https://github.com/cmlmagneville/meddivdrivers

https://github.com/cmlmagneville/meddivdrivers

Repository

README.Rmd

---
title: "README"
author: "Camille Magneville"
date: "2025-04-25"
output: md_document
---

This repository contains the data and code for our paper:

> Magneville et al, (202.). *...*. ...
> link to the paper once it's out

Our pre-print is online here: (soon)

### How to cite

Please cite this compendium as:

> Magneville et al, (2025). *Compendium of R code and data for Past Climate Stability Shapes Diversity*. Accessed ... Online at
> 

#### Long-Term Climate Stability Shapes FD and PD In Euro-Mediterranean Forests

The goal of this R project is to reproduce all analyses, figures, and
tables of drivers of FD and PD of Mediterranean forests (multidiversity
and muti taxon approach) Past climate stability, Present habitat
characteristics, Disturbances and Past and Present human impact.

## Content

The directory contains:

-   [:file_folder: R](/R):  Folder containing all functions
    created for the analyses. These functions can be loaded using
    **devtools::load_all()**. They are called in the scripts coded in
    the analysis folder.
    
-   [:file_folder: analysis](/analysis):  Folder containing all script to
    prepare data and analyse it. It uses the functions coded in the R
    folder.
    
-   [:file_folder: integradiv_db](/integradiv_db):  Folder containing the data from the INTEGRADIV database. It more specifically contains:

    - traits data with all traits gathered in the INTEGRADIV database (only a subset were used in this paper - cf first analyses) _version from September 2024_
  
    - phylogenies (some of them being pruned in this paper - cf first analyses) _version from September 2024_
  
    - occurrences in 50*50km grid cells _version from September 2024_
  
    - spatial grid of the studied area
  
    - land mask of the studied area
  
-   [:file_folder: transformed_data](/transformed_data): Folder containing all intermediate dataframe/list/vector created during the analyses, and  used to get final outputs. Data has been transformed from the raw data  (INTEGRADIV database).

-   [:file_folder: outputs](/outputs): Folder containing all the outputs of the project, created in the analyses scripts. It also includes specific folders [:file_folder: residual_maps](/outputs/residual_maps) which contains maps the residuals from each random forest model, to visualize whether the model was better at predicting specific areas or not ; [:file_folder: drivers_maps](/outputs/drivers_maps) which contains maps of specific individual drivers ; [:file_folder: directionality](/outputs/directionality) which contains plots (biplots and mosaic plots) representing the directionality of the effect of individual drivers on each dimension of diversity and for each facet. Only the individual drivers having a relative importance > 75% were studied here.

-   make.R File: Script to run the whole project. Be careful, some steps might be time consuming, and have been run on a server.

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