BioticResistance_InvasionContinuum

This repository contains all the required data and code to reproduce the analyses and visualization in the following study:

• Kun Guo, Petr Pyšek, Milan Chytrý, Jan Divíšek, Martina Sychrová, Zdeňka Lososová, Mark van Kleunen, Simon Pierce, Wen-Yong Guo. Stage dependence of Elton’s biotic resistance hypothesis of biological invasions. Nature Plants 10:1484-1492.

How to use

• 1. Download this repo as .zip file and unzip it to a folder.
• 2. Open WorldPlantInvasion.Rproj with Rstudio.
• 3. Open BioticResistance_InvasionContinuum.qmd and load Data4BioticResistance_InvasionContinuum.RData to access all the code and data used for analyses and figure reproduction.
• 4. The folder figures contains all figures included in main text and supplementary. While all figures were generated in R, Adobe Illustrator was used for refinements.
• 5. The folder results contains all intermediate results of the SES values of phylogenetic and functional metrics. Due to potential long calculation times, you may import pd.mpd.mntd2024.RDS for further analyses.

File structure

• BioticResistance_InvasionContinuum.qmd: Main analysis script
• Data4BioticResistance_InvasionContinuum.RData: Primary dataset
• figures: Folder containing all generated figures
• results: Folder containing intermediate calculation results

NOTE on computation

• Calculating SES values for phylogenetic and functional metrics with large datasets (>10,000 plots and > 1,000 species) is computationally intensive. This study used custom functions i.e., fst.ses.pd, fst.ses.mpd, fst.ses.mntd from the R package ecoloop, with parallelization implemented via R package furrr.

• Even with a high-performance server (2 Intel Xeon Gold 6226 R CPU and 256 GB memory), calculation took approximately 2 hours. Computation time may vary significantly depending on your hardware.

Contact

• For any questions or issues, please open an issue in this respository.