foieGras

fit latent variable movement models to animal tracking data

Lifecycle: maturing Project Status: Active – The project has reached a stable, usable state and is being actively developed. Coverage status CRAN_Status_Badge CRAN_Downloads CRAN_Downloads DOI

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Build Status

foieGras - fit latent variable movement models to animal tracking data for location quality control and behavioural inference

foieGras is an R package that fits a continuous-time model (RW or CRW) in state-space form to filter Argos (or GLS) satellite location data. Template Model Builder (TMB) is used for fast estimation. Argos data can be either (older) Least Squares-based locations, (newer) Kalman Filter-based locations with error ellipse information, or a mixture of the two. The state-space model estimates two sets of location states: 1) corresponding to each observation, which are usually irregularly timed (fitted states); and 2) corresponding to (usually) regular time intervals specified by the user (predicted states). Locations are returned as both LongLat and on the Mercator projection (units=km). Additional models are provided to infer movement behaviour along the SSM-estimated most-probable track.

Help

Read ?fit_ssm for details and an example of how to use the package or read the vignette in your web-browser for extended details:

browseVignettes(package = "foieGras")

Installation

First, ensure you have R version >= 3.6.0 installed:

R.Version()

From CRAN

foieGras is on CRAN and can be downloaded within R, e.g., install.packages("foieGras") or, more completely: install.packages("foieGras", depedencies = c("Imports","LinkingTo","Suggests"))

From GitHub (source)

On PC’s running Windows, ensure you have installed Rtools

On Mac’s, ensure you have installed Xcode and Xcode developer tools. If installation is needed, make sure you start Xcode after install to ensure final setup of developer tools is completed. Both Xcode and Xcode developer tools can be installed from the Mac App Store

To get the very latest foieGras stable version, you can install from GitHub:

remotes::install_github("ianjonsen/foieGras", dependencies = c("Imports","LinkingTo","Suggests"))

Note: there can be issues getting compilers to work properly, especially on a Mac with OS X 10.13.x or higher. If you encounter install and compile issues, I recommend you consult the excellent information on the glmmTMB GitHub.