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 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::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/.
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.