[Vegan-commits] r2209 - in branches/2.0: R inst man

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

Author: jarioksa
Date: 2012-06-02 12:47:59 +0200 (Sat, 02 Jun 2012)
New Revision: 2209

Modified:
   branches/2.0/R/metaMDS.R
   branches/2.0/R/monoMDS.R
   branches/2.0/R/print.metaMDS.R
   branches/2.0/inst/ChangeLog
   branches/2.0/man/metaMDS.Rd
   branches/2.0/man/monoMDS.Rd
Log:
merge selected commits in 2172 thru 2187: metaMDS warns about too good stress

Modified: branches/2.0/R/metaMDS.R
===================================================================
--- branches/2.0/R/metaMDS.R	2012-06-02 05:39:41 UTC (rev 2208)
+++ branches/2.0/R/metaMDS.R	2012-06-02 10:47:59 UTC (rev 2209)
@@ -37,6 +37,11 @@
     out <- metaMDSiter(dis, k = k, trymax = trymax, trace = trace, 
                        plot = plot, previous.best = previous.best,
                        engine = engine, ...)
+    ## Nearly zero stress is usually not a good thing but a symptom of
+    ## a problem: you may have insufficient data for NMDS
+    if (out$stress < 1e-3) {
+        warning("Stress is (nearly) zero - you may have insufficient data")
+    }     
     points <- postMDS(out$points, dis, plot = max(0, plot - 1), ...)
     if (is.null(rownames(points))) 
         rownames(points) <- rownames(comm)

Modified: branches/2.0/R/monoMDS.R
===================================================================
--- branches/2.0/R/monoMDS.R	2012-06-02 05:39:41 UTC (rev 2208)
+++ branches/2.0/R/monoMDS.R	2012-06-02 10:47:59 UTC (rev 2209)
@@ -89,13 +89,8 @@
         iregn <- 3
         nobj <- nrow(mat)
     }
-    ## ndis: number dissimilarities
+    ## ndis: number of >0 dissimilarities (distinct points)
     ndis <- length(dist)
-    ## some people try to use NMDS with too few points and too many
-    ## dimensions
-    if (ndis <= k * nobj)
-        stop(gettextf("Not enough data for NMDS: you have %d dissimilarities,\n  and you ask %d scores (%d dimensions times %d points)",
-                      ndis, k * nobj, k, nobj))
     ## starting configuration
     if (missing(y)) {
         y <- matrix(runif(nobj*k, -1, 1), nobj, k)

Modified: branches/2.0/R/print.metaMDS.R
===================================================================
--- branches/2.0/R/print.metaMDS.R	2012-06-02 05:39:41 UTC (rev 2208)
+++ branches/2.0/R/print.metaMDS.R	2012-06-02 10:47:59 UTC (rev 2209)
@@ -17,11 +17,13 @@
             cat(", ", c("weak", "strong")[x$ities], " ties", sep = "")
         cat("\n")
     }
-    if (x$converged) 
+    if (x$converged) { 
         cat("Two convergent solutions found after", x$tries, 
             "tries\n")
-    else cat("No convergent solutions - best solution after", 
-             x$tries, "tries\n")
+    } else {
+        cat("No convergent solutions - best solution after", 
+            x$tries, "tries\n")
+    }
     z <- x$points
     scal <- c(if (attr(z, "centre")) "centring",
               if (attr(z, "pc")) "PC rotation",

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2012-06-02 05:39:41 UTC (rev 2208)
+++ branches/2.0/inst/ChangeLog	2012-06-02 10:47:59 UTC (rev 2209)
@@ -12,6 +12,8 @@
 	* merge r2178, 2180: ordipointlabel gains 'select' argument.
 	* merge r2173-2176, 2185: ordihull labels, semintransparent
 	colours in ordihull & ordiellipse.
+	* merge r2172,2179,2181,2184,2186,2187: metaMDS warns about too
+	good stress.
 	* merge r2170: bioenv accepts dissimilarities as input.
 	* merge r2167: warn about unequal aspect ratio in ordiplot3d.
 	* merge r2162: set equal axis scales for ordiplot3d.

Modified: branches/2.0/man/metaMDS.Rd
===================================================================
--- branches/2.0/man/metaMDS.Rd	2012-06-02 05:39:41 UTC (rev 2208)
+++ branches/2.0/man/metaMDS.Rd	2012-06-02 10:47:59 UTC (rev 2209)
@@ -54,7 +54,9 @@
     In the latter case all other stages are skipped except random 
     starts and centring and pc rotation of axes. }
   \item{distance}{Dissimilarity index used in \code{\link{vegdist}}.}
-  \item{k}{Number of dimensions in \code{\link[MASS]{isoMDS}}.}
+  \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 in
+    non-metric MDS.}
   \item{trymax}{Maximum number of random starts in search of stable
     solution.}
 

Modified: branches/2.0/man/monoMDS.Rd
===================================================================
--- branches/2.0/man/monoMDS.Rd	2012-06-02 05:39:41 UTC (rev 2208)
+++ branches/2.0/man/monoMDS.Rd	2012-06-02 10:47:59 UTC (rev 2209)
@@ -26,7 +26,10 @@
   \item{dist}{Input dissimilarities.}
   \item{y}{Starting configuration. A random configuration will be
     generated if this is missing.}
-  \item{k}{Number of dimensions.}
+  
+  \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 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