foieGras: Fit Continuous-Time State-Space and Latent Variable Models for Filtering Argos Satellite (and Other) Telemetry Data and Estimating Movement Behaviour

Fits continuous-time random walk and correlated random walk state-space models to filter animal tracking data ('Argos', processed light-level 'geolocation', 'GPS'). Template Model Builder ('TMB') is used for fast estimation. The 'Argos' data can be: (older) least squares-based locations; (newer) Kalman filter-based locations with error ellipse information; or a mixture of both. The models estimate two sets of location states corresponding to: 1) each observation, which are (usually) irregularly timed; and 2) user-specified time intervals (regular or irregular). Latent variable models are provided to estimate move persistence along tracks as an index of behaviour. 'Jonsen I', 'McMahon CR', 'Patterson TA', 'Auger-Methe M', 'Harcourt R', 'Hindell MA', 'Bestley S' (2019) Movement responses to environment: fast inference of variation among southern elephant seals with a mixed effects model. Ecology 100:e02566 <doi:10.1002/ecy.2566>.

Version: 0.4.0
Depends: R (≥ 3.5.0)
Imports: dplyr (≥ 0.8.0), tibble (≥ 2.1.3), argosfilter, ggplot2 (≥ 3.0.0), gridExtra, lubridate, TMB (≥ 1.7.15), sf (≥ 0.8-0), stringr, tidyr, future (≥ 1.13.0), furrr (≥ 0.1.0), rworldmap, parallel
LinkingTo: TMB (≥ 1.7.15), RcppEigen
Suggests: testthat, covr, knitr, rmarkdown, units, rgeos
Published: 2019-10-07
Author: Ian Jonsen [aut, cre], Toby Patterson [aut, ctb]
Maintainer: Ian Jonsen <ian.jonsen at>
License: MIT + file LICENSE
NeedsCompilation: yes
SystemRequirements: C++11, GDAL (>= 2.4.2), GEOS (>= 3.7.0), PROJ (>= 5.2.0)
Materials: README NEWS
In views: SpatioTemporal
CRAN checks: foieGras results


Reference manual: foieGras.pdf
Vignettes: foieGras-basics
Package source: foieGras_0.4.0.tar.gz
Windows binaries: r-devel:, r-devel-gcc8:, r-release:, r-oldrel:
OS X binaries: r-release: foieGras_0.4.0.tgz, r-oldrel: foieGras_0.4.0.tgz
Old sources: foieGras archive


Please use the canonical form to link to this page.