Scripts and datasets required for native niche quantification and Niche Margin Index calculation for 45 invasive alien plants

The file "allData_nmi_EASIN_species_kde_99.rds" presents the main results of this research- the Niche Margin Index (NMI) values for every out-of-the-native-range occurrence point of 45 invasive alien plants, calculated using three different methods of quantifying the native climatic niche of the target species.Included here also are the R scripts used to calculate the NMI based on three different methods of native niche quantification. In addition, code and data are provided to select the optimal SDMs for one method of the native climatic niche quantification, fit the optimal SDMs, geographically project the results, sum the projections and finally polygonize them. No files are provided to generate background points as per our unique method of sampling stratified randomly in environmental space. Instead, the background point files for each species are provided. When running the R scripts, all data and scripts provided are assumed to be located in the work directory specified by the user, and .zip folders provided are assumed to be extracted to there, as well. The file "pca_world_all_land.rds" is a PCA result of the chosen CHELSA climatic variables across all terrestrial surfaces of the world. It is required to quantify the native climatic niche. If the user wishes to run the scripts on a slurm environment, both provided bash scripts are needed, but the "submit_jobs.sh" scripts calls the "NMI_run_SDMs_array_short_jobs.sh" script. This is to ensure that only one array job for one species runs at a time. This in turn is to optimize slurm cluster economy. The bash script contains an array function to make the jobs smaller and use up less time.The R scripts contain brief explanations on how to run the code outside of a slurm cluster environment, but the size of the "pca_world_all_land.rds" file when loaded in R will possibly make the full analysis impossible to run outside of a HPC cluster environment.