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 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.
To get started, check out our tutorial vignette, available here and our introductory paper, available here. For installation instructions, see below.
Install the latest CRAN release of flocker with
install.packages("flocker")Install the current development version of flocker
with
# install.packages("remotes")
remotes::install_github("jsocolar/flocker")flocker requires a working version of either
rstan or cmdstan, which are interfaces to Stan, 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::install_cmdstan()Both rstan and cmdstan require a working
C++ toolchain, which has posed occasional complications for Stan users.
See
here for rstan focused advice on installing the
toolchain, and see here
for cmdstan focused advice. If you encounter toolchain
issues that you are unable to troubleshoot, ask for help at
https://discourse.mc-stan.org/.
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.
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.
