Inputs, outputs and scripts of "Combined threats of land use, climate change and nitrogen deposition to global vascular plant diversity"

Data inputs, outputs and scripts necessary to reproduce the analysis of the paper "Combined threats of land use, climate change and nitrogen deposition to global vascular plant diversity" run_framework_per_ecoregion.R - file calls the functions needed to run the model.LRSL_functions.R - function to calculate local relative species loss at grid cellsLPDF_functions.R - function to calculate local extinction threats at grid cellRPDF_functions.R - function to calculate regional extinction threats at ecoregionsGPDF_functions.R - function to calculate global extinction threats at ecoregions Scripts to fit beta regressions of land use and nitrogen deposition: fit_model_land_use.R and fit_model_ndep.RScript to perform MESS analysis: MESS_analysis.RScript to simulate beta regression coefficients from multivariate normal distribution: simulate_beta_regression_coefficients.R Folder structure:My_folder/source/ All scripts should be in the folder called "source".My_folder/data/output - where preprocessed data and results are savedMy_folder/data/input - where inputs necessary for the model should be placed Data to be placed in the data/input/ folder:lookup_table.csv - table with codes and names of land use types Data to be placed in the data/output/ folder:ecoregions_info_latlon.rds - Shapefile of ecoregions in latitude/longitudeinput_landuse_latlon.tif - Raster of the land use types in latitude/longitude. This raster is available at https://www.globio.info/globio-data-downloadsinput_globalwarming_latlon.tif - Raster with the global mean temperature increase since pre industrial times (all cells receive the same value) in latitude/longitudeinput_nitrogendeposition_latlon.tif - Stacked raster of nitroden depositon and soil cation exchange capacity (CEC) in latitude/longitude. This raster is available at: https://doi.org/10.5061/dryad.f1vhhmgx7 from Gallego-Zamorano et al. (2022)mask_primary_vegetation_latlon.tif - Raster of only primary vegetation. This raster is the primary vegetation category available in the raster with all land use types at https://www.globio.info/globio-data-downloadsmask_landmass_latlon.tif - Raster of only land massecoregions_info_latlon.rds - Shapefile with zj values and relative endemism richness per ecoregion The results of the model are per ecoregion. We put all the results of local, ecoregional and global extinction threats together to facilitate data access:Results of global extinction threats: get_default.rds, get_per_pressure_and_ecoregion.rds, ger_per_pressure_and_biome_default.rds, get_per_pressure_default.rds Results of global extinction threats under the assumptions of negative and positive co-tolerance to pressures: get_max.rds, ger_per_pressure_and_biome_max.rds, get_per_pressure_max.rds, get_sum.rds, ger_per_pressure_and_biome_sum.rds, get_per_pressure_sum.rds Results of global extinction threat from Monte Carlo simulation: get_total_uncertainty.rds, get_per_pressure_uncertainty.rds Results of global extinction threat when model is applied only within the applicability domain: get_mess.rds, get_per_pressure_and_ecoregion_mess.rds, ger_per_pressure_and_biome_mess.rds, get_per_pressure_mess.rds