animovement

An R toolbox for analysing animal movement across space and time

https://github.com/roaldarbol/animovement

Keywords

Repository

An R toolbox for analysing animal movement across space and time

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```


# animovement

[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![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")
```

Owner

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------

cff-version: 1.2.0
message: 'To cite package "animovement" in publications use:'
type: software
license: MIT
title: 'animovement: An R toolbox for analysing animal movement across space and time.'
version: 0.6.0
date-released: 2025-01-03
abstract: An R toolbox for analysing animal movement across space and time.
authors:
- family-names: Roald-Arbøl
  given-names: Mikkel
  email: trackballr.htmc8@passmail.net
  orcid: https://orcid.org/0000-0002-9998-0058
url: http://www.roald-arboel.com/animovement/
contact:
- family-names: Roald-Arbøl
  given-names: Mikkel
  email: trackballr.htmc8@passmail.net
  orcid: https://orcid.org/0000-0002-9998-0058

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