Flexible Occupancy Estimation with Stan.
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.