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hSDM

:package: R package for hierarchical Bayesian species distribution models

https://github.com/ghislainv/hsdm

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.5%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

:package: R package for hierarchical Bayesian species distribution models

Basic Info
Statistics
  • Stars: 9
  • Watchers: 3
  • Forks: 1
  • Open Issues: 10
  • Releases: 0
Created over 10 years ago · Last pushed almost 3 years ago
Metadata Files
Readme Contributing Code of conduct

README.md

hSDM R Package

R-CMD-check CRAN Status DOI Downloads

hSDM is an R package for estimating parameters of hierarchical Bayesian species distribution models. 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.

Installation

Install the latest stable version of hSDM from CRAN with:

r install.packages("hSDM")

Or install the development version of hSDM from GitHub with:

r devtools::install_github("ghislainv/hSDM")

Vignettes and manual

In the wild

Contributing

The hSDM R package is Open Source and released under the GNU GPL version 3 license. Anybody who is interested can contribute to the package development following our Contributing guide. Every contributor must agree to follow the project's Code of conduct.

References

Diez J. M. and Pulliam H. R. 2007. Hierarchical analysis of species distributions and abundance across environmental gradients. Ecology. 88(12): 3144-3152.

Gelfand A. E., Silander J. A., Wu S. S., Latimer A., Lewis P. O., Rebelo A. G. and Holder M. 2006. Explaining species distribution patterns through hierarchical modeling. Bayesian Analysis. 1(1): 41-92.

Latimer, A. M.; Wu, S. S.; Gelfand, A. E. & Silander, J. A. 2006. Building statistical models to analyze species distributions. Ecological Applications. 16(1): 33-50.

MacKenzie, D. I.; Nichols, J. D.; Lachman, G. B.; Droege, S.; Andrew Royle, J. and Langtimm, C. A. 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology. 83: 2248-2255.

Royle, J. A. 2004. N-mixture models for estimating population size from spatially replicated counts. Biometrics. 60: 108-115.

Owner

  • Name: Ghislain Vieilledent
  • Login: ghislainv
  • Kind: user
  • Location: Pacific / Noumea
  • Company: Cirad

Researcher in ecology and applied statistics at Cirad

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 136
  • Total Committers: 2
  • Avg Commits per committer: 68.0
  • Development Distribution Score (DDS): 0.331
Past Year
  • Commits: 21
  • Committers: 1
  • Avg Commits per committer: 21.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Ghislain Vieilledent g****t@c****r 91
ghislainv q****l@g****m 45
Committer Domains (Top 20 + Academic)
cirad.fr: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 13
  • Total pull requests: 0
  • Average time to close issues: over 1 year
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 0
  • Average comments per issue: 0.31
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ghislainv (11)
  • Bgy1sae (1)
  • jabiologo (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 379 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
cran.r-project.org: hSDM

Hierarchical Bayesian Species Distribution Models

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 379 Last month
Rankings
Stargazers count: 19.8%
Forks count: 28.8%
Dependent packages count: 29.8%
Average: 34.3%
Dependent repos count: 35.5%
Downloads: 57.8%
Maintainers (1)
ghislain.vieilledent@cirad.fr
Last synced: 11 months ago

Dependencies

.github/workflows/check-standard.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • coda * imports
  • bookdown * suggests
  • knitr * suggests
  • raster * suggests
  • rmarkdown * suggests
  • sp * suggests