[Vegan-commits] r2182 - pkg/vegan/inst/doc

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

Author: jarioksa
Date: 2012-05-24 14:08:01 +0200 (Thu, 24 May 2012)
New Revision: 2182

Modified:
   pkg/vegan/inst/doc/FAQ-vegan.texi
Log:
FAQ about insufficient data in NMDS

Modified: pkg/vegan/inst/doc/FAQ-vegan.texi
===================================================================
--- pkg/vegan/inst/doc/FAQ-vegan.texi	2012-05-24 08:35:23 UTC (rev 2181)
+++ pkg/vegan/inst/doc/FAQ-vegan.texi	2012-05-24 12:08:01 UTC (rev 2182)
@@ -298,6 +298,7 @@
 * Can you analyse binary or cover class data?::  
 * Why dissimilarities in @pkg{vegan} differ from other sources?::  
 * Why NMDS stress is sometimes 0.1 and sometimes 10?::  
+* I get zero stress but no convergent solutions in @code{metaMDS}::  
 * Zero dissimilarities in isoMDS::  
 * How the RDA results are scaled?::  
 * cca fails with ``data.frame expected'' or ``"site.env" missing''::  
@@ -351,9 +352,9 @@
 Another reason may be that indices indeed are defined differently,
 because people use same names for different indices.
 
- at node Why NMDS stress is sometimes 0.1 and sometimes 10?, Zero dissimilarities in isoMDS, Why dissimilarities in @pkg{vegan} differ from other sources?, Ordination
+ at node Why NMDS stress is sometimes 0.1 and sometimes 10?, I get zero stress but no convergent solutions in @code{metaMDS}, Why dissimilarities in @pkg{vegan} differ from other sources?, Ordination
 @section Why @acronym{NMDS} stress is sometimes 0.1 and sometimes 10?
-
+q
 Stress is a proportional measure of badness of fit. The proportions can
 be expressed either as parts of one or as percents.  Function
 @code{isoMDS} (@pkg{MASS} package) uses percents, and function @code{monoMDS}
@@ -363,7 +364,25 @@
 100 times higher in @code{isoMDS} than in @code{monoMDS}.  Both of these
 conventions are equally correct.
 
- at node Zero dissimilarities in isoMDS, How the RDA results are scaled?, Why NMDS stress is sometimes 0.1 and sometimes 10?, Ordination
+ at node I get zero stress but no convergent solutions in @code{metaMDS}, Zero dissimilarities in isoMDS, Why NMDS stress is sometimes 0.1 and sometimes 10?, Ordination
+ at section I get zero stress but no convergent solutions in @code{metaMDS}
+
+Most common reason is that you have too few observations for your
+ at acronym{NMDS}. For @code{n} observations (points) and @code{k}
+dimensions you need to estimate @code{n*k} parameters (ordination
+scores) using @code{n*(n-1)/2} dissimilarities.  For @code{k} dimensions
+you must have @code{n > 2*k + 1}, or for two dimensions at least six
+points.  In some degenerate situations you may need even a larger number
+of points.  If you have a lower number of points, you can find an
+undefined number of perfect (stress is zero) but different solutions.
+Conventional wisdom due to Kruskal is that you should have @code{n > 4*k
++ 1} points for @code{k} dimensions.  A typical symptom of insufficient
+data is that you have (nearly) zero stress but no two convergent
+solutions.  In those cases you should reduce the number of dimensions
+(@code{k}) and with very small data sets you should not use @code{NMDS},
+but rely on metric methods.
+
+ at node Zero dissimilarities in isoMDS, How the RDA results are scaled?, I get zero stress but no convergent solutions in @code{metaMDS}, Ordination
 @section Zero dissimilarities in isoMDS
 
 Function @code{metaMDS} uses function @code{monoMDS} as its default