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.

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

8.00 score 49 stars 1 dependents 65 scripts

bsam - Bayesian State-Space Models for Animal Movement

Tools to fit Bayesian state-space models to animal tracking data. Models are provided for location filtering, location filtering and behavioural state estimation, and their hierarchical versions. The models are primarily intended for fitting to ARGOS satellite tracking data but options exist to fit to other tracking data types. For Global Positioning System data, consider the 'moveHMM' package. Simplified Markov Chain Monte Carlo convergence diagnostic plotting is provided but users are encouraged to explore tools available in packages such as 'coda' and 'boa'.

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cran-downloadsjagscpp

5.45 score 19 stars 30 scripts 669 downloads

ArgosQC - Quality Control Process for the Integrated Marine Observing System's Argos Location Data

An automated Argos location quality control process for Argos location data from satellite tags. Functions automatically download and collate data from one of several potential remote source: a user-supplied URL, a user-supplied Google Drive link, a user-supplied Dropbox link, the SMRU server, or the Wildlife Computers Portal API. The package matches deployment data with user-supplied deployment metadata; projects location data from lon,lat to a user-supplied projection or a default projection; fits user-specified SSM's in 2 passes to estimate most plausible locations; collates results by species & deployment program; generates diagnostic plots & maps; appends predicted locations at tag-measured event times to the tag manufacturer activity files such as CTD profiles, dive records, haulout records, and the Argos and (when present) GPS location files; saves activity files as .csv in one of several possible schema (IMOS ATF, ATN, User-defined); pushes QC'd files to a user-specified server or saves to a local archive (zipfile).

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4.93 score 1 stars 4 scripts

simfish - simulate fish tracks & acoustic detections

facilitates simulation of fish tracks in featureless and semi-realistic environments (coastal oceans, fjords, and lakes). A user-defined raster defining the water body - land boundaries is used to constrain simulated tracks. Fish movements are simulated (currently) as either a correlated random walk or a biased & correlated random walk, with the bias toward a defined Centre-of-Attraction. A potential function is used to ensure the tracks avoid land. The package can also be used to simulate detections of acoustically-tagged fish by acoustic receivers at user-defined locations.

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2.74 score 11 scripts

mpmm - (Animal) Movement Persistence Mixed-Effects Models

Fit covariates as linear mixed-effects to latent, time-varying movement persistence (autocorrelation).

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tmb-projectcpp

2.40 score 5 stars 6 scripts