[Vegan-commits] r772 - in branches/1.15: R inst man

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

Author: jarioksa
Date: 2009-03-31 18:33:49 +0200 (Tue, 31 Mar 2009)
New Revision: 772

Modified:
   branches/1.15/R/ordisurf.R
   branches/1.15/inst/ChangeLog
   branches/1.15/man/ordisurf.Rd
Log:
updated ordisurf in branches/1.15: grid item and 'bubble' argument

Modified: branches/1.15/R/ordisurf.R
===================================================================
--- branches/1.15/R/ordisurf.R	2009-03-30 18:29:17 UTC (rev 771)
+++ branches/1.15/R/ordisurf.R	2009-03-31 16:33:49 UTC (rev 772)
@@ -1,7 +1,8 @@
 "ordisurf" <-
     function (x, y, choices = c(1, 2), knots = 10, family = "gaussian", 
               col = "red", thinplate = TRUE, add = FALSE, display = "sites", 
-              w = weights(x), main, nlevels = 10, levels, labcex = 0.6,  ...) 
+              w = weights(x), main, nlevels = 10, levels, labcex = 0.6,
+              bubble = FALSE, cex = 1, ...) 
 {
     weights.default <- function(object, ...) NULL
     GRID = 25
@@ -32,7 +33,12 @@
                  inpoly = as.integer(inpoly), PACKAGE="vegan")$inpoly
     is.na(fit) <- inpoly == 0
     if (!add) {
-        plot(X, asp = 1, ...)
+        if (bubble) {
+            if (is.numeric(bubble))
+                cex <- bubble
+            cex <- (y -  min(y))/diff(range(y)) * (cex-0.4) + 0.4
+        }
+        plot(X, asp = 1, cex = cex, ...)
     }
     if (!missing(main) || (missing(main) && !add)) {
         if (missing(main)) 
@@ -45,5 +51,7 @@
     contour(xn1, xn2, matrix(fit, nrow=GRID), col = col, add = TRUE,
             levels = levels, labcex = labcex,
             drawlabels = !is.null(labcex) && labcex > 0)
+    mod$grid <- list(x = xn1, y = xn2, z = matrix(fit, nrow = GRID))
+    class(mod) <- c("ordisurf", class(mod))
     return(mod)
 }

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-03-30 18:29:17 UTC (rev 771)
+++ branches/1.15/inst/ChangeLog	2009-03-31 16:33:49 UTC (rev 772)
@@ -5,6 +5,9 @@
 
 Version 1.15-2 (opened January 14, 2009)
 
+	* merged rev532, 596 to ordisurf: returns a grid item of fitted
+	surface, and gains option for bubble plots of observed values.
+
 	* merged new beals code by Miquel de Caceres (rev 528:531).
 
 	* copied dispindmorisita at rev769 from pkg/vegan.

Modified: branches/1.15/man/ordisurf.Rd
===================================================================
--- branches/1.15/man/ordisurf.Rd	2009-03-30 18:29:17 UTC (rev 771)
+++ branches/1.15/man/ordisurf.Rd	2009-03-31 16:33:49 UTC (rev 772)
@@ -9,7 +9,8 @@
 \usage{
 ordisurf(x, y, choices=c(1, 2), knots=10, family="gaussian", col="red",
      thinplate = TRUE, add = FALSE, display = "sites",
-     w = weights(x), main, nlevels = 10, levels, labcex = 0.6,  ...)
+     w = weights(x), main, nlevels = 10, levels, labcex = 0.6,
+     bubble = FALSE, cex = 1, ...)
 }
 
 \arguments{
@@ -34,13 +35,20 @@
     \code{nlevels} if \code{levels} are not supplied.}
   \item{labcex}{Label size in contours.  Setting this zero will suppress
     labels.}
+  \item{bubble}{Use \dQuote{bubble plot} for points, or vary the point
+    diameter by the value of the plotted variable. If \code{bubble} is
+    numeric, its value is used for the maximum symbol size (as in
+    \code{cex}), or if \code{bubble = TRUE}, the value of \code{cex} gives
+    the maximum. The minimum size will always be \code{cex = 0.4}.  The
+    option only has an effect if \code{add = FALSE}.}
+  \item{cex}{Character expansion of plotting symbols.}
   \item{\dots}{ Other graphical parameters. }
 }
 \details{
   Function \code{ordisurf} fits a smooth surface using thinplate splines
   in \code{\link[mgcv]{gam}}, and uses \code{\link[mgcv]{predict.gam}}
   to find fitted values in a regular grid.
-  Function plots the fitted contours with convex hull of data poitns 
+  Function plots the fitted contours with convex hull of data points 
   either over an existing ordination diagram or draws a new plot
   The function uses
   \code{\link{scores}} to extract ordination scores, and \code{x} can be
@@ -56,10 +64,21 @@
   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
@@ -78,7 +97,7 @@
 library(MASS)
 vare.dist <- vegdist(varespec)
 vare.mds <- isoMDS(vare.dist)
-with(varechem, ordisurf(vare.mds, Baresoil))
+with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
 ## Cover of Cladina arbuscula
 with(varespec, ordisurf(vare.mds, Cla.arb, family=quasipoisson)) 
 }