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")
.
### 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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