animovement

An R toolbox for analysing animal movement across space and time

The primary aim of the animovement package is to provide a unified, standardised workflow for analysing animal movement data in a tidyverse-friendly syntax.

We work actively with the developers of the Python movement package, to reach a similar data standards, workflow and use cases; if you prefer analysing your data in Python, we highly recommend using movement.

Installation

You can install the development version of animovement with:

Type	Source	Command
Development	R-universe	install.packages("animovement", repos = c("https://roaldarbol.r-universe.dev", "https://cloud.r-project.org"))

Once you have installed the package, you can load it with:

library("animovement")

Documentation

Analysis of animal movement follows a similar workflow irrespective of the type of data (e.g. pose estimation, centroid tracking, trackball, treadmill). See our docs to go through the steps, one-by-one:

• Introduction to animovement
• Read trackball data
• Clean tracks
• Calculate kinematics
• Calculate summary statistics

Status

Warning

🏗️ The package is currently in early development and the interface is subject to change. Feel free to play around and provide feedback.

Roadmap

We envision this package to support a unified workflow for most animal movement analysis.

To provide a one-stop solution, we aim to provide reader functions for a variety of data sources:

• Readers for pose estimation
  • DeepLabCut
  • SLEAP
  • Lightning Pose
  • Anipose
• Readers for centroid tracking
  • TRex
  • idtracker.ai
  • AnimalTA
• Readers for trackballs
  • Optical mouse sensors, free configuration
  • Optical mouse sensors, fixed configuration
  • FicTrac

At this point in time, we explicitly plan not to support GPS tracking data, as many other packages already exist for this purpose.

Contribute

If your favourite type of movement data is not currently supported, we would love to get a sample of your data to support it!

If you enjoy the package, please make sure to cite it. If you find a bug, feel free to open an issue.

Citation

To cite animovement in publications use:

citation("animovement")
#> To cite package 'animovement' in publications use:
#> 
#>   Roald-Arbøl M (2024). "animovement: An R toolbox for analysing animal
#>   movement across space and time."
#>   <http://www.roald-arboel.com/animovement/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Misc{roaldarbol:2024,
#>     title = {animovement: An R toolbox for analysing animal movement across space and time.},
#>     author = {Mikkel Roald-Arbøl},
#>     year = {2024},
#>     url = {http://www.roald-arboel.com/animovement/},
#>     abstract = {An R toolbox for analysing animal movement across space and time.},
#>     version = {0.2.0},
#>   }