Data

Tools

Indexes

Applications

Experiments

Open Source Science

detect

R package for analyzing wildlife data with detection error

https://github.com/psolymos/detect

Science Score: 39.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 21 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.0%) to scientific vocabulary

Keywords from Contributors

ecology estimation lele rsf rspf solymos weighted-distributions progress-bar rstats-package
Last synced: 10 months ago · JSON representation

Repository

R package for analyzing wildlife data with detection error

Basic Info
Statistics
  • Stars: 5
  • Watchers: 3
  • Forks: 2
  • Open Issues: 0
  • Releases: 2
Created over 11 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog

README.md

detect: analyzing wildlife data with detection error

CRAN version CRAN download stats Build status License: GPL v2

The R package implements models to analyze site occupancy and count data models with detection error. The package development was supported by the Alberta Biodiversity Monitoring Institute and the Boreal Avian Modelling (BAM) Project.

Main functions:

  • svocc: single visit occupancy model (Lele et al. 2012, Moreno et al. 2010).
  • svabu: single visit Poisson and Negative Binomial abundance model based on conditional maximum likelihood (Solymos et al. 2012, Denes et al. 2016, Solymos & Lele 2016).
  • cmulti: conditional multinomial maximum likelihood estimation for QPAD approach combining removal and (point count) distance sampling, efficient and flexible setup for varying methodologies (Solymos et al. 2013, Solymos et al. 2018).
  • sqpad: single bin QPAD (SQPAD) approach for robust analysis of point count data (Lele & Solymos 2025).

Versions

Install CRAN release version (recommended):

R install.packages("detect")

Development version:

R install.packages("detect", repos = "https://psolymos.r-universe.dev")

User visible changes in the package are listed in the NEWS file.

Use the issue tracker to report a problem.

References

Denes, F., Solymos, P., Lele, S. R., Silveira, L. & Beissinger, S. 2017. Biome scale signatures of land use change on raptor abundance: insights from single-visit detection-based models. Journal of Applied Ecology, 54, 1268--1278. DOI: 10.1111/1365-2664.12818

Lele, S.R., Moreno, M. and Bayne, E. 2012. Dealing with detection error in site occupancy surveys: What can we do with a single survey? Journal of Plant Ecology, 5(1), 22--31. DOI: 10.1093/jpe/rtr042

Lele, S. R., Solymos, P. 2025. Single bin QPAD (SQPAD) approach for robust analysis of point count data with detection error. Ornithological Applications, xx, xx--xx. (in press)

Moreno, M. and Lele, S. R. 2010. Improved estimation of site occupancy using penalized likelihood. Ecology, 91, 341--346. DOI: 10.1890/09-1073.1

Solymos, P., Lele, S. R. and Bayne, E. 2012. Conditional likelihood approach for analyzing single visit abundance survey data in the presence of zero inflation and detection error. Environmetrics, 23, 197--205. DOI: 10.1002/env.1149

Solymos, P., Matsuoka, S. M., Bayne, E. M., Lele, S. R., Fontaine, P., Cumming, S. G., Stralberg, D., Schmiegelow, F. K. A. & Song, S. J., 2013. Calibrating indices of avian density from non-standardized survey data: making the most of a messy situation. Methods in Ecology and Evolution, 4, 1047--1058. DOI: 10.1111/2041-210X.12106

Solymos, P., Lele, S. R. 2016. Revisiting resource selection probability functions and single-visit methods: clarification and extensions. Methods in Ecology and Evolution, 7, 196--205. DOI: 10.1111/2041-210X.12432

Solymos, P., Matsuoka, S. M., Cumming, S. G., Stralberg, D., Fontaine, P., Schmiegelow, F. K. A., Song, S. J., and Bayne, E. M., 2018. Evaluating time-removal models for estimating availability of boreal birds during point-count surveys: sample size requirements and model complexity. Condor, 120, 765--786. DOI: 10.1650/CONDOR-18-32.1

Supporting info, including a tutorial for the QPAD method.

Owner

  • Name: Peter Solymos
  • Login: psolymos
  • Kind: user
  • Location: Edmonton, Canada

Tech-bio-nerd

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 1
  • Push event: 11
  • Pull request event: 1
  • Fork event: 1
  • Create event: 1
Last Year
  • Issues event: 2
  • Issue comment event: 1
  • Push event: 11
  • Pull request event: 1
  • Fork event: 1
  • Create event: 1

Committers

Last synced: almost 2 years ago

All Time
  • Total Commits: 1,257
  • Total Committers: 3
  • Avg Commits per committer: 419.0
  • Development Distribution Score (DDS): 0.154
Past Year
  • Commits: 4
  • Committers: 1
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
psolymos p****s@e****b 1,064
Peter Solymos p****s@g****m 192
stefan7th s****h@e****b 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 9
  • Total pull requests: 2
  • Average time to close issues: 4 months
  • Average time to close pull requests: 1 minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.78
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: 14 days
  • Average time to close pull requests: less than a minute
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • psolymos (9)
Pull Request Authors
  • psolymos (2)
Top Labels
Issue Labels
bug (2) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 375 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 3
  • Total versions: 14
  • Total maintainers: 1
cran.r-project.org: detect

Analyzing Wildlife Data with Detection Error

  • Versions: 14
  • Dependent Packages: 1
  • Dependent Repositories: 3
  • Downloads: 375 Last month
Rankings
Dependent repos count: 16.5%
Dependent packages count: 18.1%
Forks count: 21.0%
Average: 21.6%
Stargazers count: 22.0%
Downloads: 30.5%
Maintainers (1)
psolymos@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • Formula * depends
  • R >= 2.13.0 depends
  • pbapply * depends
  • stats4 * depends
  • Matrix * imports
  • dclone * suggests
  • dcmle * suggests
.github/workflows/check.yml actions
  • JamesIves/github-pages-deploy-action 4.0.0 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v1 composite