[Vegan-commits] r376 - pkg/man

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

Author: wagnerh1
Date: 2008-05-29 16:12:49 +0200 (Thu, 29 May 2008)
New Revision: 376

Modified:
   pkg/man/mso.Rd
Log:
Added mite example. Changed call of plot.mso to msoplot in examples.

Modified: pkg/man/mso.Rd
===================================================================
--- pkg/man/mso.Rd	2008-05-29 14:11:47 UTC (rev 375)
+++ pkg/man/mso.Rd	2008-05-29 14:12:49 UTC (rev 376)
@@ -104,12 +104,31 @@
 ## Canonical correspondence analysis (cca):
 Example.cca <- cca(X, Y)
 Example.cca <- mso(Example.cca, tmat)
-plot(Example.cca)
+msoplot(Example.cca)
 Example.cca$vario
 
 ## Correspondence analysis (ca):
 Example.ca <- mso(cca(X), tmat)
-plot(Example.ca)
+msoplot(Example.ca)
+
+
+## Unconstrained ordination with test for autocorrelation
+## using oribatid mite data set as in Wagner (2004)
+data(mite)
+data(mite.env)
+data(mite.xy)
+
+mite.cca <- cca(log(mite + 1))
+mite.cca <- mso(mite.cca, mite.xy, grain =  1, permutations = 100)
+msoplot(mite.cca)
+mite.cca$vario
+
+## Constrained ordination with test for residual autocorrelation
+## and scale-invariance of species-environment relationships
+mite.cca <- cca(log(mite + 1) ~ SubsDens + WatrCont + Substrate + Shrub + Topo, mite.env)
+mite.cca <- mso(mite.cca, mite.xy, permutations = 100)
+msoplot(mite.cca)
+mite.cca$vario
 }
 \keyword{ spatial }
 \keyword{ multivariate }