REBA: Rapid EOO-Based Assessment

This repository contains code, data, and figures that support:

Levin, M.O., J.B. Meek, B. Boom, S.M. Kross, and E.A. Eskew. 2022. Using publicly available data to conduct rapid assessments of extinction risk. Conservation Science and Practice 4: e12628.

Repository Structure

/data contains raw and intermediate data files necessary for the analysis
- /fit_models contains the fit Bayesian model objects
- /gbif_miscellaneous contains metadata associated with the GBIF data pull
- /IUCN contains assessment, plant type, and plant threat data from the IUCN
- /modeling_data contains datasets for statistical modeling
- /NatureServe contains NatureServe data on plant conservation status, for comparison
- /rcat contains conservation metrics, as calculated with rCAT
/outputs contains all figures output from the data visualization script
/R contains code for functions that are sourced in the analysis scripts
/scripts contains the primary analysis scripts, ordered sequentially by number
- 01_data_acquisition.R uses rgbif to harvest plant occurrence records
- 02_data_cleaning.R cleans the resulting occurrence data
- 03_data_analysis.R uses rCAT and custom methods to generate conservation metrics for each species
- 04_generate_modeling_data.R cleans and organizes the data for statistical modeling purposes
- 05_statistical_modeling.R fits Bayesian models
- 06_data_visualization.R generates all relevant figures