[Vegan-commits] r965 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2009-08-31 12:32:33 +0200 (Mon, 31 Aug 2009)
New Revision: 965

Removed:
   pkg/vegan/R/ripley.subs.R
   pkg/vegan/R/ripley.subsets.R
Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/bioenv.default.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/bioenv.Rd
Log:
use combn() instead of ripley.subs() in bioenv.default

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2009-08-27 13:30:53 UTC (rev 964)
+++ pkg/vegan/DESCRIPTION	2009-08-31 10:32:33 UTC (rev 965)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-25
-Date: August 23, 2009
+Version: 1.16-26
+Date: August 31, 2009
 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/vegan/R/bioenv.default.R
===================================================================
--- pkg/vegan/R/bioenv.default.R	2009-08-27 13:30:53 UTC (rev 964)
+++ pkg/vegan/R/bioenv.default.R	2009-08-31 10:32:33 UTC (rev 965)
@@ -41,7 +41,7 @@
                 "...", sep = "")
             flush.console()
         }
-        sets <- ripley.subs(i, 1:n)
+        sets <- t(combn(1:n, i))
         if (!is.matrix(sets)) 
             sets <- as.matrix(t(sets))
         est <- numeric(nrow(sets))

Deleted: pkg/vegan/R/ripley.subs.R
===================================================================
--- pkg/vegan/R/ripley.subs.R	2009-08-27 13:30:53 UTC (rev 964)
+++ pkg/vegan/R/ripley.subs.R	2009-08-31 10:32:33 UTC (rev 965)
@@ -1,5 +0,0 @@
-"ripley.subs" <-
-    function(x, string)
-{
-    ripley.subsets(length(string), x, string)
-}

Deleted: pkg/vegan/R/ripley.subsets.R
===================================================================
--- pkg/vegan/R/ripley.subsets.R	2009-08-27 13:30:53 UTC (rev 964)
+++ pkg/vegan/R/ripley.subsets.R	2009-08-31 10:32:33 UTC (rev 965)
@@ -1,15 +0,0 @@
-"ripley.subsets" <-
-    function(n, r, s = 1:n)
-{
-    if(mode(n) != "numeric" || length(n) != 1
-       || n < 1 || (n %% 1) != 0) stop("bad value of n")
-    if(mode(r) != "numeric" || length(r) != 1
-       || r < 1 || (r %% 1) != 0) stop("bad value of r")
-    if(!is.atomic(s) || length(s) < n)
-        stop("s is either non-atomic or too short")
-    fun <- function(n, r, s)
-        if(r <= 0) vector(mode(s), 0) else if(r >= n) s[1:n] else
-    rbind(cbind(s[1], Recall(n - 1, r - 1, s[-1])),
-          Recall(n - 1, r, s[-1]))
-    fun(n, r, s)
-}

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-08-27 13:30:53 UTC (rev 964)
+++ pkg/vegan/inst/ChangeLog	2009-08-31 10:32:33 UTC (rev 965)
@@ -2,8 +2,14 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-25 (opened August 23, 2009)
+Version 1.16-26 (opened August 31,2009)
 
+	* bioenv: uses standard R function combn() and removes
+	ripley.subs() and ripley.subsets() from vegan. The result should
+	be unchanged.
+
+Version 1.16-25 (closed August 31, 2009)
+
 	* mantel.correlog: updated to the version 1.4 of Pierre Legendre's
 	package. 
 

Modified: pkg/vegan/man/bioenv.Rd
===================================================================
--- pkg/vegan/man/bioenv.Rd	2009-08-27 13:30:53 UTC (rev 964)
+++ pkg/vegan/man/bioenv.Rd	2009-08-31 10:32:33 UTC (rev 965)
@@ -5,8 +5,6 @@
 \alias{print.bioenv}
 \alias{summary.bioenv}
 \alias{print.summary.bioenv}
-\alias{ripley.subsets}
-\alias{ripley.subs}
 
 \title{Best Subset of Environmental Variables with
   Maximum (Rank) Correlation with Community Dissimilarities }
@@ -80,8 +78,7 @@
   community structure to environmental variables. \emph{Marine Ecology
     Progress Series}, 92, 205--219.
 }
-\author{ Jari Oksanen. The code for selecting all possible subsets was
-  posted to the R mailing list by Prof. B. D. Ripley in 1999. }
+\author{ Jari Oksanen }
 
 \note{
   If you want to study the \sQuote{significance} of \code{bioenv}