diveMove - Dive Analysis and Calibration

Utilities to represent, visualize, filter, analyse, and summarize time-depth recorder (TDR) data. Miscellaneous functions for handling location data are also provided.

Last updated 8 months ago

animal-behaviorbehavioural-ecologybiologydivingscience

6 stars 4.31 score 82 dependencies

moveHMM - Animal Movement Modelling using Hidden Markov Models

Provides tools for animal movement modelling using hidden Markov models. These include processing of tracking data, fitting hidden Markov models to movement data, visualization of data and fitted model, decoding of the state process, etc. <doi:10.1111/2041-210X.12578>.

Last updated 6 months ago

35 stars 4.23 score 56 dependencies

momentuHMM - Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.

Last updated 2 years ago

40 stars 3.30 score 51 dependencies

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.

Last updated 2 months ago

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

37 stars 2.97 score 90 dependencies

actel - Acoustic Telemetry Data Analysis

Designed for studies where animals tagged with acoustic tags are expected to move through receiver arrays. This package combines the advantages of automatic sorting and checking of animal movements with the possibility for user intervention on tags that deviate from expected behaviour. The three analysis functions (explore(), migration() and residency()) allow the users to analyse their data in a systematic way, making it easy to compare results from different studies. CJS calculations are based on Perry et al. (2012) <https://www.researchgate.net/publication/256443823_Using_mark-recapture_models_to_estimate_survival_from_telemetry_data>.

Last updated 2 months ago

acoustic-telemetryfish-packagestelemetry-data

26 stars 2.62 score 86 dependencies

remora - Rapid Extraction of Marine Observations for Roving Animals

R Package to access and integrate animal tracking data from the IMOS Animal Tracking Facility database and web-app, and environmental data from the AODN database.

Last updated 12 days ago

13 stars 2.00 score 132 dependencies

otndo - Understand your OTN data

This package provides functions to summarize the various type of OTN-style data.

Last updated 2 months ago

animal-trackingbiotelemetryfishfisheriesvisualization

3 stars 1.85 score 102 dependencies 1 dependents

glatos - A package for the Great Lakes Acoustic Telemetry Observation System

Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.

Last updated 5 months ago

9 stars 1.85 score 79 dependencies

yaps - Track Estimation using YAPS (Yet Another Positioning Solver)

Estimate tracks of animals tagged with acoustic transmitters. 'yaps' was introduced in 2017 as a transparent open-source tool to estimate positions of fish (and other aquatic animals) tagged with acoustic transmitters. Based on registrations of acoustic transmitters on hydrophones positioned in a fixed array, 'yaps' enables users to synchronize the collected data (i.e. correcting for drift in the internal clocks of the hydrophones/receivers) and subsequently to estimate tracks of the tagged animals. The paper introducing 'yaps' is available in open access at Baktoft, Gjelland, Økland & Thygesen (2017) <doi:10.1038/s41598-017-14278-z>. Also check out our cookbook with a completely worked through example at Baktoft, Gjelland, Økland, Rehage, Rodemann, Corujo, Viadero & Thygesen (2019) <DOI:10.1101/2019.12.16.877688>. Additional tutorials will eventually make their way onto the project website at <https://baktoft.github.io/yaps/>.

Last updated 10 months ago

17 stars 1.80 score 46 dependencies

movepub - Prepare Movebank Data for Publication

Prepare animal tracking data from 'Movebank' (<https://movebank.org>) for publication in a research repository or the Global Biodiversity Information Facility ('GBIF' <https://www.gbif.org>).

Last updated 18 days ago

oscibio

3 stars 1.58 score 73 dependencies

matos - Interface with the Mid-Atlantic Acoustic Telemetry Observing System (MATOS)

This package provides HTML-scaping functions to interact with the MATOS website (https://matos.asascience.com/), allowing aggregation of data and the downloading and posting of files.

Last updated 4 months ago

animal-trackingapiapi-wrapperbiotelemetryfishfisheriesfisheries-research

3 stars 1.58 score 114 dependencies

RSP - Refined Shortest Paths

The RSP toolkit is a method for analysing the fine scale movements of aquatic animals tracked with passive acoustic telemetry in estuarine environments, that accounts for the surrounding land masses. The animal movements between detections are recreated to have occurred exclusively in water and the utilisation distribution areas are limited by the land contours, providing realistic estimations of space use.

Last updated 8 months ago

13 stars 1.58 score 118 dependencies

rvdat - Lightweight Access to 'VDAT' Shell Commands

Provides lightweight, R-friendly syntax for 'VDAT' shell functions.

Last updated 2 months ago

1.38 score 2 dependencies 1 dependents

mort - Identifying Potential Mortalities and Expelled Tags in Aquatic Acoustic Telemetry Arrays

A toolkit for identifying potential mortalities and expelled tags in aquatic acoustic telemetry arrays. Designed for arrays with non-overlapping receivers.

Last updated 4 days ago

acoustic-telemetryaquaticmortality-estimation

3 stars 1.18 score 5 dependencies

sporeg - A package to reconstruct sporadic passive tracking data and measure the bias and uncertainty incurred through the process

This package is the corresponding code for the Methods in Ecology and Evolution article, "A novel process to infer the reliability of ecological information derived from passive acoustic telemetry track reconstruction". The intended workflow is to simulate tracks inside a specified polygon, calculate quadrat counts inside grid cells, derive passive detection data from the simulated tracks using geolocations of listening stations, reconstruct the tracks using continuous-time correlated random walk models, re-route any spurious track intersections with a specified boundary, calculate quadrat counts of reconstructed tracks within grid cells, and compare quadrat counts between simulated and reconstructed tracks. This process is designed to be iterated to achieve statistical power. The user can then proceed with modeling the relationship between environmental variables and a desirable result (i.e., a good fit) to determine what environmental variables affect the odds of a good fit in grid cells.

Last updated 8 days ago

4 stars 1.08 score 102 dependencies

miscYAPS - Miscellaneous data and helper functions for using YAPS

Provides a bit of data and helper functions for wrapping around the key YAPS functions. The main function is swim_yaps, which will allow you to pass a data.table that is formatted with columns ts, epo, frac, tag, serial to the function. You must have a synchronisation model already available that is named sync_model and a data.table object for the hydrophones and their locations named hydros, as per the YAPS specifications. You should be familiar with YAPS in order to use this package but it will hopefully help make your life easier by looping through YAPS runs N (user specified number) of times and taking the best fit among those runs for each fish day. You will also find some data in the package to help you try.

Last updated 8 months ago

2 stars 0.82 score 57 dependencies

telemetar - Archetypes for Targets and Fish Telemetry

What the package does (one paragraph).

Last updated 7 months ago

0.36 score 44 dependencies