[Vegan-commits] r651 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2009-01-07 15:19:06 +0100 (Wed, 07 Jan 2009)
New Revision: 651

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/nestednodf.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/nestedtemp.Rd
Log:
nestednodf gained an option not to arrange rows and columns allowing tests of user-specified orderings

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2008-12-21 08:00:52 UTC (rev 650)
+++ pkg/vegan/DESCRIPTION	2009-01-07 14:19:06 UTC (rev 651)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-8
-Date: December 17, 2008
+Version: 1.16-9
+Date: Januay 7, 2009
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: pkg/vegan/R/nestednodf.R
===================================================================
--- pkg/vegan/R/nestednodf.R	2008-12-21 08:00:52 UTC (rev 650)
+++ pkg/vegan/R/nestednodf.R	2009-01-07 14:19:06 UTC (rev 651)
@@ -1,10 +1,11 @@
 `nestednodf` <- 
-    function(comm)
+    function(comm, order = TRUE)
 {
     comm <- ifelse(comm > 0, 1, 0)
     ## Order rows and columns
-    comm <- comm[order(rowSums(comm), decreasing=TRUE),
-                 order(colSums(comm), decreasing=TRUE)]    
+    if (order)
+        comm <- comm[order(rowSums(comm), decreasing=TRUE),
+                     order(colSums(comm), decreasing=TRUE)]    
     dimensions <- dim(comm)
     fill <- sum(comm)/length(comm)
     N.paired <- 0

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2008-12-21 08:00:52 UTC (rev 650)
+++ pkg/vegan/inst/ChangeLog	2009-01-07 14:19:06 UTC (rev 651)
@@ -2,8 +2,14 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-8 (opened Dec 17, 2008)
+Version 1.16-9 (opened Jan 7, 2009)
 
+	* nestednodf: gained argument 'order = TRUE' allowing tests for
+	other orderings than using marginal frequencies (default)
+	following suggestion by Almeida-Neto et al. (2008).
+	
+Version 1.16-8 (closed Jan 7, 2009)
+
 	* Fixed unescaped $-signs in documentation files after Ripley told
 	to do so ("[Rd] Misuse of $<matn expressions>$ in Rd files",
 	https://stat.ethz.ch/pipermail/r-devel/2008-December/051634.html) 

Modified: pkg/vegan/man/nestedtemp.Rd
===================================================================
--- pkg/vegan/man/nestedtemp.Rd	2008-12-21 08:00:52 UTC (rev 650)
+++ pkg/vegan/man/nestedtemp.Rd	2009-01-07 14:19:06 UTC (rev 651)
@@ -26,7 +26,7 @@
 nestedn0(comm)
 nesteddisc(comm)
 nestedtemp(comm, ...)
-nestednodf(comm)
+nestednodf(comm, order = TRUE)
 \method{plot}{nestedtemp}(x, kind = c("temperature", "incidendce"),
     col=rev(heat.colors(100)),  names = FALSE, ...)
 }
@@ -37,7 +37,9 @@
   \item{col}{Colour scheme for matrix temperatures.}
   \item{kind}{The kind of plot produced.}
   \item{names}{Label columns and rows in the plot using names in \code{comm}.
-    If it is a logical vector of length 2, row and column labels are returned accordingly.}
+    If it is a logical vector of length 2, row and column labels are
+    returned accordingly.}
+  \item[order}{Order rows and columns by frequencies.}
   \item{\dots}{Other arguments to functions.}
 }
 
@@ -97,8 +99,11 @@
   right to left columns and from down to up rows, and (2) decreasing
   marginal totals between all pairs of columns and all pairs of
   rows. The nestedness statistic is evaluated separately for columns
-  (\code{N columns}) for rows (\code{N rows}) and combined for the
-  whole matrix (\code{NODF}). 
+  (\code{N columns}) for rows (\code{N rows}) and combined for the whole
+  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).
 }
 
 \value{