trinaryMaps

Overview

The trinaryMaps package is a collection of functions designed to create, analyze, and visualize trinary maps. A trinary map is a categorization of a continuous raster species range estimates where each pixel has one of three possible values: 0 (definitely unoccupied habitat), 1 (marginal, occasional, or uncertain occupied habitat), or 2 (likely occupied habitat).

Installation

To install the Trinary Maps package, use the following command:

remotes:install_github("gepinillab/trinaryMaps") # Change to cmerow when published.

Then, load the package using:

library(trinaryMaps)

Functions

The Trinary Maps package includes several functions to create and analyze trinary maps. Some of the key functions include:

• trinaryMapWorkflow(): This function takes in the species presence and background data, along with a model prediction, and generates trinary maps. It also calculates the information for ROC curves.
• trinaryROCRoots(): Fit a smoothed ROC curve, find bounds for threshold and report partial AUC statistics. Used internally also in trinaryMapWorkflow().
• trinaryROCPlot(): Plot trinary ROC curve and, optionally, save the output as pdf file.
• trinaryMap(): Function to generate trinary map (spatRaster) based on thresholds calculated in trinaryROCRoots(). Used internally also in trinaryMapWorkflow().

Examples

For more information and examples, refer to the package vignette:

browseVignettes("trinarymaps")

Troubleshooting

For any issues or questions, please refer to the package documentation and vignette.

License

The trinaryMaps package is licensed under the MIT License. See LICENSE.md for more information.

Contributing

We welcome contributions from users and developers. Please submit pull requests or open issues on GitHub.

Acknowledgments

This project was developed with support from NSF Grant 1046328 and NASA grant 80NSSC18K0435.