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:
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.