[Vegan-commits] r805 - branches/1.15/inst branches/1.15/man pkg/vegan/inst pkg/vegan/man

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

Author: jarioksa
Date: 2009-04-15 08:48:20 +0200 (Wed, 15 Apr 2009)
New Revision: 805

Modified:
   branches/1.15/inst/ChangeLog
   branches/1.15/man/nestedtemp.Rd
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/nestedtemp.Rd
Log:
nestedtemp.Rd tells that bipartite::nestedness ports BINMATNEST

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-04-14 19:21:18 UTC (rev 804)
+++ branches/1.15/inst/ChangeLog	2009-04-15 06:48:20 UTC (rev 805)
@@ -5,6 +5,10 @@
 
 Version 1.15-2 (opened January 14, 2009)
 
+	* nestedtemp.Rd tells that bipartite::nestedness is a direct port
+	of BINMATNEST of Rodriquez-Girones & Santamaria. Parallel change
+	with pkg/vegan.
+
 	* merged r800 (adonis uses less memory in permutation tests) and
 	r802 (example enhanced in adonis.Rd, with formatting).
 

Modified: branches/1.15/man/nestedtemp.Rd
===================================================================
--- branches/1.15/man/nestedtemp.Rd	2009-04-14 19:21:18 UTC (rev 804)
+++ branches/1.15/man/nestedtemp.Rd	2009-04-15 06:48:20 UTC (rev 805)
@@ -95,8 +95,10 @@
   matrix (\code{NODF}).  If you set \code{order = FALSE}, the statistic
   is evaluated with the current matrix ordering allowing tests of other
   meaningful hypothesis of matrix structure than ordering by row and
-  column totals (see Almeida-Neto et al. 2008).
-}
+  column totals (see Almeida-Neto et al. 2008). Function
+  \code{\link[bipartite]{nestedness}} in the \pkg{bipartite} package is
+  a direct port of the BINMATNEST programme of
+  \enc{Rodríguez-Gironés}{Rodriguez-Girones} & Santamaria (2006).  }
 
 \value{
   The result returned by a nestedness function contains an item called

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-04-14 19:21:18 UTC (rev 804)
+++ pkg/vegan/inst/ChangeLog	2009-04-15 06:48:20 UTC (rev 805)
@@ -4,6 +4,10 @@
 
 Version 1.16-17
 
+	* nestedtemp: docs tell that Carsten Dormann's bipartite package
+	has a direct port of BINMATNEST programme of Rodriquez-Girones &
+	Santamaria. 
+
 	* anosim: uses much less memory allowing analysis of larger
 	problems (number of rows, number of iterations). The change
 	concerns only internal data structures, and the permutation

Modified: pkg/vegan/man/nestedtemp.Rd
===================================================================
--- pkg/vegan/man/nestedtemp.Rd	2009-04-14 19:21:18 UTC (rev 804)
+++ pkg/vegan/man/nestedtemp.Rd	2009-04-15 06:48:20 UTC (rev 805)
@@ -71,26 +71,28 @@
   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
-  the matrix, and the surprise of the absence or presences is the
-  diagonal distance from the fill line (Atmar & Patterson
-  1993). Function tries to pack species and sites to a low
-  temperature (\enc{Rodríguez-Gironés}{Rodriguez-Girones} & Santamaria
-  2006), but this is an iterative procedure, and the temperatures
-  usually vary among runs.  Function \code{nestedtemp} also has a
-  \code{plot} method which can display either incidences or temperatures
-  of the surprises. Matrix temperature was rather vaguely described
-  (Atmar & Patterson 1993), but
+  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 the matrix, and the
+  surprise of the absence or presences is the diagonal distance from the
+  fill line (Atmar & Patterson 1993). Function tries to pack species and
+  sites to a low temperature (\enc{Rodríguez-Gironés}{Rodriguez-Girones}
+  & Santamaria 2006), but this is an iterative procedure, and the
+  temperatures usually vary among runs.  Function \code{nestedtemp} also
+  has a \code{plot} method which can display either incidences or
+  temperatures of the surprises. Matrix temperature was rather vaguely
+  described (Atmar & Patterson 1993), but
   \enc{Rodríguez-Gironés}{Rodriguez-Girones} & Santamaria (2006) are
   more explicit and their description is used here. However, the results
   probably differ from other implementations, and users should be
-  cautious in interpreting the results. The details of calculations
-  are explained in the \code{\link{vignette}} \emph{Design decisions
-  and implementation} that you can read using functions
-  \code{\link{vignette}} or \code{\link{vegandocs}}.
+  cautious in interpreting the results. The details of calculations are
+  explained in the \code{\link{vignette}} \emph{Design decisions and
+  implementation} that you can read using functions
+  \code{\link{vignette}} or \code{\link{vegandocs}}. Function
+  \code{\link[bipartite]{nestedness}} in the \pkg{bipartite} package is
+  a direct port of the BINMATNEST programme of
+  \enc{Rodríguez-Gironés}{Rodriguez-Girones} & Santamaria (2006).
 
   Function \code{nestednodf} implements a nestedness metric based on
   overlap and decreasing fill (Almeida-Neto et al., 2008). Two basic