[Vegan-commits] r907 - in pkg/vegan: inst man

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

Author: jarioksa
Date: 2009-07-27 02:37:34 +0200 (Mon, 27 Jul 2009)
New Revision: 907

Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/metaMDS.Rd
Log:
metaMDS actually does only random starts if input data were dissimilarities

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-07-26 17:19:06 UTC (rev 906)
+++ pkg/vegan/inst/ChangeLog	2009-07-27 00:37:34 UTC (rev 907)
@@ -5,7 +5,7 @@
 Version 1.16-22 (opened July 15, 2009)
 
 	* metaMDS: accepts now user supplied dissimilarities either as a
-	"dist" structure or as symmetric square matrix (on Susan Letcher's
+	"dist" structure or as symmetric square matrix (Susan Letcher's
 	wish). As a side effect, dissimilarity matrices are now correctly
 	detected and will not be wrongly treated as raw data.
 

Modified: pkg/vegan/man/metaMDS.Rd
===================================================================
--- pkg/vegan/man/metaMDS.Rd	2009-07-26 17:19:06 UTC (rev 906)
+++ pkg/vegan/man/metaMDS.Rd	2009-07-27 00:37:34 UTC (rev 907)
@@ -49,8 +49,8 @@
 \arguments{
   \item{comm}{Community data. Alternatively, dissimilarities either as
     a \code{\link{dist}} structure or as a symmetric square matrix. 
-    In the latter case, species scores are not calculated and
-    \code{\link{stepacross}} is not used. }
+    In the latter case all other stages are skipped except random 
+    starts. }
   \item{distance}{Dissimilarity index used in \code{\link{vegdist}}.}
   \item{k}{Number of dimensions in \code{\link[MASS]{isoMDS}}.}
   \item{trymax}{Maximum number of random starts in search of stable
@@ -171,7 +171,8 @@
     may have found good and relatively stable solutions although the
     function is not yet satisfied. Setting \code{trace = TRUE} will
     monitor the final stresses, and \code{plot = TRUE} will display
-    Procrustes overlay plots from each comparison.
+    Procrustes overlay plots from each comparison. This is the only
+    step performed if input data (\code{comm}) were dissimilarities. 
 
     \item Scaling of the results: \code{metaMDS} will run
     \code{postMDS} for the final result. Function \code{postMDS}
@@ -205,8 +206,6 @@
     calculation of species scores can be suppressed with \code{wascores
     = FALSE}. 
   }
-  Only steps 4 and 5 are performed if dissimilarities were suppied
-  instead of the community data.  
 }
 
 \value{