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https://github.com/roaldarbol/animovement

An R toolbox for analysing animal movement across space and time
https://github.com/roaldarbol/animovement

animal-behaviour animal-movement neuroethology neuroscience rstats

Last synced: 19 days ago
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An R toolbox for analysing animal movement across space and time

Host: GitHub
URL: https://github.com/roaldarbol/animovement
Owner: roaldarbol
License: other
Created: 2024-03-17T15:24:00.000Z (8 months ago)
Default Branch: main
Last Pushed: 2024-10-24T07:23:36.000Z (22 days ago)
Last Synced: 2024-10-25T02:57:34.398Z (21 days ago)
Topics: animal-behaviour, animal-movement, neuroethology, neuroscience, rstats
Language: R
Homepage: http://www.roald-arboel.com/animovement/
Size: 12 MB
Stars: 5
Watchers: 2
Forks: 0
Open Issues: 32
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff

Awesome Lists containing this project

README

        ---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# animovement

[![DOI](https://zenodo.org/badge/773406370.svg)](https://zenodo.org/doi/10.5281/zenodo.13235277)

[![R-CMD-check](https://github.com/roaldarbol/animovement/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/roaldarbol/animovement/actions/workflows/R-CMD-check.yaml)

[![animovement status

badge](https://roaldarbol.r-universe.dev/badges/animovement)](https://roaldarbol.r-universe.dev)

[![Codecov test coverage](https://codecov.io/gh/roaldarbol/animovement/graph/badge.svg)](https://app.codecov.io/gh/roaldarbol/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`](https://movement.neuroinformatics.dev/) package, to reach a similar data standards, workflow and use cases; if you prefer analysing your data in Python, we highly recommend using [`movement`](https://movement.neuroinformatics.dev/).*

## Installation

You can install the development version of *animovement* with:

Type | Source | Command

---|---|-----------------------

Development | R-universe | `install.packages("animovement", repos = "https://roaldarbol.r-universe.dev")`

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

```{r, eval=FALSE}

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`](https://www.roald-arboel.com/animovement/articles/animovement.html)

- [Read trackball data](https://www.roald-arboel.com/animovement/articles/read-trackball.html)

- [Clean tracks](https://www.roald-arboel.com/animovement/articles/clean-tracks.html)

- [Calculate kinematics](https://www.roald-arboel.com/animovement/articles/calculate-kinematics.html)

- [Calculate summary statistics](https://www.roald-arboel.com/animovement/articles/calculate-summary-statistics.html)

## 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](https://deeplabcut.github.io/DeepLabCut/README.html)

  - [SLEAP](https://sleap.ai/)

  - [Lightning Pose](https://lightning-pose.readthedocs.io/en/latest/)

  - [Anipose](https://anipose.readthedocs.io/en/latest/)

- **Readers for centroid tracking**

  - [TRex](https://trex.run/)

  - [idtracker.ai](https://idtracker.ai/latest/)

  - [AnimalTA](http://vchiara.eu/index.php/animalta)

- **Readers for trackballs**

  - Optical mouse sensors, free configuration

  - Optical mouse sensors, fixed configuration

  - [FicTrac](https://github.com/rjdmoore/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](#citation). If you find a bug, feel free to open an issue.

## Citation {#citation}

To cite *animovement* in publications use:

```{r}

citation("animovement")

```