Defaunation-causing-biotic-homogenization: Version for publication in Ecology

Version: v1.0.0

Purpose: Public reproducibility package for the analyses in the manuscript: Mammal defaunation leads to biotic homogenization of plant communities in tropical rainforests, Ecology.

Luiz Guilherme dos Santos Ribas, Nacho Villar, Valesca Zipparro, Sérgio Nazareth, Yuri Souza, Carlos Rodrigo Brocardo, Gabriela Schmaedecke, Luana Hortenci, Rafael Souza Cruz Alves, Mauro Galetti.

Contents

Raw data (Excel workbooks, one per site; multiple sheets = timepoints): Cardoso_T0_T156.xlsx (CAR), Carlos_Botelho_T0_T108.xlsx (CBO), Itamambuca_T0_T156.xlsx (ITA), Vargem_Grande_T0_T156.xlsx (VG).

Annotated analysis workflows (R Markdown + HTML): CAR_analysis.Rmd/.html, CBO_analysis.Rmd/.html, ITA_analysis.Rmd/.html, VG_analysis.Rmd/.html (site-level alpha/beta diversity processing, modeling, and plotting).

Cross-site synthesis: Meta_analysis.Rmd/.html (cross-site meta-analysis/pairwise contrasts and comparative plots).

Documentation: README.md describing repository structure, requirements, and step-by-step usage.

How to reproduce

Place the site .xlsx files in the data/ directory (as described in README.md).

Knit/run the four site-specific .Rmd files (CAR, CBO, ITA, VG). Outputs are saved to the user's Desktop by default under: Desktop/Defaunation_biotic_homogenization/<SITE>/

Knit/run Meta_analysis.Rmd after site scripts to generate cross-site comparative figures/tables (also saved to Desktop by default).

Notes

Default output location is the user's Desktop on Windows; macOS/Linux users may need to adjust desktop_path at the top of each .Rmd.

This Zenodo archive represents the version of record for reproducibility (v1.0.0). Future updates will be versioned via GitHub releases.

Recommended citation

Use the Zenodo DOI minted from this release to cite the data and code package in the manuscript's Open Research statement.