Package: flocker 1.0-2

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:Jacob B. Socolar [aut, cre, cph], Simon C. Mills [aut], Paul-Christian Bürkner [ctb]

flocker_1.0-2.tar.gz
flocker_1.0-2.zip(r-4.7)flocker_1.0-2.zip(r-4.6)flocker_1.0-2.zip(r-4.5)
flocker_1.0-2.tgz(r-4.6-any)flocker_1.0-2.tgz(r-4.5-any)
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flocker_1.0-2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flocker/json (API)

# 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/docs site:https://jsocolar.github.io

Datasets:
  • mfd_single - Data for example single-season flocker model

On CRAN:

Conda:

7.36 score 32 stars 36 scripts 257 downloads 18 exports 78 dependencies

Last updated from:b440938938. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK323
source / vignettesOK209
linux-release-x86_64OK315
macos-release-arm64OK210
macos-oldrel-arm64OK239
windows-develOK348
windows-releaseOK335
windows-oldrelOK380
wasm-releaseOK139

Exports:example_flocker_model_singlefitted_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:abindassertthatbackportsbayesplotBHbootbridgesamplingbrmsBrobdingnagcallrcheckmateclicodacodetoolscpp11descdigestdistributionaldplyrfarverfuturefuture.applygenericsggplot2ggridgesglobalsgluegridExtragtableinlineisobandlabelinglatticelifecyclelistenvloomagrittrMASSMatrixmatrixStatsmgcvmvtnormnleqslvnlmenumDerivotelparallellypillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsS7scalesStanHeadersstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr

Advanced brms custom families: occupancy models and the flocker_data format
The problem | Two key tricks: unlooped families and vint terms | The flocker_data format for a single-season model | A note on performance | Even fancier families | The multi-season format | The data augmented format
Rendered fromflocker_format.Rmdusingknitr::rmarkdown

Last update: 2026-06-22
Started: 2023-10-21

Fitting occupancy models with flocker
Terms and definitions | Installation and feedback | Data simulation | Data formatting | Model fitting | The single-season rep-varying model | The single-season rep-constant model | Multi-season models | Data-augmented multi-species models | Post-processing | brms-native post-processing | Fitted values | The posterior occupancy state | Posterior prediction | Model comparison | brms tips and tricks | Priors | Model formulas | Random effects | Nonlinear models | Phylogenetic models | Spatial and autoregressive structures | Measurement error in covariates | Additional fitting arguments
Rendered fromflocker_tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-06-22
Started: 2021-08-21

Nonlinear models in flocker
Parametric nonlinear predictor | Spatially varying coefficients via a Gaussian process
Rendered fromnonlinear_models.Rmdusingknitr::rmarkdown

Last update: 2026-06-22
Started: 2023-10-17

Data-augmented models in flocker
Rendered fromaugmented_models.Rmdusingknitr::rmarkdown

Last update: 2026-02-26
Started: 2023-10-17

Multiseason models in flocker
Multiseason models as HMMs | Emission probabilities | Colonization and extinction | Initial occupancy | Examples
Rendered frommultiseason_models.Rmdusingknitr::rmarkdown

Last update: 2023-12-09
Started: 2023-07-12