https://doi.org/10.5061/dryad.p5hqbzksd

In this repository, you can find the processed data used as inputs for the model. These inputs are stored in .rds files that can be read in R.

The land use classes and area derived from GLOBIO land use map:

land_class_area_ecoregions_globio4.rds
GLOBIO4_LU_legend_harmonized.rds

    - Columns of land_class_area_ecoregions_globio4.rds:
        - zone and land_use_id: code that indicates the land use type
        - land_use: label of land use type
        - ecoregion: code that indicates ecoregion
        - area_km2: area of a given land use type in a given ecoregion in km2
    - Columns of GLOBIO4_LU_legend_harmonized.rds:
        - land_use: label indicate a land use type
        - land_use_id: identification code of a land use type that correspondes to a label

The land use classes and area derived from LUH2 land use map:

land_class_area_ecoregions_LUH2.rds

As the LUH2 land use map does not have land use intensities, we assigned intensely used pasture and intensely used cropland based on the inorganic nitrogen fertilization rate, assuming that a rate above 100 kg/ha characterizes intense use (Schipper et al., 2020; Temme & Verburg, 2011);

    - Columns of land_class_area_ecoregions_LUH2.rds:
        - land_use: label to indicates the land use type∅
        - eco_code: code that indicates ecoregion
        - area_km2: area of a given land use type in a given ecoregion in km2
        - land_use_id: code that indicates the land use type

Endemism richness per ecoregion relative to the global richness of vascular plant species derived from the GBIF data set:

endemism_weighted_richness_per_ecoregion_globio.rds
endemism_weighted_richness_per_ecoregion_luh2.rds

    - Columns of endemism_weighted_richness_per_ecoregion_globio.rds
        - eco_code: code that indicates the ecoregion
        - biome: code that indicates the biome
        - realm: code that indicates the realm
        - end_w_rich: endemism richness of a given ecoregion
        - end_w_rich_rel: relative endemism richness of a given ecoregion
        - richness: species richness of a given ecoregion 

Total global number of vascular plant species derived from the GBIF data set :

richness_global_globio.rds and richness_global_luh2.rds

    - column s_org_global: one value indicating the global richness

z-values and Local relative species richness values were written directly in the script number 12.

The outputs are stored in .rds files and can be read in R. Outputs:

results_globio.rds and results_luh2.rds

Results of model using GLOBIO and LUH2 land use map. It is a list containing three elements:
- The first list, named "extirpation", it is a data table with the estimated regional extinction threats per ecoregion.
    - column ecoregion: code that indicates the ecoregion.
    - column biome_id: code that indicates the biome.
    - column biome: indicates the biome name.
    - column Richness: indicates the richness in the ecoregion.
    - column s_new: indicates the richness in the ecoregion after habitat conversion due to land use.
    - column s_loss: indicates the richness under threat of extinction in the ecoregion due to land use.
    - column class_name: indicates the group of organisms included in the analysis.
    - column realm_id: indicates the code of the realm. It is the same as the first two letters of the ecoregion column.
    - column s_loss_rel: indicates the relative richness under threat of extinction in the ecoregion due to land use.

- The second list, named "extirpation_lu", it is a data table with the estimated regional extinction threats per land use type and per ecoregion.
    - column ecoregion: code that indicates the ecoregion.
    - column biome_id: code that indicates the biome.
    - column land_use_id: code that indicates the land use type.
    - column land_use: indicates the name of the land use type.
    - column biome: indicates the biome name.
    - column s_loss_eco_i: indicates the richness under threat of extinction in the given land use type and ecoregion due to land use.
    - column ecoregion_name: indicates the name of the ecoregion.
    - column realm_id: indicates the code of the realm. It is the same as the first two letters of the ecoregion column.
    - column s_loss_eco_i: indicates the relative richness under threat of extinction in the given land use type and ecoregion due to land use.

- The third list, named "extinction", it is a list with all the results of the global extinction threat of vascular plants due to land use.
- List named "s_loss_glob_i", shows the percentage of species under extinction threat due to land use.
    - column land_use: indicates the name of the land use type.
    - column s_loss_glob_i_rel: indicates the relative number of global richness under global extinction threat due to a given land use type 
    - column s_loss_glob_i_per: indicates the percentage of global richness under global extinction threat due to a given land use type
- List named "s_loss_glob_i_j", shows the percentage of species under extinction threat due to land use per land use type and ecoregion.
    - column ecoregion: code that indicates the ecoregion.
    - column biome_id: code that indicates the biome.
    - column land_use: indicates the name of the land use type.
    - column land_use_id: code that indicates the land use type.
    - column ecoregion_name: indicates the name of the ecoregion.
    - column biome: indicates the biome name.
    - column realm_id: indicates the code of the realm. It is the same as the first two letters of the ecoregion column.
    - column s_loss_glob_i_j_rel: indicates the relative number of global richness under global extinction threat due to a given land use type in a given ecoregion 
    - column s_loss_glob_i_j_per: indicates the percentage of global richness under global extinction threat due to a given land use type in a given ecoregion
- List named "s_loss_glob_j", shows the percentage of species under extinction threat due to land use per ecoregion.
    - column ecoregion: code that indicates the ecoregion.
    - column biome_id: code that indicates the biome.
    - column biome: indicates the biome name.
    - column realm_id: indicates the code of the realm. It is the same as the first two letters of the ecoregion column.
    - column s_loss_glob_j_rel: indicates the relative number of global richness under global extinction threat due to land use in a given ecoregion 
    - column s_loss_glob_j_per: indicates the percentage of global richness under global extinction threat due to land use in a given ecoregion 
- List named "global_summary", shows the total number of species globally and the relative number estimated to be under extinction threat due to land use
    - column s_org_global: global number of vascular plant species
    - column s_loss: number of species estimated to be threatened to extinction due to land use
    - column s_loss_rel: relative number of species estimated to be threatened to extinction due to land use
- List named "s_loss_glob_realm", shows the relative number of species estimated to be under extinction threat due to land use at realm level
    - column realm_id: indicates the code of the realm. It is the same as the first two letters of the ecoregion column.
    - column s_loss_glob_j_rel: relative number of species estimated to be threatened to extinction due to land use in a given realm
    - column s_loss_glob_j_per: perentage of species estimated to be threatened to extinction due to land use in a given realm
- List named "s_loss_glob_realm_lu", shows the contribution of a given land use type to the relative number of species estimated to be under extinction threat due to land use at realm level
    - column realm_id: indicates the code of the realm. It is the same as the first two letters of the ecoregion column.
    - column s_loss_glob_i_j_rel: relative number of species estimated to be threatened to extinction due to land use in a given realm due to a given land use type
    - column s_loss_glob_i_j_per: perentage of species estimated to be threatened to extinction due to land use in a given realm  due to a given land use type
    - column land_use: indicates the name of the land use type.
    - column per_lu_loss_within_realm: indicates how much the given land use type contributes to the extinction threat in that given realm

Results from model where variables were randomized
results_random_z_values_globio.rds and results_random_relative_endemism_richness_globio and results_random_RR_pv_globio.rds and results_random_natural_fractions_globio.rds

Respectively: results of model in which z-values are randomized among biomes; results of model in which relative endemism richness are randomized among ecoregions; results of model in which local relative plant species richness are randomized among land uses, with expectation of values for primary vegetation; results of model in which the fraction of natural and non-natural vegetation is randomized among ecoregions. These results are organized in lists containing the results of the simulations. Each list shows the percentage of species under extinction threat due to land use per ecoregion.
    - column ecoregion: code that indicates the ecoregion.
    - column biome_id: code that indicates the biome.
    - column biome: indicates the biome name.
    - column realm_id: indicates the code of the realm. It is the same as the first two letters of the ecoregion column.
    - column s_loss_glob_j_rel: indicates the relative number of global richness under global extinction threat due to land use in a given ecoregion 
    - column s_loss_glob_j_per: indicates the percentage of global richness under global extinction threat due to land use in a given ecoregion

Scripts (at Zenodo repository):

    - Script to calculate regional extinction threat (7_function_calculate_extirpation.R); It calculates affinity and countryside species-area relationship according to equations 3 and 1 in the paper.
    - Script to allocate regional extinction threat to land use (8_function_allocate_extirpation.R); It allocates regional extinction threats to land use types according to equation 4 in the paper
    - Script to calculate global extinction threat per ecoregion and land use (9_function_calculate_extinction.R);    It calculates global extinction threat using the relative endemism richness (equation 2 in the paper) and according to the regional extinction threats calculated with 7_function_calculate_extirpation
    - Script to create the map and the stacked bar plot presented in the results (10_function_make_plots.R); Script to prepare all the plots presented in the paper. It reads the results from the model and prepares the figures.
    - Script to create figure presented in the sensitivity analysis (11_function_make_sensitivity_plots.R); Script to prepare the figures of the sensitivity analysis. It reads the results from the randomized models and prepare the figures.
    - Script to run the model (12_Model_estimate_extinction_threat.R). In this script all the above mentioned functions are called. The model runs and saves all the results. The script can be run for the default land use map (GLOBIO), for the LUH2 map and for the models in which z-values, relative endemism richness, local relative plant species richness and percentage of natural and non-natural area are randomized.
    - Script to compare allocation using equations S1 and S2 (Compare_allocations_to_land_use.R).