Package: aniMotum 1.2-17

Ian Jonsen

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

Fits continuous-time random walk, correlated random walk and move persistence state-space models for location estimation and behavioural inference from animal tracking data ('Argos', processed light-level 'geolocation', 'GPS'). Template Model Builder ('TMB') is used for fast random-effects 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). A track re-routing function is provided to adjust location estimates for known movement barriers. Track simulation functions are provided. Latent variable models are also provided to estimate move persistence from track data not requiring state-space model filtering.

Authors:Ian Jonsen [aut, cre, cph], W. James Grecian [aut, ctb], Toby Patterson [aut, ctb]

aniMotum_1.2-17.tar.gz
aniMotum_1.2-17.zip(r-4.7)aniMotum_1.2-17.zip(r-4.6)aniMotum_1.2-17.zip(r-4.5)
aniMotum_1.2-17.tgz(r-4.6-x86_64)aniMotum_1.2-17.tgz(r-4.6-arm64)aniMotum_1.2-17.tgz(r-4.5-x86_64)aniMotum_1.2-17.tgz(r-4.5-arm64)
aniMotum_1.2-17.tar.gz(r-4.7-arm64)aniMotum_1.2-17.tar.gz(r-4.7-x86_64)aniMotum_1.2-17.tar.gz(r-4.6-arm64)aniMotum_1.2-17.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
aniMotum/json (API)

# Install 'aniMotum' in R:
install.packages('aniMotum', repos = c('https://benjaminhlina.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ianjonsen/animotum/issues

Pkgdown/docs site:https://ianjonsen.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ellie - Southern elephant seal Argos satellite data
  • sese - Southern elephant seal Argos satellite data
  • sese2 - Southern elephant seal Argos satellite data
  • sese2_n - Southern elephant seal Argos satellite data
  • wese_sb - Weddell seal Argos satellite data

On CRAN:

Conda:

animal-movementanimal-trackingrandom-effects-modelstate-space-modelstmbcpp

8.00 score 49 stars 1 packages 65 scripts 20 exports 87 dependencies

Last updated from:ceb8bc8650. Checks:11 NOTE, 1 OK, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE437
linux-devel-x86_64NOTE629
source / vignettesOK445
linux-release-arm64NOTE402
linux-release-x86_64NOTE441
macos-release-arm64NOTE281
macos-release-x86_64NOTE904
macos-oldrel-arm64NOTE260
macos-oldrel-x86_64NOTE885
windows-develNOTE487
windows-releaseNOTE488
windows-oldrelNOTE511
wasm-releaseFAIL230

Exports:aes_lstemffit_mpmfit_ssmfmapformat_datagrabjoinmapmpm_controlosarroute_pathsimsim_filtersim_fitsim_postsimilarity_flagsimilarity_varsmru_hauloutssm_control

Dependencies:abindaskpassbootCircStatsclassclassIntclicpp11crsmetacurlDBIdeldirdplyre1071farvergenericsgeodistgeographiclibggplot2gluegmmgoftestgridExtragtablehttrisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmimemvtnormnlmeopensslpatchworkpillarpkgconfigpolyclipPROJproj4proxypurrrR6rasterRColorBrewerRcppRcppEigenreprojrlangrnaturalearths2S7sandwichscalessfspspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsystensorterratibbletidyrtidyselectTMBtmvtnormtraipsetripunitsutf8vctrsviridisviridisLitewithrwkzoo

Mapping
map() | Map an SSM fit to data, using default settings | Control track components | Change projection
Rendered fromMapping.Rmdusingknitr::rmarkdown

Last update: 2024-02-06
Started: 2022-05-19

Move_persistence_models
Rendered fromMove_persistence_models.Rmdusingknitr::rmarkdown

Last update: 2024-02-06
Started: 2022-05-03

Overview
Disclaimer | Models | Data | Argos Least-Squares (LS) location data | Argos Kalman Filter (KF) location data | GPS location data | Light-level geolocation data | Projected location data | A mixture of location data types | Fitting a model | Custom data formats | Access results | Visualising a model fit | References
Rendered fromOverview.Rmdusingknitr::rmarkdown

Last update: 2024-02-06
Started: 2022-05-19

SSM_fitting
Processing data | Fit an SSM | emf: specifying error multiplication factors | map: fixing model parameters | control: controlling the optimization | References
Rendered fromSSM_fitting.Rmdusingknitr::rmarkdown

Last update: 2024-02-06
Started: 2022-04-26

SSM_validation
References
Rendered fromSSM_validation.Rmdusingknitr::rmarkdown

Last update: 2024-02-06
Started: 2022-04-26

Track_simulation
sim() | Simulate tracks from each of the 3 process models | Plot simulated tracks | Fit SSM to simulated lon,lat locations (with Argos error) | sim_fit() | Simulate tracks from an SSM fit and plot: | Simulate tracks with a potential function to help avoid land: | Simulate central place foraging tracks | sim_filter() | route_path() | Simulate tracks from the posterior of SSM fit(s) - sim_post() | References
Rendered fromTrack_simulation.Rmdusingknitr::rmarkdown

Last update: 2024-02-06
Started: 2022-05-19

Path_rerouting
Example | route_path() | re-route Weddell seal SSM-predicted locations
Rendered fromPath_rerouting.Rmdusingknitr::rmarkdown

Last update: 2022-12-09
Started: 2022-05-19