[Vegan-commits] r1964 - pkg/vegan/man

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

Author: jarioksa
Date: 2011-10-29 19:22:16 +0200 (Sat, 29 Oct 2011)
New Revision: 1964

Modified:
   pkg/vegan/man/goodness.metaMDS.Rd
   pkg/vegan/man/metaMDS.Rd
Log:
clarify iso/monoMDS differences in stress + version history

Modified: pkg/vegan/man/goodness.metaMDS.Rd
===================================================================
--- pkg/vegan/man/goodness.metaMDS.Rd	2011-10-28 16:50:04 UTC (rev 1963)
+++ pkg/vegan/man/goodness.metaMDS.Rd	2011-10-29 17:22:16 UTC (rev 1964)
@@ -20,7 +20,7 @@
 \arguments{
   \item{object}{A result object from \code{\link{metaMDS}}, 
     \code{\link{monoMDS}} or \code{\link[MASS]{isoMDS}}. }
-  \item{dis}{Dissimilarities.  This should  not used with
+  \item{dis}{Dissimilarities.  This should not be used with
     \code{\link{metaMDS}} or \code{\link{monoMDS}}, but must be used with
     \code{\link[MASS]{isoMDS}}.}
   \item{pch}{Plotting character for points.  Default is dependent on the
@@ -32,9 +32,14 @@
   \item{\dots}{Other parameters to functions, e.g. graphical parameters.}
 }
 \details{
-  Function \code{goodness.metaMDS} finds a goodness of fit statistic for
-  observations (points).  This is defined so that sum of squared values
-  is equal to squared stress.  Large values indicate poor fit. 
+  Function \code{goodness.metaMDS} finds a goodness of fit statistic
+  for observations (points).  This is defined so that sum of squared
+  values is equal to squared stress.  Large values indicate poor fit.
+  The absolute values of the goodness statistic depend on the
+  definition of the stress: \code{\link[MASS]{isoMDS}} expresses
+  stress in percents, and therefore its goodness values are 100 times
+  higher than those of \code{\link{monoMDS}} which expresses the
+  stress as a proportion.
 
   Function \code{stressplot} draws a Shepard diagram which is a plot
   of ordination distances and monotone or linear fit line against

Modified: pkg/vegan/man/metaMDS.Rd
===================================================================
--- pkg/vegan/man/metaMDS.Rd	2011-10-28 16:50:04 UTC (rev 1963)
+++ pkg/vegan/man/metaMDS.Rd	2011-10-29 17:22:16 UTC (rev 1964)
@@ -252,17 +252,19 @@
 
 \value{ Function \code{metaMDS} returns an object of class
   \code{metaMDS}. The final site ordination is stored in the item
-  \code{points}, and species ordination in the item
-  \code{species}. The other items store the information on the steps
-  taken and the items returned by the \code{engine} function. The
-  object has \code{print}, \code{plot}, \code{points} and \code{text}
-  methods.  Functions \code{metaMDSdist} and \code{metaMDSredist}
-  return \code{\link{vegdist}} objects.  Function \code{initMDS}
-  returns a random configuration which is intended to be used within
+  \code{points}, and species ordination in the item \code{species},
+  and the stress in item \code{stress} (NB, the scaling of the stress
+  depends on the \code{engine}: \code{\link[MASS]{isoMDS}} uses
+  percents, and \code{\link{monoMDS}} proportions in the range \eqn{0
+  \ldots 1}). The other items store the information on the steps taken
+  and the items returned by the \code{engine} function. The object has
+  \code{print}, \code{plot}, \code{points} and \code{text} methods.
+  Functions \code{metaMDSdist} and \code{metaMDSredist} return
+  \code{\link{vegdist}} objects.  Function \code{initMDS} returns a
+  random configuration which is intended to be used within
   \code{\link[MASS]{isoMDS}} only.  Functions \code{metaMDSiter} and
   \code{postMDS} returns the result of NMDS with updated
-  configuration.  
-}
+  configuration.  }
 
 
 \references{
@@ -306,11 +308,10 @@
   to \code{FALSE} with a warning.  
 }
 
-\section{Warning}{ \code{metaMDS} used \code{\link[MASS]{isoMDS}} as
-  its NMDS engine till version 1.18-28, when this was replaced with
-  the \code{\link{monoMDS}} function. You can set argument
-  \code{engine} to select the old engine.
-}
+\section{Warning}{\code{metaMDS} uses \code{\link{monoMDS}} as its
+  NMDS \code{engine} from \pkg{vegan} version 2.0-0, when it replaced
+  the \code{\link[MASS]{isoMDS}} function. You can set argument
+  \code{engine} to select the old engine.}
 
 \seealso{\code{\link{monoMDS}} (and \code{\link[MASS]{isoMDS}}), 
   \code{\link{decostand}},