[Vegan-commits] r532 - in pkg: . R inst man

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

Author: jarioksa
Date: 2008-10-27 09:02:55 +0100 (Mon, 27 Oct 2008)
New Revision: 532

Modified:
   pkg/DESCRIPTION
   pkg/R/ordisurf.R
   pkg/inst/ChangeLog
   pkg/man/ordisurf.Rd
Log:
ordisurf: returns a mgcv:::gam object amended with item 'grid' containing x, y and z values used by contour() for the surface

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-10-22 03:47:43 UTC (rev 531)
+++ pkg/DESCRIPTION	2008-10-27 08:02:55 UTC (rev 532)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-2
-Date: October 21, 2008
+Version: 1.16-3
+Date: October 27, 2008
 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/R/ordisurf.R
===================================================================
--- pkg/R/ordisurf.R	2008-10-22 03:47:43 UTC (rev 531)
+++ pkg/R/ordisurf.R	2008-10-27 08:02:55 UTC (rev 532)
@@ -45,5 +45,7 @@
     contour(xn1, xn2, matrix(fit, nrow=GRID), col = col, add = TRUE,
             levels = levels, labcex = labcex,
             drawlabels = !is.null(labcex) && labcex > 0)
+    mod$grid <- list(x = xn1, y = xn2, z = matrix(fit, nrow = GRID))
+    class(mod) <- c("ordisurf", class(mod))
     return(mod)
 }

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-10-22 03:47:43 UTC (rev 531)
+++ pkg/inst/ChangeLog	2008-10-27 08:02:55 UTC (rev 532)
@@ -2,15 +2,18 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-2 (opened October 10, 2008)
+Version 1.16-3 (opened October 27, 2008)
 
+	* ordisurf: returns x, y and z used by contour() following a query
+	"[R-sig-eco] output from ordisurf" on Oct 23, 2008.
+	
+Version 1.16-2 (closed October 27, 2008) --- for Annukka
+
 	* beals: replaced old beals.R with the new code by Miquel de
 	Caceres with new methods described in De Caceres & Legendre
 	(Oecologia 156, 657-669; 2008). This also implements the
 	cross-validatory Beals of Munzbergova & Herben (Oikos 104,
-	408-414; 2004) plus many new options of unbiasing estimates. In
-	addition to new beals, there is a function for bealsing only one
-	target species.
+	408-414; 2004) plus many new options of unbiasing estimates. 
 
 	* permatfull: bug of row/col marins is fixed, shuffle argument is
 	added to enable individual and sample based randomisation of count

Modified: pkg/man/ordisurf.Rd
===================================================================
--- pkg/man/ordisurf.Rd	2008-10-22 03:47:43 UTC (rev 531)
+++ pkg/man/ordisurf.Rd	2008-10-27 08:02:55 UTC (rev 532)
@@ -56,10 +56,21 @@
   accordance with constrained \code{\link{cca}}, you should set
   \code{display = "lc"} (and possibly \code{scaling = 2}).
 }
+
 \value{
-  Function is usually called for its side effect of drawing the contour
-  plot, but it returns the result object of \code{\link[mgcv]{gam}}.
+  Function is usually called for its side effect of drawing the
+  contour plot. The function returns the result object of class
+  \code{"ordisurf"} that inherits from \code{\link[mgcv]{gam}} used
+  internally to fit the surface, but adds an item \code{grid} that
+  contains the data for the grid surface. The item \code{grid} has
+  elements \code{x} and \code{y} which are vectors of axis coordinates,
+  and element \code{z} that is a matrix of fitted values for
+  \code{\link{contour}}. The values outside the convex hull of observed
+  points are \code{NA} in \code{z}. The \code{\link[mgcv]{gam}}
+  component of the result can be used for further analysis like
+  predicting new values (see \code{\link[mgcv]{predict.gam}}).
 }
+
 \author{ Dave Roberts and Jari Oksanen }
 \note{   
   The default is to use thinplate splines.  These make sense in