R script overview:
Scripts include preprocessing data, generating models, and post processing data. All scripts are numbered in the order that they were originally ran.
R scripts (see each script for individual goals, notes, dates the script was written):
1.1_reprojecting_all_rasters
2.1_reprojecting_study_extents
2.2_cropping_rasters_to_range_study_extents
3.1_filtering_input_localities
3.2_reprojecting_input_localities
3.3_removing_duplicates_input_localities_dismo
3.4_removing_independent_data_from_input_localities
3.5_subsetting_input_localities
4.1_tuning_features_regularization
5.1_extracting_envi_vars_values_under_input_localities
5.2_subsetting_kfolds
6.1_Maxent_Random_pts_kfolds
6.2_Maxent_Random_pts_all_localities
7.1_extract_continuous_surface_predictions_WLNP_sites
7.2_independent_AUC_WLNP
8.1_determine_binary_threshold
8.2_binary_surface_counts
9.1_summed_binary_surfaces
9.2_summed_binary_surface_counts
10.1_density_response_curves_supmat
Data included here:
Input_locs_extracted_vars: Separated into folders for each species. Within each species folder there are three csv files (one for each study extent). The csv file has species scientific name, type (1=presence), and the extracted values of the climate variables used in the model under each presence point. NOTE: Due to data sharing agreements with various government agencies and researchers we are unable to share the lat and long locations of the input localities.
Maxent_outputs: There are two folders 1) Models, 2) Prediction_surfaces. Within the "Models" folder there is the saved model object file for each Maxent model that the prediction surfaces were based off. Within the "Prediction_surfaces" folder there is the saved TIFF files for the logistic prediction surfaces for each model.
Study_extent_shp: Separated itno folders for each species. Within each species folder there are the shape files for each study extent used to generate the models.
NOTE: Climate variables were downloaded from Climate NA using the climate normals of 1991-2020 period
(https://adaptwest.databasin.org/pages/adaptwest-climatena/)