Replication archive for: Global distribution of avian plumage coloration and patterning: The relative influence of climate, ecology, and sexual selection
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### OverviewThis repository contains the complete replication archive—including the final integrated comparative dataset, and functional analytical R scripts—required to reproduce the macroevolutionary models, phylogenetic signal estimations, and phylogenetic path analyses presented in the manuscript: **"Global distribution of avian plumage coloration and patterning: The relative influence of climate, ecology, and sexual selection"** (Published in *Ecography*, 2026). --- ### Repository Structure & ContentsThe data and code are structured into a self-contained, reproducible pipeline. Upon unzipping the archive, you will find the following core components: * **`data/raw/`**: Contains `All_factors.csv`, the integrated species-level master dataset combining avian plumage phenotypic data (colorimetric RGB and patterning scores) with multi-source geospatial predictors (climate, ecology, and sexual selection metrics). * **`data/processed/`**: Contains simulated data gradients generated for robustness and sensitivity testing.* **`data/results/`**: Contains both automated script outputs and human-curated summary tables consolidated for manuscript readability.* **`scripts/`**: Sequential R scripts (organized from 01 to 04) covering: 1. Phylogenetic signal estimations (with automated `clootl` repository dependency checking). 2. Multivariate Bayesian PGLMMs (`MCMCglmm`). 3. Phylogenetic Path Analyses (`phylopath`). 4. Multi-threaded sensitivity and validation simulations. --- ### Basic Usage & Replication Instructions1. Download and unzip the `replication_archive.zip` file.2. Open RStudio and set the unzipped root directory as your working directory (e.g., using `setwd()`).3. Execute the analytical R scripts inside `scripts/data_processed_and_analysis/` in chronological order (01 through 04). All file paths within the scripts are relative to the root directory to guarantee out-of-the-box execution. ### Contact & CitationFor any inquiries regarding the code or datasets, please contact:* **Principal Investigator:** Yuqing Han (hanyq25@mail.sysu.edu.cn)* **Affiliation:** School of Ecology, Sun Yat-sen University* **Citation:** Please cite both the original *Ecography* paper (Han et al., 2026; DOI:10.1002/ecog.08536) and this Zenodo repository DOI if you utilize these resources in your research.
