Darwin's Naturalization Conundrum explained by gradients of environmental stress and disturbance_R code

These R scripts contain the code used for data processing, phylogenetic, and statistical analyses presented in the manuscript titled "Darwin's Naturalization Conundrum Explained by Gradients of Environmental Stress and Disturbance".This study analyzed the phylogenetic distances between non-native and native plant species across globally distributed plant communities along elevational and disturbance gradients. The input data, comprising records of native and non-native vascular plant species collected along mountain roads, was provided by the Mountain Invasion Research Network (MIREN) and is publicly available on Zenodo (DOI: 10.5281/zenodo.5529071). The scripts are organized as follows: "Data handling & phylogenetic tree.R": This script includes code for data processing, community selection, and the generation of a phylogenetic tree of the plant species. "Phylogenetic distances & Null model functions.R": This script calculates the phylogenetic distances between non-native and native species within each plant community. It also includes code for the null model, comparing observed phylogenetic distances with random patterns. "Statistical Analyses_Null model & Global and Regional Mixed Models.R": This script contains the code for linear mixed-effects models used to analyze the data and test the study's hypotheses.