[Vegan-commits] r1417 - branches/1.17/man

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2010-12-13 20:37:39 +0100 (Mon, 13 Dec 2010)
New Revision: 1417

Added:
   branches/1.17/man/vegan-package.Rd
Log:
copied vegan-package.Rd to branches/1.17

Copied: branches/1.17/man/vegan-package.Rd (from rev 1416, pkg/vegan/man/vegan-package.Rd)
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--- branches/1.17/man/vegan-package.Rd	                        (rev 0)
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+\name{vegan-package}
+\alias{vegan-package}
+\alias{vegan}
+\docType{package}
+\title{
+Community Ecology Package: Ordination, Diversity and Dissimilarities
+}
+
+\description{ The \pkg{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.  }
+
+\details{The functions in the \pkg{vegan} package contain tools for
+diversity analysis (see \code{\link{vignette}}
+\code{vegandocs("diversity")}), ordination and analysis of
+dissimilarities (see \code{\link{vignette}}
+\code{vegandocs("intro")}). Together with the \pkg{labdsv} package,
+the \pkg{vegan} package provides most standard tools of descriptive
+community analysis. Package \pkg{ade4} provides an alternative
+comprehensive package, and several other packages complement
+\pkg{vegan} and provide tools for deeper analysis in specific
+fields. Package \pkg{BiodiversityR} provides a GUI for a large subset
+of \pkg{vegan} functionality.
+
+The \pkg{vegan} package is developed at R-Forge
+(\url{http://vegan.r-forge.r-project.org}).  The R-Forge provides
+up-to-date information and mailing lists for help queries and bug
+reports. Bug reports can also be emailed to the function authors or to
+the package maintainers.
+
+The \pkg{vegan} documents can be read with \code{\link{vegandocs}}
+function. In addition to \code{\link{vignette}}s of basic usage, you
+can read \code{NEWS} on the new features and bug fixes in the release
+version (\code{vegandocs("NEWS")}), and more technical and fine
+grained \code{ChangeLog} (\code{vegandocs("Change")}).  Several
+frequently asked questions really are answered in the vegan FAQ
+(\code{vegandocs("FAQ")}). The discussion on design decisions can be
+read with \code{vegandocs("decision")}.  A tutorial of the package at
+\url{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
+\code{citation("vegan")}.  
+}
+
+\author{ The \pkg{vegan} development team is Jari Oksanen,
+F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, R. B. O'Hara,
+Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene
+Wagner.  Many other people have contributed to individual functions: see
+credits in function help pages.
+
+The maintainers at the R-Forge are Jari Oksanen <jari.oksanen at oulu.fi>
+and Gavin Simpson <gavin.simpson at ucl.ac.uk>.
+}
+\examples{
+### 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)
+## Overall permutation test for all variables
+anova(mod1)
+## Permutation test for terms added sequentially
+anova(mod1, by = "term")
+## Automatic selection of variables by permutation P-values
+mod <- ordistep(mod0, scope=formula(mod1))
+mod
+plot(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)
+}
+
+\keyword{ package }
+\keyword{ multivariate }
+\keyword{ univar }
+\keyword{ models }
+\keyword{ spatial }
+\keyword{ nonparametric }
+\keyword{ htest }
+\keyword{ regression }
\ No newline at end of file