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

Fits continuous-time random walk and correlated random walk state-space models for quality control 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. Track simulation functions are provided. 'Jonsen I', 'McMahon CR', 'Patterson TA', 'Auger-Méthé 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: 0.7-6
Depends: R (≥ 3.6.0)
Imports: tibble (≥ 2.1.3), ggplot2 (≥ 3.0.0), lubridate, TMB (≥ 1.7.15), sf (≥ 0.9-4), stringr, tidyr, purrr, dplyr (≥ 1.0.0), trip, assertthat, patchwork, future, furrr, CircStats, mvtnorm, tmvtnorm, parallel, lifecycle
LinkingTo: TMB (≥ 1.7.15), RcppEigen
Suggests: testthat, covr, knitr, rmarkdown, rgeos, rworldmap
Published: 2021-04-26
Author: Ian Jonsen [aut, cre, cph], Toby Patterson [aut, ctb]
Maintainer: Ian Jonsen <ian.jonsen at>
License: MIT + file LICENSE
NeedsCompilation: yes
SystemRequirements: GDAL (>= 2.4.2), GEOS (>= 3.7.0), PROJ (>= 5.2.0), pandoc (>=2.7.3)
Citation: foieGras citation info
Materials: README NEWS
In views: SpatioTemporal, Tracking
CRAN checks: foieGras results


Reference manual: foieGras.pdf
Vignettes: basics
Package source: foieGras_0.7-6.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release: foieGras_0.7-6.tgz, r-oldrel: foieGras_0.7-6.tgz
Old sources: foieGras archive


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