No packages match

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

animal-movementhidden-markov-modelhmmmovement-ecologyopenblascpp

8.90 score 44 stars 151 scripts 864 downloads

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

animal-movementhidden-markov-modelhmmtelemetry-datatime-series-analysisopenblascpp

8.48 score 55 stars 302 scripts 851 downloads

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

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

8.07 score 50 stars 1 dependents 81 scripts

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.

Last updated

acoustic-telemetryanimal-movement-tracking

6.62 score 17 stars 1 dependents 202 scripts

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

6.25 score 19 stars 26 scripts

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

animal-behaviorbehavioural-ecologybiologydivingscience

6.07 score 6 stars 32 scripts 1.2k downloads

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

acoustic-telemetryfish-packagestelemetry-data

6.05 score 28 stars 20 scripts 689 downloads

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

acoustic-telemetryaquaticmortality-estimation

5.51 score 4 stars 23 scripts 222 downloads

otndo - Understand your OTN data

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

Last updated

animal-trackingbiotelemetryfishfisheriesvisualizationquarto

5.36 score 7 stars 2 dependents 12 scripts

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).

Last updated

5.11 score 2 stars 6 scripts

movepub - Prepare Movebank Data for Publication

Prepare animal tracking data from 'Movebank' (<https://www.movebank.org/>) for publication in a research repository. With 'movepub' you can document data with metadata following the Data Package standard and transform these to Darwin Core and Ecological Metadata Language ('EML') for publication to the Global Biodiversity Information Facility ('GBIF') and the Ocean Biodiversity Information System ('OBIS').

Last updated

animal-movementanimal-trackingbiologgingoscibio

5.08 score 5 stars 6 scripts

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

5.00 score 20 stars 20 scripts 366 downloads

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).

Last updated

onetbbcpp

4.22 score 11 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/>.

Last updated

cpp

4.16 score 21 stars 69 scripts 16 downloads

pathroutr - An R Package for (Re-)Routing Paths Around Barriers

The `pathroutr` package aims to provide a set of tools for routing marine animal tracks around land barriers based on the shortest path through a visibility graph network. The foundation of the package is a graph network created from a Delaunay Triangle mesh created from the vertices of land polygons within the study area. Any network edges that cross or fall completely within the land (barrier) polygons are removed.

Last updated

4.08 score 1 dependents 20 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.

Last updated

animal-trackingapiapi-wrapperbiotelemetryfishfisheriesfisheries-researchquarto

3.78 score 4 stars 9 scripts

surimi - Convert Acoustic Telemetry Data Between Institutional Formats

Surimi takes as input data files representing acoustic telemetry, which may have column names and structures specific to particular institutions. It can convert, with minimal code on the user's part, data from one format to another, allowing data from one institution to be easily used across software packages that may expect different formats.

Last updated

3.54 score 7 stars 4 scripts

rvdat - Lightweight Access to 'VDAT' Shell Commands

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

Last updated

3.48 score 15 scripts

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

3.01 score 7 stars 29 scripts

kaltoa - Kalman filtered time-of-arrival positioning

State-space models for time-of-arrival positioning in underwater acoustic telemetry arrays.

Last updated

cpp

2.65 score

wcUtils - Utilities to Access the Wildlife Computers Data Portal API

This package provides basic access and capabilities for interacting with and downloading data from the Wildilfe Computers Data Portal API. Where appropriate functions to specify data types and tidy the data are employed.

Last updated

animal-trackingbiologging

2.54 score 7 stars 7 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.

Last updated

1.60 score 2 stars 1 scripts