The goal of bayesmove is to analyze animal movement using a non-parametric Bayesian framework, which addresses a number of limitations of existing segmentation methods and state-space models. This package currently offers two different model frameworks on which to make behavioral inference from animal telemetry data: 1) segment-level behavioral state estimation and 2) observation-level behavioral state estimation.
The model that makes segment-level inference is a two-stage framework that first partitions individual tracks into segments and subsequently clusters these segments into latent behavioral states. This framework allows the analysis of multiple telemetry and biologging data streams, which must first be discretized into a set of bins before they can be analyzed. The model that makes behavioral inference at the observation-level also requires that data streams are first discretized, but then directly clusters these observations together into behavioral states within a single step. While the outcome is similar to that from state-space and hidden Markov models, this observation-level model does not assume an underlying Markov property or use a mechanistic process (e.g., correlated random walk).
This package also includes features to check model convergence based on the log-likelihood for each MCMC iteration. Model output are often returned in a format that is
tidyverse-friendly, which allows for easy visualization using
You can install the latest CRAN release with:
You can install the latest stable version of the package from GitHub with:
# install.packages("remotes") remotes::install_github("joshcullen/bayesmove")
or latest development (unstable) version with:
# install.packages("remotes") remotes::install_github("joshcullen/bayesmove@dev")
If installing from GitHub, ensure that you have a tool installed for compiling C++ code:
For PC’s running Windows, install Rtools if you have not already done so.
For Mac’s, install the Command Line Tools for Xcode by executing
xcode-select --install in the terminal; or you can download the latest version from the URL (free developer registration may be required). A full Xcode install uses up a lot of disk space and is not required.