[Vegan-commits] r546 - pkg/man

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

Author: jarioksa
Date: 2008-11-02 17:05:36 +0100 (Sun, 02 Nov 2008)
New Revision: 546

Modified:
   pkg/man/nestedtemp.Rd
Log:
nesteddisc: docs tell about reordering of tied columns

Modified: pkg/man/nestedtemp.Rd
===================================================================
--- pkg/man/nestedtemp.Rd	2008-11-02 15:56:02 UTC (rev 545)
+++ pkg/man/nestedtemp.Rd	2008-11-02 16:05:36 UTC (rev 546)
@@ -51,7 +51,13 @@
   (Patterson & Atmar 1986).  Function \code{nesteddisc} implements
   discrepancy index which is the number of ones that should be shifted
   to fill a row with ones in a table arranged by species frequencies
-  (Brualdi & Sanderson 1999). Function \code{nestedtemp} finds the
+  (Brualdi & Sanderson 1999). The original definition arranges species
+  (columns) by their frequencies, but did not have any method of
+  handling tied frequencies. The \code{nesteddisc} function tries to
+  order tied columns to minimize the discrepancy statistic but this is
+  rather slow, and with a large number of tied columns there is no
+  guarantee that the best ordering was found. In that case a warning
+  of tied columns will be issued. Function \code{nestedtemp} finds the
   matrix temperature which is defined as the sum of \dQuote{surprises}
   in arranged matrix.  In arranged unsurprising matrix all species
   within proportion given by matrix fill are in the upper left corner of