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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# animovement
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://zenodo.org/doi/10.5281/zenodo.13235277)
[](https://github.com/roaldarbol/animovement/actions/workflows/R-CMD-check.yaml)
[](https://roaldarbol.r-universe.dev)
[](https://app.codecov.io/gh/roaldarbol/animovement)
<!-- badges: end -->
*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.
<!-- ## Acknowledgements -->
<!-- *animovement* is all about the data, and we are deeply grateful for all those who have shared data with us to implement and test our code. Thank you! -->
<!-- - [Stan Edwards](): Trackball with optical flow, free. -->
<!-- - [Estelle Moubarak](): Trackball with optical flow, fixed. -->
<!-- - [Maria Cozan](): Treadmill with rotary encoder. -->
<!-- - [Violette Chiara](): AnimalTA -->
## Citation {#citation}
To cite *animovement* in publications use:
```{r}
citation("animovement")
```