[Vegan-commits] r2860 - in pkg/vegan: R man

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

Author: jarioksa
Date: 2014-02-21 11:37:54 +0100 (Fri, 21 Feb 2014)
New Revision: 2860

Added:
   pkg/vegan/man/scores.hclust.Rd
Removed:
   pkg/vegan/R/scores.hclust.Rd
Log:
scores.hclust.Rd was in the wrong directory

Deleted: pkg/vegan/R/scores.hclust.Rd
===================================================================
--- pkg/vegan/R/scores.hclust.Rd	2014-02-21 10:31:22 UTC (rev 2859)
+++ pkg/vegan/R/scores.hclust.Rd	2014-02-21 10:37:54 UTC (rev 2860)
@@ -1,70 +0,0 @@
-\name{scores.hclust}
-\alias{scores.hclust}
-
-\title{
-  Coordinates of Leaves and Internal Nodes in a hclust Tree
-}
-
-\description{ The function finds the coordinates that will be used for
-  internal nodes and leaves when an \code{\link{hclust}} object is
-  plotted. These help in annotating the plotted dendrogram.  }
-
-\usage{
-scores.hclust(x, display = "internal", ...)
-}
-
-\arguments{
-  \item{x}{
-  An \code{\link{hclust}} result object.
-}
-  \item{display}{
-  Return \code{"internal"} nodes or \code{"terminal"} nodes (also
-  called \code{"leaves"}.
-}
-  \item{\dots}{
-  Other arguments passed to the function (ignored).
-}
-}
-
-\details{
-
-  The function returns the coordinates of nodes in an
-  \code{\link{hclust}} plot as two-column matrix. First column called
-  \code{x} gives the horizontal coordinates which for \eqn{n} terminal
-  nodes (leaves) is an integer sequence \eqn{1..n}. The second column
-  called \code{height} gives the merge value. For terminal nodes
-  (leaves) this the value at which the item is merged to the tree, and
-  in plots the labels can still hang below this level, as defined by
-  the argument \code{hang} in \code{\link{plot.hclust}}.
-
-  The function only works with \code{\link{hclust}} objects; it does
-  not work with \code{\link{dendrogram}}.
-
-}
-
-\value{
-  A two-column matrix of coordinates.
-}
-
-\author{
-  Jari Oksanen.
-}
-
-\note{
-  This function may be removed as useless.  
-}
-
-
-\seealso{
-  \code{\link{hclust}}, \code{\link{plot.hclust}}.
-}
-\examples{
-## Show values that were used in reordering a tree
-data(mite, mite.env)
-hc <- hclust(vegdist(mite))
-hc <- with(mite.env, reorder(hc, WatrCont))
-with(mite.env, plot(hc, labels=round(WatrCont), cex=0.7))
-ordilabel(scores(hc), label=round(hc$value), cex=0.7)
-}
-\keyword{ multivariate }
-

Copied: pkg/vegan/man/scores.hclust.Rd (from rev 2859, pkg/vegan/R/scores.hclust.Rd)
===================================================================
--- pkg/vegan/man/scores.hclust.Rd	                        (rev 0)
+++ pkg/vegan/man/scores.hclust.Rd	2014-02-21 10:37:54 UTC (rev 2860)
@@ -0,0 +1,70 @@
+\name{scores.hclust}
+\alias{scores.hclust}
+
+\title{
+  Coordinates of Leaves and Internal Nodes in a hclust Tree
+}
+
+\description{ The function finds the coordinates that will be used for
+  internal nodes and leaves when an \code{\link{hclust}} object is
+  plotted. These help in annotating the plotted dendrogram.  }
+
+\usage{
+scores.hclust(x, display = "internal", ...)
+}
+
+\arguments{
+  \item{x}{
+  An \code{\link{hclust}} result object.
+}
+  \item{display}{
+  Return \code{"internal"} nodes or \code{"terminal"} nodes (also
+  called \code{"leaves"}.
+}
+  \item{\dots}{
+  Other arguments passed to the function (ignored).
+}
+}
+
+\details{
+
+  The function returns the coordinates of nodes in an
+  \code{\link{hclust}} plot as two-column matrix. First column called
+  \code{x} gives the horizontal coordinates which for \eqn{n} terminal
+  nodes (leaves) is an integer sequence \eqn{1..n}. The second column
+  called \code{height} gives the merge value. For terminal nodes
+  (leaves) this the value at which the item is merged to the tree, and
+  in plots the labels can still hang below this level, as defined by
+  the argument \code{hang} in \code{\link{plot.hclust}}.
+
+  The function only works with \code{\link{hclust}} objects; it does
+  not work with \code{\link{dendrogram}}.
+
+}
+
+\value{
+  A two-column matrix of coordinates.
+}
+
+\author{
+  Jari Oksanen.
+}
+
+\note{
+  This function may be removed as useless.  
+}
+
+
+\seealso{
+  \code{\link{hclust}}, \code{\link{plot.hclust}}.
+}
+\examples{
+## Show values that were used in reordering a tree
+data(mite, mite.env)
+hc <- hclust(vegdist(mite))
+hc <- with(mite.env, reorder(hc, WatrCont))
+with(mite.env, plot(hc, labels=round(WatrCont), cex=0.7))
+ordilabel(scores(hc), label=round(hc$value), cex=0.7)
+}
+\keyword{ multivariate }
+