Documentation site

essicolo.github.io/nuee

The Problem

Community ecology leans on a specific toolkit of multivariate methods (ordinations, diversity indices, permutation tests), and in R that toolkit is mature, above all in the vegan package. Python has no real equivalent. What exists is fragmented or incomplete, so ecologists end up switching languages or reimplementing standard methods by hand.

The Approach

nuee is a Python implementation inspired by the renowned R package vegan. It provides:

• Ordination methods: NMDS, RDA, CCA, PCA with environmental fitting (envfit) and Procrustes analysis
• Diversity analyses: Shannon, Simpson, Fisher’s alpha indices, Renyi entropy, species richness, evenness, rarefaction
• Dissimilarity measures: Bray-Curtis, Jaccard, Euclidean, and 15+ other distances
• Statistical tests: PERMANOVA, ANOSIM, MRPP, Mantel test, beta dispersion
• Integrated visualizations: ordination plots, biplots, rarefaction curves, confidence ellipses
• Classic datasets: varespec, dune, BCI, mite with their environmental variables

The package maintains a familiar interface for vegan users while leveraging the Python scientific ecosystem (NumPy, SciPy, pandas, scikit-learn).

Technical Implementation

• Pure Python library with standard dependencies (NumPy, SciPy, pandas, matplotlib, seaborn, scikit-learn)
• Formula interface via patsy for specifying statistical models
• Integration with statsmodels for advanced analyses
• Simple installation via pip or git clone
• Built-in datasets for learning and testing

Current Status

Active project under development. Core ordination, diversity, and statistical testing functionalities are implemented. The package is usable for standard ecological analyses. Contributions are welcome to expand capabilities and improve compatibility with vegan.