Package: aniMotum 1.2-06

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_1.2-06.tar.gz
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aniMotum_1.2-06.tgz(r-4.4-x86_64)aniMotum_1.2-06.tgz(r-4.4-arm64)aniMotum_1.2-06.tgz(r-4.3-x86_64)aniMotum_1.2-06.tgz(r-4.3-arm64)
aniMotum_1.2-06.tar.gz(r-4.5-noble)aniMotum_1.2-06.tar.gz(r-4.4-noble)
aniMotum.pdf |aniMotum.html
aniMotum/json (API)
NEWS

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

Peer review:

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

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:

animal-movementanimal-trackingrandom-effects-modelstate-space-modelstmb

19 exports 38 stars 7.12 score 90 dependencies 50 scripts

Last updated 3 months agofrom:e599da1808. Checks:OK: 4 NOTE: 5. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 30 2024
R-4.5-win-x86_64NOTESep 30 2024
R-4.5-linux-x86_64NOTESep 30 2024
R-4.4-win-x86_64NOTESep 30 2024
R-4.4-mac-x86_64NOTESep 30 2024
R-4.4-mac-aarch64NOTESep 30 2024
R-4.3-win-x86_64OKSep 30 2024
R-4.3-mac-x86_64OKSep 30 2024
R-4.3-mac-aarch64OKSep 30 2024

Exports:aes_lstemffit_mpmfit_ssmfmapformat_datagrabjoinmapmpm_controlosarroute_pathsimsim_filtersim_fitsim_postsimilarity_flagsimilarity_varssm_control

Dependencies:abindaskpassbootCircStatsclassclassIntclicolorspacecpp11crsmetacurlDBIdeldirdplyre1071fansifarvergenericsgeodistgeosphereggplot2gluegmmgoftestgridExtragtablehttrisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellmvtnormnlmeopensslpatchworkpillarpkgconfigpolyclipPROJproj4proxypurrrR6rasterRColorBrewerRcppRcppEigenreprojrlangrnaturalearths2sandwichscalessfspspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsystensorterratibbletidyrtidyselectTMBtmvtnormtraipsetripunitsutf8vctrsviridisviridisLitewithrwkzoo

Mapping

Rendered fromMapping.Rmdusingknitr::rmarkdownon Sep 30 2024.

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

Move_persistence_models

Rendered fromMove_persistence_models.Rmdusingknitr::rmarkdownon Sep 30 2024.

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

Overview

Rendered fromOverview.Rmdusingknitr::rmarkdownon Sep 30 2024.

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

Path_rerouting

Rendered fromPath_rerouting.Rmdusingknitr::rmarkdownon Sep 30 2024.

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

SSM_fitting

Rendered fromSSM_fitting.Rmdusingknitr::rmarkdownon Sep 30 2024.

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

SSM_validation

Rendered fromSSM_validation.Rmdusingknitr::rmarkdownon Sep 30 2024.

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

Track_simulation

Rendered fromTrack_simulation.Rmdusingknitr::rmarkdownon Sep 30 2024.

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