[Vegan-commits] r2179 - pkg/vegan/R

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

Author: jarioksa
Date: 2012-05-23 18:47:53 +0200 (Wed, 23 May 2012)
New Revision: 2179

Modified:
   pkg/vegan/R/monoMDS.R
   pkg/vegan/R/print.metaMDS.R
   pkg/vegan/R/print.monoMDS.R
Log:
only warn about insufficient data in NMDS, but more loudly

Modified: pkg/vegan/R/monoMDS.R
===================================================================
--- pkg/vegan/R/monoMDS.R	2012-05-23 15:24:31 UTC (rev 2178)
+++ pkg/vegan/R/monoMDS.R	2012-05-23 16:47:53 UTC (rev 2179)
@@ -90,12 +90,9 @@
         nobj <- nrow(mat)
     }
     ## ndis: number of >0 dissimilarities (distinct points)
-    ndis <- sum(dist > 0)
-    ## some people try to use NMDS with too few points and too many
-    ## dimensions
-    if (ndis <= k * nobj)
-        stop(gettextf("Not enough data: you have %d dissimilarities >0,\n  and you ask %d scores (%d dimensions times %d points)",
-                      ndis, k * nobj, k, nobj))
+    ndis <- length(dist)
+        warning(gettextf("Not enough data: you have %d dissimilarities >0,\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: pkg/vegan/R/print.metaMDS.R
===================================================================
--- pkg/vegan/R/print.metaMDS.R	2012-05-23 15:24:31 UTC (rev 2178)
+++ pkg/vegan/R/print.metaMDS.R	2012-05-23 16:47:53 UTC (rev 2179)
@@ -17,11 +17,18 @@
             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")
+        if (x$stress < 1e-3) {
+            cat("Stress is (nearly) zero - you may have too few points for NMDS:\n")
+            cat(gettextf("You have %d dissimilarities >0, and you ask for %d scores\n", sum(x$dist > 0), prod(dim(x$points))))
+            cat(gettextf("(%d points x %d dimensions).\n", nrow(x$points), ncol(x$points)))
+        }                 
+    }
     z <- x$points
     scal <- c(if (attr(z, "centre")) "centring",
               if (attr(z, "pc")) "PC rotation",

Modified: pkg/vegan/R/print.monoMDS.R
===================================================================
--- pkg/vegan/R/print.monoMDS.R	2012-05-23 15:24:31 UTC (rev 2178)
+++ pkg/vegan/R/print.monoMDS.R	2012-05-23 16:47:53 UTC (rev 2179)
@@ -36,6 +36,13 @@
                       "Stress nearly unchanged",
                       "Scale factor of gradient nearly zero")
     cat("Stopped after ", x$iters, " iterations: ", stoplab, "\n", sep="")
+    if (x$stress < 1e-3) {
+        cat("Stress is (nearly) zero: check your analysis\n")
+        ndis <- sum(x$dist > 0)
+        pdim <- dim(x$points)
+        cat(gettextf("You asked % d scores (%d points x %d dimensions)\nand  you have %d dissimilarities > 0\n",
+                    prod(pdim), pdim[1], pdim[2], ndis))
+    }
     invisible(x)
 }