Jr.

Contributor

Show 2 more contributorsHide 2 contributors

Adam M. Wilson

Contributor

Shanshan Wu

Contributor · added in 1.4.1

CIRAD

Copyright holder, Funder · added in 1.4.1

Listed in earlier versions (1)

Frederic Mortier

no longer listed · 1.0

Releases (6)

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
R
R 4.4.0 released · 2024-04-24
1.4.4Latest
record
2023-09-06 · current release · diff ↗
1.4.3
record
2023-08-28 · diff ↗
unarchivedReturned to CRAN
2023-05-25
1.4.2
record
2023-05-25 · diff ↗
archivedRemoved from CRAN
2023-05-05
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.4.1
record
2019-05-13 · diff ↗ ·
added 1 export
hSDM.Nmixture.K
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21

Show 7 earlier eventsHide 7 earlier events

R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
1.4
record
2014-07-02 · diff ↗ ·
removed 2 exports
hSDM.hierarchical.binomial, hSDM.hierarchical.poisson

added 10 exports
hSDM.ZIB, hSDM.ZIB.iCAR, hSDM.ZIB.iCAR.alteration, hSDM.siteocc, hSDM.siteocc.iCAR, hSDM.ZIP, hSDM.ZIP.iCAR, hSDM.ZIP.iCAR.alteration, hSDM.Nmixture, hSDM.Nmixture.iCAR
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
1.0
record
2012-12-04
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-12-04
Total releases: 6 / 14 yrs
License: GPL-3 OSI
Bundled data: 278 KB / 7 files
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hSDM")

Format

Vieilledent, G., CIRAD, Autier, M., Gelfand, A. E., Guélat, J., Kéry, M., Latimer, A. M., Merow, C., Mortier, F., Silander Jr., J. A., Wilson, A. M., & Wu, S. (2023). hSDM: Hierarchical Bayesian Species Distribution Models (Version 1.4.4) [Computer software]. https://doi.org/10.32614/CRAN.package.hSDM

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 hSDM version 1.4.4 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →