[Vegan-commits] r932 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-08-20 18:48:34 +0200 (Thu, 20 Aug 2009)
New Revision: 932

Added:
   pkg/vegan/R/summary.ordiellipse.R
   pkg/vegan/R/summary.ordihull.R
Modified:
   pkg/vegan/R/ordiellipse.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/ordihull.Rd
Log:
ordihull & ordiellipse got summary method that returns centres and areas

Modified: pkg/vegan/R/ordiellipse.R
===================================================================
--- pkg/vegan/R/ordiellipse.R	2009-08-20 14:04:21 UTC (rev 931)
+++ pkg/vegan/R/ordiellipse.R	2009-08-20 16:48:34 UTC (rev 932)
@@ -43,6 +43,7 @@
             if (label)
                 ordiArgAbsorber(mat$center[1], mat$center[2], labels=is,
                                FUN = text, ...)
+            mat$scale <- t
             res[[is]] <- mat
         }
     }

Added: pkg/vegan/R/summary.ordiellipse.R
===================================================================
--- pkg/vegan/R/summary.ordiellipse.R	                        (rev 0)
+++ pkg/vegan/R/summary.ordiellipse.R	2009-08-20 16:48:34 UTC (rev 932)
@@ -0,0 +1,12 @@
+### Centres and areas of plotted ellipses. The principal axes of the
+### conic (oblique ellipse) are found from the eigenvalues of the
+### covariance matrix.
+`summary.ordiellipse` <-
+    function(object, ...)
+{
+    cnts <- sapply(object, function(x) x$center)
+    areas <- sapply(object,
+                    function(x)
+                    prod(sqrt(eigen(x$cov)$values)) * pi * x$scale^2)
+    rbind(cnts, `Area` = areas)
+}

Added: pkg/vegan/R/summary.ordihull.R
===================================================================
--- pkg/vegan/R/summary.ordihull.R	                        (rev 0)
+++ pkg/vegan/R/summary.ordihull.R	2009-08-20 16:48:34 UTC (rev 932)
@@ -0,0 +1,29 @@
+### Centres and areas of convex hulls. The area of the *convex* polygon
+### is found as the *sum* of the areas of triangles. 
+`summary.ordihull` <-
+    function(object, ...)
+{
+    ## The area of triangle from vertices using eq. 8.10 of Spiegel,
+    ## Liu & Lipschitz (1999), Mathematical Handbook of Formulas and
+    ## Tables (2nd ed.), McGraw & Hill. The hull is closed, so that
+    ## first and last point are identical.
+    triarea <- function(x) {
+        ones <- rep(1, 3)
+        if (nrow(x) < 4)
+            return(0)
+        if (nrow(x) == 4)
+            return(abs(det(cbind(x[-1,], ones))/2))
+        else {
+            sol <- 0
+            cnt <- colMeans(x[-1,])
+            for (i in 2:nrow(x)) {
+                mat <- cbind(rbind(cnt, x[(i-1):i,]), ones)
+                sol <- sol + abs(det(mat)/2)
+            }
+            return(sol)
+        }
+    }
+    areas <- sapply(object, function(x) triarea(x))
+    cnts <- sapply(object, function(x) colMeans(x[-1,]))
+    rbind(cnts, `Area` = areas)
+}

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-08-20 14:04:21 UTC (rev 931)
+++ pkg/vegan/inst/ChangeLog	2009-08-20 16:48:34 UTC (rev 932)
@@ -8,10 +8,9 @@
 	name of the group in the centre of the ellipse or the hull. The
 	functions now return invisibly data on their plots for each
 	plotted item: ordiellipse() the covariance matrix (cov.wt()
-	result), and ordihull() the coordinates of the hull
-	vertices. Nothing is done with these yet, but the intention is to
-	write a summary() method to give the coordinates of the centres
-	and surface areas of the plotted hulls or ellipses.
+	result), and ordihull() the coordinates of the hull vertices.
+	These inivisible results have a summary() method that displays the
+	centres of the hulls or ellipses and their surface areas.
 
 	* ordiellipse: does not depend on the 'ellipse' package, but finds
 	the coordinates of ellipse using the equation taken from the 'car'

Modified: pkg/vegan/man/ordihull.Rd
===================================================================
--- pkg/vegan/man/ordihull.Rd	2009-08-20 14:04:21 UTC (rev 931)
+++ pkg/vegan/man/ordihull.Rd	2009-08-20 16:48:34 UTC (rev 932)
@@ -9,6 +9,8 @@
 \alias{weights.cca}
 \alias{weights.rda}
 \alias{weights.decorana}
+\alias{summary.ordihull}
+\alias{summary.ordiellipse}
 
 \title{Add Graphical Items to Ordination Diagrams}
 \description{
@@ -97,6 +99,14 @@
   An ellipsoid hull can be drawn with function
   \code{\link[cluster]{ellipsoidhull}} of package \pkg{cluster}.
 
+  Functions \code{ordihull} and \code{ordiellipse} return the
+  \code{\link{invisible}} plotting structure. In \code{ordihull} this
+  is a list of coordinates of the hull and in \code{ordiellipse} a
+  list of covariance matrices and scales used in drawing the
+  ellipses. These result objects have a summary method that returns
+  the coordinates of the centroids of the ellipses or hulls and their
+  surface areas in user units.
+
   Function \code{ordiarrows} draws
   \code{\link{arrows}} and \code{ordisegments} draws line
   \code{\link{segments}} between successive items in the
@@ -143,13 +153,17 @@
 attach(dune.env)
 ## pass non-graphical arguments without warnings
 plot(mod, type="n", scaling = 3)
-ordihull(mod, Management, scaling = 3, label = TRUE)
+## Catch the invisible result of ordihull...
+pl <- ordihull(mod, Management, scaling = 3, label = TRUE)
+## ... and find centres and areas of the hulls
+summary(pl)
 ordispider(mod, col="red", scaling = 3)
 plot(mod, type = "p", display="sites")
 ordicluster(mod, hclust(vegdist(dune)), prune=3, col = "blue")
 plot(mod, type="n", display = "sites")
 text(mod, display="sites", labels = as.character(Management))
-ordiellipse(mod, Management, kind="se", conf=0.95, lwd=2, col="blue")
+pl <- ordiellipse(mod, Management, kind="se", conf=0.95, lwd=2, col="blue")
+summary(pl)
 }
 \keyword{aplot }