[Vegan-commits] r2160 - pkg/vegan/man

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

Author: jarioksa
Date: 2012-05-10 10:21:51 +0200 (Thu, 10 May 2012)
New Revision: 2160

Modified:
   pkg/vegan/man/ordiplot3d.Rd
Log:
example on envfit & ordiplot3d interfaces

Modified: pkg/vegan/man/ordiplot3d.Rd
===================================================================
--- pkg/vegan/man/ordiplot3d.Rd	2012-05-10 08:19:40 UTC (rev 2159)
+++ pkg/vegan/man/ordiplot3d.Rd	2012-05-10 08:21:51 UTC (rev 2160)
@@ -194,6 +194,14 @@
 ### Add species using xyz.convert function returned by ordiplot3d
 sp <- scores(ord, choices=1:3, display="species", scaling=3)
 text(pl$xyz.convert(sp), rownames(sp), cex=0.7, xpd=TRUE)
+### Two ways of adding fitted variables to ordination plots
+ord <- cca(dune)
+ef <- envfit(ord ~ Moisture + A1, dune.env, choices = 1:3)
+### 1. use argument 'envfit'
+ordiplot3d(ord, envfit = ef)
+### 2. use returned envfit.convert function for better user control
+pl3 <- ordiplot3d(ord)
+plot(pl3$envfit.convert(ef), at = pl3$origin)
 ### ordirgl
 ordirgl(ord, size=2)
 ordirgl(ord, display = "species", type = "t")