vegan-package: Community Ecology Package: Ordination, Diversity and Dissimilarities

Description

The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well.

Arguments

Details

The functions in the vegan package contain tools for diversity analysis, ordination methods and tools for the analysis of dissimilarities. Together with the labdsv package, the vegan package provides most standard tools of descriptive community analysis. Package ade4 provides an alternative comprehensive package, and several other packages complement vegan and provide tools for deeper analysis in specific fields. Package BiodiversityR provides a GUI for a large subset of vegan functionality.

The vegan package is developed at GitHub (https://github.com/vegandevs/vegan/). GitHub provides up-to-date information and forums for bug reports.

Most important changes in vegan documents can be read with news(package="vegan") and vignettes can be browsed with browseVignettes("vegan"). The vignettes include a vegan FAQ, discussion on design decisions, short introduction to ordination and discussion on diversity methods. A tutorial of the package at http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf provides a more thorough introduction to the package.

To see the preferable citation of the package, type citation("vegan").

Examples

Run this code

### Example 1: Unconstrained ordination
## NMDS
data(varespec)
data(varechem)
ord <- metaMDS(varespec)
plot(ord, type = "t")
## Fit environmental variables
ef <- envfit(ord, varechem)
ef
plot(ef, p.max = 0.05)
### Example 2: Constrained ordination (RDA)
## The example uses formula interface to define the model
data(dune)
data(dune.env)
## No constraints: PCA
mod0 <- rda(dune ~ 1, dune.env)
mod0
plot(mod0)
## All environmental variables: Full model
mod1 <- rda(dune ~ ., dune.env)
mod1
plot(mod1)
## Automatic selection of variables by permutation P-values
mod <- ordistep(mod0, scope=formula(mod1))
mod
plot(mod)
## Permutation test for all variables
anova(mod)
## Permutation test of "type III" effects, or significance when a term
## is added to the model after all other terms
anova(mod, by = "margin")
## Plot only sample plots, use different symbols and draw SD ellipses 
## for Managemenet classes
plot(mod, display = "sites", type = "n")
with(dune.env, points(mod, disp = "si", pch = as.numeric(Management)))
with(dune.env, legend("topleft", levels(Management), pch = 1:4,
  title = "Management"))
with(dune.env, ordiellipse(mod, Management, label = TRUE))
## add fitted surface of diversity to the model
ordisurf(mod, diversity(dune), add = TRUE)
### Example 3: analysis of dissimilarites a.k.a. non-parametric
### permutational anova
adonis(dune ~ ., dune.env)
adonis(dune ~ Management + Moisture, dune.env)

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