DOI: 10.5061/dryad.w0vt4b94h
title: Data and code from: Echoes of the past: Long-term climate stability shapes functional and phylogenetic diversity in Euro-Mediterranean forests

description: This dataset contains the processed inputs, null-model outputs, and R
 scripts used to quantify functional and phylogenetic diversity across
 multiple vertebrate and plant taxa in Euro-Mediterranean forests. It
 includes gridded environmental and anthropogenic drivers (50 × 50 km),
 indices of functional and phylogenetic richness, dispersion, and
 originality derived from observed data, and the corresponding values
 generated by null models. All analyses—from data preparation to random
 forest models and figure production—are reproducible using the provided
 scripts and the make.R workflow, beginning at the stage where null-model
 outputs are available. Raw species and trait data are not included because
 distribution rights are held by external data providers (cf., README
 file). The dataset supports reuse for comparative analyses of biodiversity
 metrics, and exploration of diversity–environment relationships across
 taxa and facets (cite as Dryad repository).
description: --- editor_options: markdown: wrap: 72 -------- This repository contains
 the data and code for our paper: &gt; Magneville et al. **Echoes of the
 Past: Long-Term Climate Stability Shapes Functional and Phylogenetic
 Diversity in Euro-Mediterranean Forests** &gt; *Accepted for publication
 in Global Ecology and Biogeography on December 2025* ### How to cite
 Though not required, a recommended citation for this compendium: &gt;
 (2025). *Compendium of R code and data for Past Climate Stability Shapes
 Diversity*. Accessed [...] Online at &gt;
 [https://doi.org/10.5061/dryad.w0vt4b94h](https://doi.org/10.5061/dryad.w0vt4b94h) #### 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 This repository contains all the R scripts used to run the analyses from the manuscript cited above. It contains data from the null models, and not the raw data used for the analyses, as the authors do not hold distribution rights for all the data. The user is then able to look at all the R scripts used for the analyses, and run all the analyses from the step of the null models onward. R packages which are needed to run the analyses are named in the DESCRIPTION file. Users who wish to access the raw species and trait data underlying the null-model outputs may request them from the INTEGRADIV project’s principal investigator, Agathe Leriche ([agathe.leriche@imbe.fr](mailto:agathe.leriche@imbe.fr)), as these datasets are not publicly distributed by the authors. **To run the make.R file and analyses easily, the files are organised as follows** * :file_folder: 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. **This folder gathers all the files with a name ending with "_fcts"** * :file_folder: analysis: 🍳 Folder containing all script to prepare data and analyse it. It uses the functions coded in the R folder. **This folder contains all the files named with numbers"** * :file_folder: env_db: 📦 Folder containing a file with the names of the drivers (used for graphic purposes), 50*50km grid cells and land masks for plotting maps. * :file_folder: transformed_data: 📦 Folder containing the dataframe gathering the drivers data (restricted or not to the final number of cells studied in the paper), and another folder "div_values_null_models", containing: * rds files containing functional and phylogenetic indices values per studied grid cells. Named "FacetName_IndicesNames_ScaleStudtied_TAXA.rds". * rds files containing outputs from the null models run. Named "FacetName_IndexNames_null_models_ScaleStudtied_TAXA.rds". * rds containing values computed out of the null models and observed diversity values. Named "FacetName_IndexNames_null_models_metrics_ScaleStudtied_TAXA.rds" * make.R File: Script to run the whole project. The steps 1 to 7 can't be run with raw data (as the authors don't do not hold distribution rights for raw data), but associated R scripts can still be looked at. These steps are related to cleaning the data and computing observed diversity indices and null models. Steps from 8-16 can be run with provided data (as they rely on the outputs of the null models which are provided). These steps are related to: random forests analyses, plotting the main Figures/Appendices, associated statistical tests and model checks.