[Vegan-commits] r1411 - pkg/vegan/man

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

Author: jarioksa
Date: 2010-12-13 14:04:30 +0100 (Mon, 13 Dec 2010)
New Revision: 1411

Modified:
   pkg/vegan/man/vegan-package.Rd
Log:
expand examples with ordiellipse and mention FAQ

Modified: pkg/vegan/man/vegan-package.Rd
===================================================================
--- pkg/vegan/man/vegan-package.Rd	2010-12-13 09:37:32 UTC (rev 1410)
+++ pkg/vegan/man/vegan-package.Rd	2010-12-13 13:04:30 UTC (rev 1411)
@@ -30,14 +30,15 @@
 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")}).  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.
+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")}.  
@@ -86,6 +87,13 @@
 ## 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