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ctmm: Continuous-Time Movement Modeling

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The R package ctmm provides functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data. The package implements all major continuous-time models that have been applied to animal movement. In comparison to discrete-time and correlated-random-walk models, continuous-time models are insensitive to sampling schedule and can account for a wider range of autocorrelation structures. Fitted models can be leveraged to estimate home range, interpolate missing data, filter/smooth errors, etc.

Compatibility with Movebank: 

The package uses the Movebank format for importing data into the package and uses the move package to allow download of data directly from Movebank.

Maintained by: 

Chris H. Fleming

How to Obtain: 

The package, user manual, and vignettes can be downloaded from https://cran.r-project.org/web/packages/ctmm/index.html

FollowDem

FollowDem allows users to track positions of animals equipped with a GPS and share their real-time position on a webmapping internet page. It is used by Parc national des Ecrins to follow ibex and share their movements with schools, partners, and tourists: see http://bouquetins.ecrins-parcnational.fr

Compatibility with Movebank: 

The application does not currently access data directly from Movebank. However it should be possible to use the tool with data from Movebank downloaded in csv format.

Maintained by: 

Parc national des Ecrins, France

How to Obtain: 

FollowDem has been published as an open-source application; it is multilingual and generic to be installed in other places and other animals. It can be downloaded, installed and modified freely at https://github.com/PnEcrins/FollowDem.

Animal Tracker

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The Animal Tracker app (available for Android, iPad, and iPhone) allows the public to follow the movements of animals being tracked using live feeds in Movebank. Users can animate recent movements, view information about the research project and individual animals, and contribute images of the animals or their habitat. Any Movebank user who is using live feeds and has their data available to the public can participate by contacting support@movebank.org.

Compatibility with Movebank: 

The app accesses data directly from Movebank.

Maintained by: 
How to Obtain: 

The app can be downloaded from Google Play and the App Store.

trip

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The R package trip provides functions to manipulate spatial data for animal tracking, in particular functions for

  • dealing with outliers, duplicate records, and irregular timestamps
  • working with Argos data
  • calculating trajectory statistics and time spent grids

It is developed by Michael D. Sumner at the Institute for Marine and Antarctic Studies, University of Tasmania and Sebastián Luque at the University of Manitoba.

Compatibility with Movebank: 

The package does not access data directly from Movebank. However, movement data can be downloaded from Movebank in csv format for use in R.

Maintained by: 

Michael D. Sumner

How to Obtain: 

The package, user manual, and vignette can be downloaded from http://cran.r-project.org/web/packages/trip

crawl

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The (C)orrelated (RA)ndom (W)alk (L)ibrary of R functions (crawl package) has functions to fit continuous-time correlated random walk models to animal telemetry data.

It is developed by Devin S. Johnson at NOAA.

Additional resources:
Johnson, D.S., London, J.M., Lea, M-A., and Durban, J.W., 2008, Continuous-time correlated random walk model for animal telemetry data: Ecology 89(5) 1208–1215. doi:10.1890/07-1032.1

Compatibility with Movebank: 

The package does not access data directly from Movebank. However, movement data can be downloaded from Movebank in csv format for use in R.

Maintained by: 

Devin S. Johnson

How to Obtain: 

The package and user manual can be downloaded from http://cran.r-project.org/web/packages/crawl.

Digiroo2

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The R package Digiroo2 can be used to generate null models of the space use of individual animals that exhibit "random" social structure, based on specified home range contours or utilization distributions. Along with observed animal locations, the null models can be used to test hypotheses about whether pairs of animals show attraction or avoidance behaviors. For further analysis, association matrices using these models can be generated using SOCPROG.

Compatibility with Movebank: 

The package does not access data directly from Movebank. However, movement data can be downloaded from Movebank in csv format for use in R.

Maintained by: 

Ross Dwyer

How to Obtain: 

The package and user manual can be downloaded from http://cran.r-project.org/web/packages/Digiroo2.

mkde

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The R package mkde provides functions to compute and visualize movement-based kernel density estimates (MKDEs) for animal utilization distributions in 2 or 3 spatial dimensions. The third Z dimension can represent altitude (for flying animals), elevation (for terrestrial animals), or depth (for aquatic animals). The calculations can incorporate raster layers of elevation or bathymetry.

It was developed by Jeff A. Tracey, James Sheppard, Jun Zhu, Robert Sinkovts, Amit Chourasia, Glenn Lock-
wood, and Robert N. Fisher.

Additional resources:

Compatibility with Movebank: 

The package does not access data directly from Movebank. However, movement data can be downloaded from Movebank in csv format for use in R.

Maintained by: 

Jeff A. Tracey

How to Obtain: 

The package and user manual can be downloaded from http://cran.r-project.org/web/packages/mkde

DCRW and DCRWS state-space models

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This code supports state-space modelling of animal movement data using two models: DCRW (first-difference correlated random walk) and DCRWS (first-difference correlated random walk with switching). These models accomodate complex error structure in tracking data and allow fitting of behavioral models.

Additional resources:

Compatibility with Movebank: 

The package does not interact directly with Movebank. 

Maintained by: 

unknown

How to Obtain: 

The scripts and sample data can be downloaded from http://www.esapubs.org/archive/ecol/E086/156/suppl-1.htm

RNCEP

The R package RNCEP provides functions to retrieve, organize, and visualize weather data from the NCEP/NCAR Reanalysis and NCEP/DOE Reanalysis II weather datasets provided online by the US National Oceanic and Atmospheric Administration (NOAA). Functions allow users to

Compatibility with Movebank: 

The package does not interact directly with Movebank. However, movement data can be downloaded from Movebank in csv format for use with R.

Maintained by: 

Michael U. Kemp

How to Obtain: 

The package and user manual can be downloaded from http://cran.r-project.org/web/packages/RNCEP

tripEstimation

The R package tripEstimation provides data handling and estimation functions for animal movement estimation using data from archival or satellite tags, including code for light-level geolocation. Helper functions are included for making image summaries, binned by time interval, from Markov chain Monte Carlo (MCMC) simulations of point data. It was developed by Michael D. Sumner and Simon Wotherspoon at the University of Tasmania.

Additional resources:

Compatibility with Movebank: 

The package does not interact directly with Movebank. However, Movebank can be used to archive raw light-level data and derived locations as described here, and movement data can be downloaded from Movebank in csv format for use with R.

Maintained by: 

Michael D. Sumner

How to Obtain: 

The package and user manual can be downloaded from http://cran.r-project.org/web/packages/tripEstimation/index.html

adehabitat

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The R package adehabitat provides over 250 functions for the analysis of habitat selection by animals, including functions for

  • habitat selection and ecological niche analysis
  • home range estimation
  • animal trajectory analysis
  • working with raster maps along with trajectory data

The functions are divided into four packages:

Compatibility with Movebank: 

These packages do not access data directly from Movebank. However, movement data can be downloaded from Movebank in csv format for use with R.

Maintained by: 

Clement Calange

Douglas Argos-Filter

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The Douglas Argos-filter (DAF) algorithm flags implausible locations based on user-defined thresholds that allow the algorithm’s performance to be tuned to species’ movement behaviours and study objectives. Users can choose from three filtering methods:

Compatibility with Movebank: 

This algorithm is implemented within Movebank and can be applied to Argos data in Movebank in the Event Editor.

Maintained by: 

David Douglas

How to Obtain: 

Instructions for running the filter in Movebank are at www.movebank.org/node/38. The SAS executable can be downloaded at http://alaska.usgs.gov/science/biology/spatial/douglas.html.

MoveMine

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MoveMine is a program for mining databases of moving objects. It allows users to mine movement data in Movebank using a user-friendly interface for interactive exploration of mining results and flexible tuning of the underlying methods. The program was developed by researchers in the Department of Computer Science at the University of Illinois Urbana-Champaign and the College of Information Sciences and Technology at Pennsylvania State University.

Additional resources:

Compatibility with Movebank: 

This program allows you to directly access data in Movebank for which you have appropriate permissions.

Maintained by: 

Tobias Lei

How to Obtain: 

The program and documentation are available at http://faculty.ist.psu.edu/jessieli/MoveMine.

Acceleration Viewer

The Acceleration Viewer visualizes acceleration and GPS data that were acquired by e-obs and madebytheo tags. In addition, users can manually annotate information, such as behavioral categories, to the acceleration datasets. GPS data can be visualized in a timeline along with acceleration values and linked to a view of the track on a map with satellite imagery.

Compatibility with Movebank: 

This program allows you to directly access acceleration data in Movebank for which you have appropriate permissions.

Maintained by: 
How to Obtain: 

The program and documentation are available at www.movebank.org/node/26108.

move

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The R package move provides functions to access movement data stored in Movebank as well as tools to visualize and statistically analyze animal movement data. It is developed by Bart Kranstauber and Marco Smolla at the Max Planck Institute for Ornithology. Functions allow users to

Compatibility with Movebank: 

This package allows you to directly access data in Movebank for which you have appropriate permissions.

Maintained by: 

Marco Smolla

How to Obtain: 

The package, user guide, and vignettes can be downloaded from http://cran.r-project.org/web/packages/move/index.html

GeoLight

The R package GeoLight provides basic functions for determining location based on geolocator data obtained from light-level loggers (light intensity measurements over time). It was developed by Simeon Lisovski, Simon Wotherspoon, Michael Sumner, Silke Bauer, Tamara Emmenegger and Steffen Hahn at the Swiss Ornithological Institute. Functions allow users to

Compatibility with Movebank: 

The package does not currently access light level data directly from Movebank. Movebank can be used to archive raw light-level data and derived locations as described here.

Maintained by: 

Simeon Lisovski

How to Obtain: 

The package and user guide can be downloaded from http://cran.r-project.org/web/packages/GeoLight/index.html

Vireo

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The software Vireo calculates heart rate from remote recordings using heart rate telemetry. It was co-developed by Isabelle-Anne Bisson, Research Associate at the Smithsonian Institution’s Migratory Bird Center, and electrical engineer, Paul Kelley of NOAA (National Oceanic and Atmospheric Association) and Severn Electronics.

Compatibility with Movebank: 

This program does not access data directly from Movebank. However, heart rate data files can be stored and shared in Movebank.

Maintained by: 

Isabelle-Anne Bisson and Paul Kelley

How to Obtain: 

Please visit www.isabellebisson.com to fill out the form and obtain Vireo files.

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