flocker

flexible occupancy estimation in R

https://github.com/jsocolar/flocker

Science Score: 49.0%

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Links to: biorxiv.org
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Low similarity (20.8%) to scientific vocabulary

Last synced: 6 months ago · JSON representation

Repository

flexible occupancy estimation in R

Basic Info

Host: GitHub
Owner: jsocolar
License: other
Language: R
Default Branch: main
Homepage:
Size: 30.6 MB

Statistics

Stars: 32
Watchers: 5
Forks: 3
Open Issues: 9
Releases: 0

Created over 4 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog License

flocker: flexible occupancy estimation in R

The flocker R package enables users to fit flexible occupancy models using the extended lme4 formula syntax provided by R package brms. Also included are functions to format data for occupancy modeling and functions for model post-processing, including posterior predictions, the posterior distribution of the latent true occupancy state, and model comparison. flocker is under active development: development priorities include new model types, better integrated functionality for posterior predictive checking, and full cross-validation.

Compared to existing R packages for fitting occupancy models, flocker is substantially more flexible in the variety of models that can be fit, and contains advanced functionality for model comparison and checking.

Getting started

To get started, check out our tutorial vignette, available here and our introductory paper, available here. For installation instructions, see below.

Installation

Install the latest CRAN release of flocker with install.packages("flocker")

Install the current development version of flocker with ```

install.packages("remotes")

remotes::installgithub("jsocolar/flocker") `flocker` requires a working version of either `rstan` or `cmdstan`, which are interfaces to [Stan](https://mc-stan.org/), a state-of-the-art the probabilistic programming language. We recommend using `cmdstan` if possible. To do so, first install R package `cmdstanr` with install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) You must additionally install `cmdstan` itself. We strongly recommend using `cmdstanr` to manage the cmdstan installation: cmdstanr::installcmdstan() ``Bothrstanandcmdstanrequire a working C++ toolchain, which has posed occasional complications for Stan users. [See here](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started) forrstanfocused advice on installing the toolchain, and [see here](https://mc-stan.org/cmdstanr/articles/cmdstanr.html) forcmdstan` focused advice. If you encounter toolchain issues that you are unable to troubleshoot, ask for help at https://discourse.mc-stan.org/.

Bugs, features, contributions

To request a feature or report a bug (much appreciated!) please open an issue at the GitHub repository. To contribute to flocker (very much appreciated!) have a look at existing open issues, or open a new issue to discuss.

Citing flocker

When using flocker, please cite the companion manuscript: * Socolar, J.B. & Mills, S.C. (2023). "Introducing flocker: an R package for flexible occupancy modeling via brms and Stan." https://doi.org/10.1101/2023.10.26.564080

Additionally, please consider citing Stan and R package brms.

AI generated

Owner

Name: Jacob B. Socolar
Login: jsocolar
Kind: user
Company: NCX

Website: jsocolar.github.io
Repositories: 6
Profile: https://github.com/jsocolar

GitHub Events

Total

Issues event: 3
Watch event: 5
Issue comment event: 16
Push event: 20
Pull request event: 2
Fork event: 1
Create event: 2

Last Year

Issues event: 3
Watch event: 5
Issue comment event: 16
Push event: 20
Pull request event: 2
Fork event: 1
Create event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 1
Total pull requests: 1
Average time to close issues: 2 months
Average time to close pull requests: 2 months
Total issue authors: 1
Total pull request authors: 1
Average comments per issue: 6.0
Average comments per pull request: 1.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 1
Average time to close issues: 2 months
Average time to close pull requests: 2 months
Issue authors: 1
Pull request authors: 1
Average comments per issue: 6.0
Average comments per pull request: 1.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

jsocolar (1)
mhollanders (1)
skeyser (1)
jdyen (1)

Pull Request Authors

jsocolar (2)

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Packages

Total packages: 1
Total downloads:
- cran 107 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 1
Total maintainers: 1

cran.r-project.org: flocker

Flexible Occupancy Estimation with Stan

Homepage: https://github.com/jsocolar/flocker
Documentation: http://cran.r-project.org/web/packages/flocker/flocker.pdf
License: BSD_3_clause + file LICENSE
Latest release: 1.0-0
published about 2 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 107 Last month

Rankings

Dependent packages count: 28.2%

Dependent repos count: 36.1%

Average: 49.6%

Downloads: 84.5%

Maintainers (1)

jacob.socolar@gmail.com