vegan is a package for use with R for the analysis of ecological communities, especially vegetation communities. It has tools for analyzing ecological diversity and for the multivariate analysis of communities (NMDS, pCCA, pRDA, etc.)
Vegan is an r package that provides ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Vegan contains many popular tools used in community ecology:
- Diversity analysis: Shannon, Simpson, Fisher indices, Rényi diversities and Hill numbers.
- Species abundance models: Fisher and Preston models, species abundance distributions.
- Analysis of species richness: species accumulation curves, extrapolated richness.
- Ordination: support and meta functions for NMDS, redundancy analysis, constrained correspondence analysis, constrained analysis of proximities (all three with partial analysis),
- Support functions for ordination: dissimilarity indices, extended dissimilarities, Procrustes analysis, ordination diagnostics, permutation tests.
- Ordination and environment: vector fitting, centroid fitting and smooth surface fitting, adding species scores as weighted averages, adding convex hull, SD ellipses, arrows etc. to ordination.
- Dissimilarity analyses: ANOVA using dissimilarities, ANOSIM, MRPP, BIOENV, Mantel and partial Mantel tests.
- Data standardization: Hellinger, Wisconsin, Chi-square, Beals smoothing.
Repositories
Vignettes
Other resources
- vegan FAQ
- Multivariate Analysis of Ecological Communities in R: vegan tutorial by Jari Oksanen
- CRAN Task View on Environmetrics
- Inside-R reference page
- Posts on R-bloggers
