Overview

This repository contains code and data for Roswell and Espíndola "Global conservation prioritization approach provides credible results at a regional scale" (doi:10.1111/ddi.13969), a manuscript about predicting which unassessed regional taxa are likely to face conservation threats... using occurrence data, covariates, and random forest classifiers.

General organization

• code contains R scripts to download occurrence data and GIS layers, process them, and fit the Random Forests.
• data contains all the downloaded and manufactured datasets (these are often large) for this project
  • data/fromR mainly contains tables generated by the scripts in code
  • data/GIS_downloads contains raster layers downloaded from various sources
  • the data files for this project are very large. As a result, this repository was created using git lfs; see note below
• figures contains .pdf files of maps and graphs generated by scripts in code
• notes is a place where I am recording code snippets and notes to myself, there is not analysis here

Workflow within code/:

Utilities

data cleanup

1. tidy_flora.R regex matching to turn .pdf into a flat file
2. robust_gbif_namesearch.R wraps an rgbif function to try to get nice matches for taxon names without returning synonyms if a valid match exists.

model fitting etc.

1. fix_mod.R klugey way to handle novel factor levels when using various predict functions.
2. RF_tuner.R specifies how to tune an fit the random forests
3. RF_setup.R creates folds for model fitting, cleans up model formulae

Data download and analysis scripts (may call 1 or more utilities above)

1. download_gis.R documents the sources of many of the GIS layers used downstream. Created a long time ago and unstable. Do not run
2. download_occurrences_and_statuses.R documents the queries in GBIF and natureserve. Largely stable but not rerun; the dataset liable to change if rerun.
3. crunch_GIS.R Should be rel. stable, all GIS work done in R
4. fit_RF.R Fits random forests
5. graphing_model_outputs.R generates figures and tabular results

large files and git lfs

This is the first time I used git lfs to handle large files in the repo. The files tracked by lfs are most likely handled dysfunctionally if you clone this repo and have not installed git lfs. For more information on git lfs, see here.