[Vegan-commits] r927 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2009-08-17 16:10:09 +0200 (Mon, 17 Aug 2009)
New Revision: 927

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/spantree.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/spantree.Rd
Log:
spantree got a 'call' item, and first argument is 'd' like in hclust()

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2009-08-13 18:56:28 UTC (rev 926)
+++ pkg/vegan/DESCRIPTION	2009-08-17 14:10:09 UTC (rev 927)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-23
-Date: August 11, 2009
+Version: 1.16-24
+Date: August 17, 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/spantree.R
===================================================================
--- pkg/vegan/R/spantree.R	2009-08-13 18:56:28 UTC (rev 926)
+++ pkg/vegan/R/spantree.R	2009-08-17 14:10:09 UTC (rev 927)
@@ -1,14 +1,14 @@
 "spantree" <-
-    function (dis, toolong = 0) 
+    function (d, toolong = 0) 
 {
-    dis <- as.dist(dis)
+    dis <- as.dist(d)
     n <- attr(dis, "Size")
     labels <- labels(dis)
     dis <- .C("primtree", dist = as.double(dis), toolong = as.double(toolong), 
               n = as.integer(n), val = double(n + 1),
               dad = integer(n + 1), NAOK = TRUE, PACKAGE = "vegan")
     out <- list(kid = dis$dad[2:n] + 1, dist = dis$val[2:n],
-                labels = labels)
+                labels = labels, call = match.call())
     class(out) <- "spantree"
     out
 }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-08-13 18:56:28 UTC (rev 926)
+++ pkg/vegan/inst/ChangeLog	2009-08-17 14:10:09 UTC (rev 927)
@@ -2,8 +2,13 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-23 (opened August 11, 2009)
+Version 1.16-24 (opened August 17, 2009)
 
+	* spantree: first argument 'd' like in hclust()instead of 'dis'.
+	Got a 'call' item so that update() works.
+	
+Version 1.16-23 (closed August 17, 2009)
+
 	* poolaccum: new function to find the extrapolated richness
 	values (or specpool() estimates) for random accumulation of
 	sites (with summary and plot methods). 

Modified: pkg/vegan/man/spantree.Rd
===================================================================
--- pkg/vegan/man/spantree.Rd	2009-08-13 18:56:28 UTC (rev 926)
+++ pkg/vegan/man/spantree.Rd	2009-08-17 14:10:09 UTC (rev 927)
@@ -11,7 +11,7 @@
   above the threshold or \code{NA}.  
 }
 \usage{
-spantree(dis, toolong = 0)
+spantree(d, toolong = 0)
 \method{cophenetic}{spantree}(x)
 \method{plot}{spantree}(x, ord, cex = 0.7, type = "p", labels, dlim,
      FUN = sammon,  ...)
@@ -19,7 +19,7 @@
 }
 
 \arguments{
-  \item{dis}{Dissimilarity data inheriting from class \code{dist} or
+  \item{d}{Dissimilarity data inheriting from class \code{dist} or
     a an object, such as a matrix, that can be converted to a
     dissimilarity matrix. Functions \code{\link{vegdist}} and
     \code{\link{dist}} are some functions producing suitable
@@ -89,6 +89,7 @@
   \item{dist }{Corresponding distance. If \code{kid = NA}, then
     \code{dist = 0}.}
   \item{labels }{Names of nodes as found from the input dissimilarities.} 
+  \item{call}{The function call.}
 }
 \references{
  Sedgewick, R. (1990). \emph{Algorithms in C}. Addison Wesley.