Effects of time, diversification, and energy on regional richness change with phylogenetic scale

# Rubio-Lopez et al. 2026: Figure Generation Pipeline ## Overview This repository contains the data, scripts, and computational environment required to reproduce the main figures presented in *Rubio-Lopez et al. (2026)*. This README describes the structure, contents, and purpose of each folder, allowing users to navigate and reproduce the analyses. ## Directory Structure - `data/`: Input datasets organized by type (phylogenies, environmental rasters, spatial boundaries, metrics, clade-level results, taxonomic backbones). - `scripts/`: - `code_figures.R` generates Figures 1–3. - `code_phyloscale_example.R` generates Figure 4. ## Reproduction Protocol 1. Install dependencies via `renv::restore()` or `conda env create -f environment.yml`. 2. Execute `source("scripts/figures.R")` from the project root. 3. Outputs are saved to the working directory as `.tif` and `.pdf` files. ## Data Provenance - Phylogenies: Time-calibrated maximum clade credibility trees derived from VertLife (https://vertlife.org). - Environmental data: CHELSA bioclimatic variables and MODIS NPP/AET rasters processed at 1° resolution. - Taxonomic backbones: Integrated from VertLife, The Reptile Database, and AmphibiaWeb. ## Licensing Code: MIT License. Data: CC-BY 4.0 (unless otherwise specified in source repositories). ## Contact Iñigo Rubio López ([e-mail])