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 direct functionality for posterior predictive checking and implementation of dynamic (multiseason) occupancy models and N-mixture models.
Compared to existing R packages for fitting occupancy models,
flocker is substantially more flexible in the variety of single-season models that can be fit, and contains advanced functionality for model comparison and checking.
To get started, check out our tutorial vignette, available here. For installation instructions, see below.
flocker in R 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
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:
If using Rstan, we strongly recommend installing the development version rather than the CRAN version. In a fresh R session, do
# Uncomment the next line if you have previously installed rstan # remove.packages(c("StanHeaders", "rstan")) install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
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.