packages.Rmd

---
title: "R packages"
description: |
  We turn the methods we develop into R packages.
---

<script src="js/for_toc.js"></script>

Here we list our main contributions. 

We also contribute to many other R packages, but our contributions are not as crucial or the projects are small and experiemental.
For more details, you can check our GitHub pages:

- [<i class='fa fa-github'></i> Alexandre Courtiol](https://github.com/courtiol)
- [<i class='fa fa-github'></i> Liam Bailey](https://github.com/LiamDBailey)

## Open source

### For natural scientists {#main_packages}

- {climwin} [<i class='fa fa-github'></i>](https://github.com/LiamDBailey/climwin) [<i class='fab fa-r-project'></i>](https://cran.r-project.org/web/packages/climwin/index.html) is a package designed to detect and visualise periods of climate sensitivity (climate windows) for a given biological response. Created and maintained by Liam.
- {IsoriX} [<i class='fa fa-github'></i>](https://github.com/courtiol/IsoriX) [<i class='fab fa-r-project'></i>](https://cran.r-project.org/web/packages/IsoriX/index.html) to build isoscapes using mixed models and infer the geographic origin of organisms based on their isotopic ratios. Created and maintained by Alex.
- {torpor} [<i class='fa fa-github'></i>](https://github.com/vullioud/torpor) to fit thermoregulatory curves in heterothermic endotherm species, while assigning metabolic rates to the correct physiological state. Created and maintained by Colin.
- {camtrapR} [<i class='fa fa-github'></i>](https://github.com/jniedballa/camtrapR) [<i class='fab fa-r-project'></i>](https://cran.r-project.org/web/packages/camtrapR/index.html) to manage camera trap photographs in wildlife studies. We helped its maintainer -- Jürgen Niedballa -- to set it up while he was still a PhD student.

### For all data scientists

- {ABMR6} [<i class='fa fa-github'></i>](https://github.com/LiamDBailey/ABMR6) an example of how to implement individual-based simulations using R6. Created by Alex, maintained by Liam.
- {lay} [<i class='fa fa-github'></i>](https://courtiol.github.io/lay/) [<i class='fab fa-r-project'></i>](https://cran.r-project.org/web/packages/lay/index.html) to perform simple but efficient rowwise jobs. Created together with [Romain François](https://github.com/romainfrancois) and maintained by Alex.
- {spaMM} [<i class='fa fa-gitlab'></i>](https://gitlab.mbb.univ-montp2.fr/francois/spamm-ref) [<i class='fab fa-r-project'></i>](https://cran.r-project.org/web/packages/spaMM/index.html) to efficiently fit linear models of varying complexity, including mixed models with spatial autocorrelation. We contribute to its development mostly by using this package a lot, debugging it and suggesting new features. Maintained by one very close collaborator ([François Rousset](https://kimura.univ-montp2.fr/~rousset)).
- {timevarcorr} [<i class='fa fa-github'></i>](https://courtiol.github.io/timevarcorr) [<i class='fab fa-r-project'></i>](https://cran.r-project.org/web/packages/timevarcorr/index.html) to estimate time varying correlation coefficients using non-parametric kernel smoothing. Created and maintained by Alex.


## Private (for now)

- {hyenaR} [<i class='fa fa-github'></i>](https://github.com/hyenaproject/hyenaR) to manage most of the data generated by the [hyena project](https://hyena-project.com). Created and maintained by Liam and Alex.
- {SHIM} [<i class='fa fa-github'></i>](https://github.com/hyenaproject/SHIM), a Spotted Hyena Individual-based Model simulating the lives of hyenas followed by the [hyena project](https://hyena-project.com). Created and maintained by Liam.

These packages will become open when we judge them ready for others to use.

```{r, fig.align='center', out.width=100, echo=FALSE}
knitr::include_graphics(path = "images/R.jpg")
```