[Vegan-commits] r2187 - in pkg/vegan: R man

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

Author: jarioksa
Date: 2012-05-24 21:39:33 +0200 (Thu, 24 May 2012)
New Revision: 2187

Modified:
   pkg/vegan/R/metaMDS.R
   pkg/vegan/man/metaMDS.Rd
   pkg/vegan/man/monoMDS.Rd
Log:
warning on data insufficiency should be more elaborate to cover local & hybrid scaling and isoMDS

Modified: pkg/vegan/R/metaMDS.R
===================================================================
--- pkg/vegan/R/metaMDS.R	2012-05-24 18:49:05 UTC (rev 2186)
+++ pkg/vegan/R/metaMDS.R	2012-05-24 19:39:33 UTC (rev 2187)
@@ -40,8 +40,7 @@
     ## Nearly zero stress is usually not a good thing but a symptom of
     ## a problem: you may have insufficient data for NMDS
     if (out$stress < 1e-3) {
-        warning(gettextf("Stress is (nearly) zero - you may have insufficient data:\n  %d dimensions x %d points = %d estimated scores with %d dissimilarities",
-                out$ndim, out$nobj, out$ndim * out$nobj, out$ndis))
+        warning("Stress is (nearly) zero - you may have insufficient data")
     }     
     points <- postMDS(out$points, dis, plot = max(0, plot - 1), ...)
     if (is.null(rownames(points))) 

Modified: pkg/vegan/man/metaMDS.Rd
===================================================================
--- pkg/vegan/man/metaMDS.Rd	2012-05-24 18:49:05 UTC (rev 2186)
+++ pkg/vegan/man/metaMDS.Rd	2012-05-24 19:39:33 UTC (rev 2187)
@@ -55,7 +55,8 @@
     starts and centring and pc rotation of axes. }
   \item{distance}{Dissimilarity index used in \code{\link{vegdist}}.}
   \item{k}{Number of dimensions.  NB., the number of points \eqn{n}
-    should be \eqn{n > 2k + 1}{n > 2*k + 1}, and preferably higher.}
+    should be \eqn{n > 2k + 1}{n > 2*k + 1}, and preferably higher in
+    non-metric MDS.}
   \item{trymax}{Maximum number of random starts in search of stable
     solution.}
 

Modified: pkg/vegan/man/monoMDS.Rd
===================================================================
--- pkg/vegan/man/monoMDS.Rd	2012-05-24 18:49:05 UTC (rev 2186)
+++ pkg/vegan/man/monoMDS.Rd	2012-05-24 19:39:33 UTC (rev 2187)
@@ -28,7 +28,8 @@
     generated if this is missing.}
   
   \item{k}{Number of dimensions. NB., the number of points \eqn{n}
-    should be \eqn{n > 2k + 1}{n > 2*k + 1}, and preferably higher.}
+    should be \eqn{n > 2k + 1}{n > 2*k + 1}, and preferably higher in
+    non-metric MDS.}
 
   \item{model}{MDS model: \code{"global"} is normal non-metric MDS
     with a monotone regression, \code{"local"} is non-metric MDS with