[Vegan-commits] r872 - branches/1.15/inst/doc

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

Author: jarioksa
Date: 2009-06-17 10:12:05 +0200 (Wed, 17 Jun 2009)
New Revision: 872

Modified:
   branches/1.15/inst/doc/FAQ-vegan.texi
Log:
merged FAQ update on negative eigenvalues in capscale (r859)

Modified: branches/1.15/inst/doc/FAQ-vegan.texi
===================================================================
--- branches/1.15/inst/doc/FAQ-vegan.texi	2009-06-12 10:41:38 UTC (rev 871)
+++ branches/1.15/inst/doc/FAQ-vegan.texi	2009-06-17 08:12:05 UTC (rev 872)
@@ -311,7 +311,6 @@
 * Can you analyse binary or cover class data?::  
 * Why dissimilarities in vegan differ from other sources?::  
 * Zero dissimilarities in isoMDS::  
-* Warnings of negative eigenvalues in capscale::  
 * Variance explained by ordination axes::  
 * Is it possible to have passive points in ordination?::  
 * Class variables and dummies::  
@@ -346,7 +345,7 @@
 Another reason may be that indices indeed are defined differently,
 because people use same names for different indices.
 
- at node Zero dissimilarities in isoMDS, Warnings of negative eigenvalues in capscale, Why dissimilarities in vegan differ from other sources?, Ordination
+ at node Zero dissimilarities in isoMDS, Variance explained by ordination axes, Why dissimilarities in vegan differ from other sources?, Ordination
 @section Zero dissimilarities in isoMDS
 
 You can use argument @code{zerodist = "add"} in @code{metaMDS} or
@@ -359,30 +358,7 @@
 zero dissimilarity, and you have to resort to the kluge (or work
 harder with your data).
 
- at node Warnings of negative eigenvalues in capscale, Variance explained by ordination axes, Zero dissimilarities in isoMDS, Ordination
- at section Warnings of negative eigenvalues in capscale
-
-Function @code{capscale} regularly and normally gives warnings of
-negative eigenvalues. These warnings are harmless, and @code{capscale}
-will ignore the axes with negative eigenvalues. The warnings are
-generated by underlying function @code{cmdscale} or metric
-multidimensional scaling (a.k.a. principal coordinates analysis), The
-metric MDS assumes that dissimilarities are metric, but most
-ecologically useful indices are semimetric. The warnings only concern
-the very last minor axes, and the axes with negative eigenvalues will
-be ignored in @code{capscale}. If the warnings are
-disturbing, you can use argument @code{add = TRUE} in @code{capscale}
-which implements ``correction method 2'' of Legendre & Legendre (1998,
-p. 434) in @code{cmdscale}.
-
-You can get a warning about negative eigenvalues also with metric
-indices if you have deficit rank data. This happens, for instance,
-when number of species (columns) is lower than number of sites (rows),
-or if some sites are linear combinations of other sites. You can find
-the rank of the data using, for instance, vegan function @code{rda}
-which is identical to @code{capscale} with Euclidean distance.
-
- at node Variance explained by ordination axes, Is it possible to have passive points in ordination?, Warnings of negative eigenvalues in capscale, Ordination
+ at node Variance explained by ordination axes, Is it possible to have passive points in ordination?, Zero dissimilarities in isoMDS, Ordination
 @section Variance explained by ordination axes.
 
 In general, vegan does not directly give any statistics on the