ryanpavlick/sister-biodiversity

sister-biodiversity

This repository contains code for calculating alpha and beta spectral diversity metrics. Methods were adapted from Féret & de Boissieu (2020) but do not exactly replicate their techniques. We have included a command line script, which can automatically generate diversity metrics with user specfied parameters, along with an interactive Jupyter notebook (recommended).

Féret, J. B., & de Boissieu, F. (2020). biodivMapR: An r package for α‐and β‐diversity mapping using remotely sensed images. Methods in Ecology and Evolution, 11(1), 64-70. https://doi.org/10.1111/2041-210X.13310

Installation

pip -r requirements.txt

Use

python spectral_diversity.py reflectance_image output_directory

Optional arguments:

• --nclusters: Number of k-means clusters, default = 25
• --window: Window size for calculating diversity metrics, default= 10
• --pca: Export PCA image, default = False
• --species: Export spectral species map, default = False
• --ncpus: Number of CPUs for MDS, default = 1
• --verbose: default = False