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.org; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.

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acoustic-telemetryanimal-movement-tracking

5.63 score 13 stars 1 dependents 152 scripts

otndo - Understand your OTN data

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

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animal-trackingbiotelemetryfishfisheriesvisualizationquarto

4.43 score 6 stars 1 dependents 6 scripts

rvdat - Lightweight Access to 'VDAT' Shell Commands

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

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4.43 score 1 dependents 15 scripts

TelemetrySpace - Spatial point process and random field models for electronic tagging data

A collection of tools to fit spatial models to several types of telemetry data. Models are provided to account for the detection process when estimating individual centers of activity from acoustic telemetry data and to incorporate data from stationary test transmitters when available. Bayesian versions of models are fitted using Stan (http://mc-stan.org/). Maximum likelihood versions are fitted using Template Model Builder (https://kaskr.github.io/adcomp/index.html).

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cpp

4.30 score 5 stars 6 scripts

TelemetrySpace - Spatial point process and random field models for electronic tagging data

A collection of tools to fit spatial models to several types of telemetry data. Models are provided to account for the detection process when estimating individual centers of activity from acoustic telemetry data and to incorporate data from stationary test transmitters when available. Bayesian versions of models are fitted using Stan (http://mc-stan.org/). Maximum likelihood versions are fitted using Template Model Builder (https://kaskr.github.io/adcomp/index.html).

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cpp

4.26 score 6 scripts

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.

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animal-trackingapiapi-wrapperbiotelemetryfishfisheriesfisheries-researchquarto

4.08 score 4 stars 9 scripts

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/>.

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cpp

4.11 score 20 stars 65 scripts 5 downloads

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

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.

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1.60 score 2 stars 1 scripts