Package: flocker 1.0-0
flocker: Flexible Occupancy Estimation with Stan
Fit occupancy models in 'Stan' via 'brms'. The full variety of 'brms' formula-based effects structures are available to use in multiple classes of occupancy model, including single-season models, models with data augmentation for never-observed species, dynamic (multiseason) models with explicit colonization and extinction processes, and dynamic models with autologistic occupancy dynamics. Formulas can be specified for all relevant distributional terms, including detection and one or more of occupancy, colonization, extinction, and autologistic depending on the model type. Several important forms of model post-processing are provided. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Socolar & Mills (2023) <doi:10.1101/2023.10.26.564080>.
Authors:
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flocker.pdf |flocker.html✨
flocker/json (API)
NEWS
| # Install 'flocker' in R: |
| install.packages('flocker', repos = c('https://jsocolar.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jsocolar/flocker/issues
Pkgdown site:https://jsocolar.github.io
- example_flocker_model_single - Example single-season flocker model
Last updated 1 months agofrom:c1c9b1297f. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 25 2025 |
| R-4.5-win | OK | Feb 25 2025 |
| R-4.5-mac | OK | Feb 25 2025 |
| R-4.5-linux | OK | Feb 25 2025 |
| R-4.4-win | OK | Feb 25 2025 |
| R-4.4-mac | OK | Feb 25 2025 |
| R-4.3-win | OK | Feb 25 2025 |
| R-4.3-mac | OK | Feb 25 2025 |
Exports:fitted_flockerflockflocker_stancodeflocker_standataget_flocker_priorget_Zlog_inv_logitlog_lik_flockerlog1m_inv_logitloo_compare_flockerloo_flockermake_flocker_datamake_flocker_data_augmentedmake_flocker_data_dynamicmake_flocker_data_staticpredict_flockersimulate_flocker_data
Dependencies:abindassertthatbackportsbayesplotBHbootbridgesamplingbrmsBrobdingnagcallrcheckmateclicodacodetoolscolorspacedescdigestdistributionaldplyrfansifarverfuturefuture.applygenericsggplot2ggridgesglobalsgluegridExtragtableinlineisobandlabelinglatticelifecyclelistenvloomagrittrMASSMatrixmatrixStatsmgcvmunsellmvtnormnleqslvnlmenumDerivparallellypillarpkgbuildpkgconfigplyrposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyselectutf8vctrsviridisLitewithr
Advanced brms custom families: occupancy models and the flocker_data format
Rendered fromflocker_format.Rmdusingknitr::rmarkdownon Feb 25 2025.Last update: 2024-02-15
Started: 2023-10-21
Data-augmented models in flocker
Rendered fromaugmented_models.Rmdusingknitr::rmarkdownon Feb 25 2025.Last update: 2023-12-11
Started: 2023-10-17
Fitting occupancy models with flocker
Rendered fromflocker_tutorial.Rmdusingknitr::rmarkdownon Feb 25 2025.Last update: 2023-12-11
Started: 2021-08-21
Multiseason models in flocker
Rendered frommultiseason_models.Rmdusingknitr::rmarkdownon Feb 25 2025.Last update: 2023-12-09
Started: 2023-07-12
Nonlinear models in flocker
Rendered fromnonlinear_models.Rmdusingknitr::rmarkdownon Feb 25 2025.Last update: 2023-12-09
Started: 2023-10-17
