[Vegan-commits] r787 - branches/1.15/R branches/1.15/inst branches/1.15/man pkg/vegan/inst

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

Author: gsimpson
Date: 2009-04-04 11:20:59 +0200 (Sat, 04 Apr 2009)
New Revision: 787

Modified:
   branches/1.15/R/betadisper.R
   branches/1.15/inst/ChangeLog
   branches/1.15/man/betadisper.Rd
   pkg/vegan/inst/ChangeLog
Log:
merge r786 to 1.15 branch and update both changelogs

Modified: branches/1.15/R/betadisper.R
===================================================================
--- branches/1.15/R/betadisper.R	2009-04-04 09:15:43 UTC (rev 786)
+++ branches/1.15/R/betadisper.R	2009-04-04 09:20:59 UTC (rev 787)
@@ -1,6 +1,8 @@
 `betadisper` <-
-    function(d, group, type = c("centroid","median"), tol = 1e-07)
+    function(d, group, type = c("centroid","median"))
 {
+    ## Tolerance for zero Eigenvalues
+    TOL <- 1e-7
     ## uses code from stats:::cmdscale by R Core Development Team
     if(!inherits(d, "dist"))
         stop("distances 'd' must be a 'dist' object")
@@ -19,14 +21,9 @@
     e <- eigen(-x/2, symmetric = TRUE)
     vectors <- e$vectors
     eig <- e$values
-    ## check d is Euclidean
-    w0 <- eig[n] / eig[1]
-    if(w0 > -tol)
-        r <- sum(eig > (eig[1] * tol))
-    else
-        r <- length(eig)
-    ## truncate eig if d is Euclidean
-    eig <- eig[(rs <- seq_len(r))]
+    ## Remove zero eigenvalues
+    eig <- eig[abs(eig/eig[1]) > TOL]
+    rs <- seq_along(eig)
     ## scale Eigenvectors
     vectors <- vectors[, rs, drop = FALSE] %*% diag(sqrt(abs(eig)))
     ## store which are the positive eigenvalues

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-04-04 09:15:43 UTC (rev 786)
+++ branches/1.15/inst/ChangeLog	2009-04-04 09:20:59 UTC (rev 787)
@@ -5,8 +5,8 @@
 
 Version 1.15-2 (opened January 14, 2009)
 
-	* merged r781 from trunk to 1.15 branch: betadisper bug fix and
-	upgrade to work more nicely with Euclidean 'd'.
+	* merged r781 and r786  from trunk to 1.15 branch: betadisper 
+	bug fix and upgrade to work more nicely with Euclidean 'd'.
 
 	* copied contribdiv from pkg/vegan at rev681 (vegan at rev775). 
 	

Modified: branches/1.15/man/betadisper.Rd
===================================================================
--- branches/1.15/man/betadisper.Rd	2009-04-04 09:15:43 UTC (rev 786)
+++ branches/1.15/man/betadisper.Rd	2009-04-04 09:20:59 UTC (rev 787)
@@ -25,7 +25,7 @@
   Tukey's 'Honest Significant Difference' method.
 }
 \usage{
-betadisper(d, group, type = c("centroid", "median"), tol = 1e-07)
+betadisper(d, group, type = c("centroid", "median"))
 
 \method{anova}{betadisper}(object, \dots)
 
@@ -51,7 +51,6 @@
     level (i.e.~one group).}
   \item{type}{the type of analysis to perform. Only \code{type =
       "centroid"} is currently supported.}
-  \item{tol}{tolerance for checking if \code{d} is Euclidean.}
   \item{display}{character; partial match to access scores for
     \code{"sites"} or \code{"species"}.}
   \item{object, x}{an object of class \code{"betadisper"}, the result of a

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-04-04 09:15:43 UTC (rev 786)
+++ pkg/vegan/inst/ChangeLog	2009-04-04 09:20:59 UTC (rev 787)
@@ -14,9 +14,8 @@
 
 	* betadisper: Fix bug corrects the way distance to centroid is
 	computed when only one group is present in the data. betadisper 
-	can now also detect if 'd' is Euclidean up to a tolerance that 
-	can be set using new argument 'tol'. Bug report and suggested
-	improvements provided by Etienne Laliberté.
+	can now also detect if 'd' is Euclidean, zapping zero Eigenvalues. 
+	Bug report and suggested improvements provided by Etienne Laliberté.
 	
 Version 1.16-16 (closed April 2, 2009)