[Vegan-commits] r1483 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2011-02-10 21:38:32 +0100 (Thu, 10 Feb 2011)
New Revision: 1483

Modified:
   pkg/vegan/R/eigenvals.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/eigenvals.Rd
Log:
eigenvals learnt labdsv pco & pca objects

Modified: pkg/vegan/R/eigenvals.R
===================================================================
--- pkg/vegan/R/eigenvals.R	2011-02-10 11:21:42 UTC (rev 1482)
+++ pkg/vegan/R/eigenvals.R	2011-02-10 20:38:32 UTC (rev 1483)
@@ -88,6 +88,32 @@
     out
 }
 
+## labdsv::pco
+
+`eigenvals.pco` <-
+    function(x)
+{
+    out <- x$eig
+    class(out) <- "eigenvals"
+    out
+}
+
+## labdsv::pca
+
+`eigenvals.pca` <-
+    function(x)
+{
+    out <- x$sdev^2
+    ## pca() may return only some first eigenvalues
+    if ((seig <- sum(out)) < x$totdev) {
+        names(out) <- paste("PC", seq_along(out), sep="")
+        out <- c(out, "Rest" = x$totdev - seig)
+    }
+    class(out) <- "eigenvals"
+    out
+}
+        
+
 `print.eigenvals` <-
     function(x, ...)
 {

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-02-10 11:21:42 UTC (rev 1482)
+++ pkg/vegan/inst/ChangeLog	2011-02-10 20:38:32 UTC (rev 1483)
@@ -4,7 +4,8 @@
 
 Version 1.18-22 (opened January 19, 2011)
 
-	* eigenvals: learnt to know 'dudi' objects of ade4 package.
+	* eigenvals: learnt to know 'dudi' objects of the ade4 package,
+	and 'pco' an 'pca' obejct of the labdsv package.
 
 	* betadisper: streamlined code somewhat.
 

Modified: pkg/vegan/man/eigenvals.Rd
===================================================================
--- pkg/vegan/man/eigenvals.Rd	2011-02-10 11:21:42 UTC (rev 1482)
+++ pkg/vegan/man/eigenvals.Rd	2011-02-10 20:38:32 UTC (rev 1483)
@@ -41,8 +41,9 @@
 \details{
   This is a generic function that has methods for \code{\link{cca}},
   \code{\link{wcmdscale}}, \code{\link{pcnm}}, \code{\link{prcomp}},
-  \code{\link{princomp}},  and\code{\link[ade4]{dudi}} (of \pkg{ade4}) 
-  result objects. The default method also
+  \code{\link{princomp}}, \code{\link[ade4]{dudi}} (of \pkg{ade4}), and 
+  \code{\link[labdsv]{pca}} and \code{\link[labdsv]{pco}} (of 
+  \pkg{labdsv}) result objects. The default method also
   extracts eigenvalues if the result looks like being from
   \code{\link{eigen}} or \code{\link{svd}}.  Functions
   \code{\link{prcomp}} and \code{\link{princomp}} contain square roots