[Vegan-commits] r1410 - pkg/vegan/man

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

Author: jarioksa
Date: 2010-12-13 10:37:32 +0100 (Mon, 13 Dec 2010)
New Revision: 1410

Modified:
   pkg/vegan/man/vegan-package.Rd
Log:
samll edits and examples (but do we need examples?)

Modified: pkg/vegan/man/vegan-package.Rd
===================================================================
--- pkg/vegan/man/vegan-package.Rd	2010-12-12 16:23:28 UTC (rev 1409)
+++ pkg/vegan/man/vegan-package.Rd	2010-12-13 09:37:32 UTC (rev 1410)
@@ -3,7 +3,7 @@
 \alias{vegan}
 \docType{package}
 \title{
-The Community Ecology Package
+Community Ecology Package: Ordination, Diversity and Dissimilarities
 }
 
 \description{ The \pkg{vegan} package provides tools for descriptive
@@ -25,19 +25,19 @@
 
 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 and fora for help queries and
-bug reports. Bug reports can also be emailed to the function authors
-of the package maintainers.
+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 also read \code{NEWS} on the new features and bug fixes in the
-relese version (\code{vegandocs("NEWS")}), or more technical and fine
-grained history in \code{vegandocs("ChangeLog")}.  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 packaage.
+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")}).  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")}.  
@@ -45,11 +45,54 @@
 
 \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.
+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")
+## 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 }