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>.

Version: 1.0-0
Depends: R (≥ 4.1.0)
Imports: abind, assertthat, boot, brms (≥ 2.20.3), loo (≥ 2.0.0), MASS, matrixStats, stats, utils, withr
Suggests: BH (≥ 1.75.0-0), knitr, RcppEigen (≥ 0.3.3.9.3), rmarkdown, rstan (≥ 2.26.0), spelling, testthat (≥ 2.1.0), tibble
Published: 2024-02-05
Author: Jacob B. Socolar [aut, cre, cph], Simon C. Mills [aut], Paul-Christian Bürkner [ctb]
Maintainer: Jacob B. Socolar <jacob.socolar at gmail.com>
BugReports: https://github.com/jsocolar/flocker/issues
License: BSD_3_clause + file LICENSE
URL: https://github.com/jsocolar/flocker, https://jsocolar.github.io/flocker/
NeedsCompilation: no
Language: en-US
Materials: README NEWS
CRAN checks: flocker results

Documentation:

Reference manual: flocker.pdf
Vignettes: Data-augmented models in flocker
Advanced brms custom families: occupancy models and the 'flocker_data' format
Fitting occupancy models with flocker
Multiseason models in flocker
Nonlinear models in flocker

Downloads:

Package source: flocker_1.0-0.tar.gz
Windows binaries: r-prerel: flocker_1.0-0.zip, r-release: flocker_1.0-0.zip, r-oldrel: flocker_1.0-0.zip
macOS binaries: r-prerel (arm64): flocker_1.0-0.tgz, r-release (arm64): flocker_1.0-0.tgz, r-oldrel (arm64): flocker_1.0-0.tgz, r-prerel (x86_64): flocker_1.0-0.tgz, r-release (x86_64): flocker_1.0-0.tgz

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