index.Rmd

---
title: "Theory-driven analysis for ecological data"
description:  |
  FRB-CESAB & GdR TheoMoDive training course, with the support of the PEPR MathsVives
  <br><br>
  <a href="https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/develop-skills/theory-driven-analysis-of-ecological-data/">
    <img class="logo" src="https://raw.githubusercontent.com/theodatasci/.github/main/profile/banner-theodatasci_150dpi.png" style="width: 100%;" />
  </a>
author:
  - name: "Vincent Calcagno"
    url: https://vcalcagnoresearch.wordpress.com/
    affiliation: INRAE Institut Sophia Agrobiotech
    affiliation_url: https://www6.paca.inrae.fr/institut-sophia-agrobiotech
    orcid_id: 0000-0002-5781-967X
  - name: "Emanuel A. Fronhofer"
    url: https://www.emanuelfronhofer.net/
    affiliation: CNRS ISEM
    affiliation_url: https://isem-evolution.fr/en/
    orcid_id: 0000-0002-2219-784X
  - name: "Isabelle Gounand"
    url: https://isabellegounand.wordpress.com/
    affiliation: CNRS iEES-Paris
    affiliation_url: https://iees-paris.fr/teams/dynamics-of-ecological-networks/
    orcid_id: 0000-0002-0675-3973
  - name: "Claire Jacquet"
    url: https://clairejacquet.weebly.com/
    affiliation: CNRS ISEM
    affiliation_url: https://isem-evolution.fr/en/
    orcid_id: 0000-0002-7913-0689
  - name: "Sonia Kéfi"
    url: https://scholar.google.nl/citations?user=JcRmX4EAAAAJ&hl=fr
    affiliation: CNRS ISEM
    affiliation_url: https://isem-evolution.fr/en/
    orcid_id: 0000-0002-9678-7770
  - name: "François Massol"
    url: https://sites.google.com/a/polytechnique.org/francoismassol/home
    affiliation: CNRS iEES-Paris
    affiliation_url: https://iees-paris.fr/teams/dynamics-of-ecological-networks/
    orcid_id: 0000-0002-4098-955X
date: "`r format(Sys.Date(), '%m-%d-%Y')`"
site: distill::distill_website
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```




::: {.box-info}
`r fontawesome::fa_i("lightbulb")`&nbsp;
**Pre-registration opens each spring and training course is provided each winter. Subscribe to the [FRB-CESAB newsletter](https://www.fondationbiodiversite.fr/en/newsletter/) to stay informed. More information is available on the [FRB-CESAB website](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/develop-skills/theory-driven-analysis-of-ecological-data/).**
:::

<br />



This workshop is co-organized by the 
[FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/) 
and the 
[GdR TheoMoDive](https://sete-moulis-cnrs.fr/en/research/centre-for-biodiversity-theory-and-modelling/theomodive).
The objective of this five-day workshop is to train young researchers in building and analyzing mathematical models that will help them better understand ecological data. By contrast with purely statistical models, **this course emphasizes a process-driven approach based on ecological theory**. The course covers a general introduction to ecological modeling and thematic sessions focused on three topics of interest (time series, spatial data, interaction networks). Each topic is explored through mathematical models as well as inferential and predictive approaches, with a mix of courses and practical.

**N.B.** This training course is **in English** and slides are available in the tab `Courses/`.


<br />

::: {.box-info}
`r fontawesome::fa_i("lightbulb")`&nbsp;
**The 2026 edition benefited from funding from the [PEPR MathsVives](https://www.maths-vives.fr/en/). **
:::

<br />

## Program


<table>
  
  <tr style="background-color:#f0f2ed">
    <td rowspan="4">**Monday**</td>
    <td>**_Speakers_**: Isabelle Gounand, Sonia Kéfi & Vincent Calcagno</td>
  </tr>
  <tr style="background-color:#f0f2ed">
    <td>Icebreaker & Introduction to the week</td>
  </tr>
  <tr style="background-color:#f0f2ed">
    <td>Mathematical modeling & Theory
    
  <!--
      <span class="btn"><a href="courses/theo-modeling/intro_why_models.html">SLIDES</a></span><span class="btn"><a href="courses/theo-modeling/TAED_2024_DEF2.pdf">SLIDES</a></span><span class="btn"><a href="courses/theo-modeling/TDAED_stats_2024.pdf">SLIDES</a></span>
  -->
    </td>
  </tr>
  <tr style="background-color:#f0f2ed">
    <td>**_Guest seminar_** by Peter B. Adler (Univ. of Utah, USA)
    </td>
  </tr>
  
  <!--
  <tr style="background-color:#f0f2ed">
    <td>**_Guest seminar_**: Kim Cuddington (Waterloo Univ., Canada) <span class="btn"><a href="https://www.ecotheory.ca/theorydata/datatheory.html">SLIDES</a></span></td>
  </tr>
  -->
  
  <tr>
    <td rowspan="3">**Tuesday**</td>
    <td>**_Speakers_**: Emanuel Fronhofer & Peter Kamal</td>
  </tr>
  <tr>
    <td>Temporal series and dynamics in ecology
    
  <!--
    <span class="btn"><a href="time-series/emmanuel/fronhofer_day2_cesab_theomodive.pdf">SLIDES</a></span>
  -->
    </td>
  </tr>
  <tr>
    <td>**_Guest seminar_** by Benjamin Rosenbaum (iDiv, Germany)
    </td>
  </tr>

  <tr style="background-color:#f0f2ed">
    <td rowspan="3">**Wednesday**</td>
    <td>**_Speakers_**: Vincent Calcagno & Quentin Petitjean</td>
  </tr>
  <tr style="background-color:#f0f2ed">
    <td>Spatial data, macro-ecology and co-occurrences
    
  <!--
    <span class="btn"><a href="courses/spatial-data/TDAED_day3_slides_2024.pdf">SLIDES</a></span>
  -->
  
  </td>
  </tr>
  
  <tr style="background-color:#f0f2ed">
    <td>**_Guest seminar_** by Kevin Painter (Politecnico Torino)
    
  <!--
    <span class="btn"><a href="courses/spatial-data/Martinetti_SDM_PopilliaJaponica2.pdf">SLIDES</a></span>
  -->
    </td>
  </tr>
  
  <tr>
    <td rowspan="4">**Thursday**</td>
    <td>**_Speakers_**: François Massol & Claire Jacquet</td>
  </tr>
  <tr>
    <td>Interaction networks, trophic networks & complexity
    
  <!--
  <span class="btn"><a href="courses/networks/Day4_Networks_2023.pdf">SLIDES</a></span><span class="btn"><a href="courses/networks/Claire/empirical_food_webs_2023.pdf">SLIDES</a></span>
  -->
  
  </td>
  </tr>
  
  <tr>
    <td>**_Guest seminar_** by Matthieu Barbier (CIRAD, Montpellier & INTP)
    
  <!--
      <span class="btn"><a href="courses/networks/matthieu/MB_cesab.pdf">SLIDES</a></span>
  -->
  
  </td>
  </tr>
  <tr>
    <td>**_Guest seminar_** by Sonia Kéfi (CNRS ISEM, Montpellier)
    
  <!--
  <span class="btn"><a href="courses/networks/2022_05_cesab_Kefi.pdf">SLIDES</a></span>
  -->
  </td>
  </tr>
  
  <tr style="background-color:#f0f2ed">
    <td>**Friday**</td>
    <td>Subgroups projects</td>
  </tr>
  
</table>



<br/>


## Summary of the course

<div class="container">
  <iframe class="responsive-iframe" src="courses/main_summary.pdf"></iframe>
</div> 

<br/>


## Prerequisites

For this course, you need to install [`R`](https://cran.r-project.org/) and [`RStudio`](https://posit.co/download/rstudio-desktop/) (optional).

You also need to install the R package [`RStan`](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started).


<br/>



## See also


Discover the other training courses provided by the FRB-CESAB and its partners: <https://frbcesab.github.io/content/courses.html>



## Citation {.appendix}



Calcagno V, Fronhofer EA, Gounand I, Jacquet C, Kéfi C & Massol F (2025) 
FRB-CESAB & GdR TheoMoDive training course: Theory-driven analysis for ecological data.