[Phylobase-commits] r362 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Dec 20 02:30:38 CET 2008
Author: bbolker
Date: 2008-12-20 02:30:38 +0100 (Sat, 20 Dec 2008)
New Revision: 362
Modified:
pkg/man/nNodes-methods.Rd
pkg/man/phylo4.Rd
pkg/man/phylo4d.Rd
pkg/man/phyloXXYY.Rd
pkg/man/tree.plot.Rd
pkg/man/treePlot-methods.Rd
Log:
various example tweaks and doc additions
Modified: pkg/man/nNodes-methods.Rd
===================================================================
--- pkg/man/nNodes-methods.Rd 2008-12-20 01:01:10 UTC (rev 361)
+++ pkg/man/nNodes-methods.Rd 2008-12-20 01:30:38 UTC (rev 362)
@@ -24,6 +24,7 @@
\alias{edgeLength-methods}
\alias{edgeLength,phylo4-method}
\alias{nodeType}
+\alias{nodeType,phylo4-method}
\alias{isRooted}
\alias{isRooted-methods}
\alias{isRooted,phylo4-method}
Modified: pkg/man/phylo4.Rd
===================================================================
--- pkg/man/phylo4.Rd 2008-12-20 01:01:10 UTC (rev 361)
+++ pkg/man/phylo4.Rd 2008-12-20 01:30:38 UTC (rev 362)
@@ -21,7 +21,7 @@
\item{\dots}{fixme?}
}
\details{
- The minimum information necessary to create a phylobase tree object is a valid edge matrix. The edge matrix describes the topology of the phylogeny. Each row describes a branch of the phylogeny, with the (descendant) node number in column 2 and it's ancestor's node number in column 1. These numbers are used internally and must be unique for each node.
+ The minimum information necessary to create a phylobase tree object is a valid edge matrix. The edge matrix describes the topology of the phylogeny. Each row describes a branch of the phylogeny, with the (descendant) node number in column 2 and its ancestor's node number in column 1. These numbers are used internally and must be unique for each node.
The labels designate either nodes or edges. The vector \code{node.label} names internal nodes, and together with \code{tip.label}, name all nodes in the tree. The vector \code{edge.label} names all branches in the tree. All label vectors are optional, and if they are not given, internally-generated labels will be assigned. The labels, whether user-specified or internally generated, must be unique as they are used to join species data with phylogenetic trees.
}
\author{phylobase team}
@@ -31,18 +31,20 @@
function to check the validity of \code{phylo4} objects. See also the \code{\link{phylo4d}} constructor, and \linkS4class{phylo4d} class.}
\examples{
# a three species tree:
-mytree <- phylo4(edge=matrix(data=c(4,1, 4,5, 5,2, 5,3), ncol=2, byrow=TRUE), tip.label=c("speciesA", "speciesB", "speciesC"))
+mytree <- phylo4(edge=matrix(data=c(4,1, 4,5, 5,2, 5,3,NA,4), ncol=2, byrow=TRUE), tip.label=c("speciesA", "speciesB", "speciesC"))
mytree
plot(mytree)
# another way to specify the same tree:
-mytree <- phylo4(edge=cbind(c(4,4,5,5), c(1,5,2,3)), tip.label=c("speciesA", "speciesB", "speciesC"))
+mytree <- phylo4(edge=cbind(c(4,4,5,5,NA), c(1,5,2,3,4)), tip.label=c("speciesA", "speciesB", "speciesC"))
# another way:
-mytree <- phylo4(edge=rbind(c(4,1), c(4,5), c(5,2), c(5,3)), tip.label=c("speciesA", "speciesB", "speciesC"))
+mytree <- phylo4(edge=rbind(c(4,1), c(4,5), c(5,2), c(5,3), c(NA,4)), tip.label=c("speciesA", "speciesB", "speciesC"))
# with branch lengths:
-mytree <- phylo4(edge=rbind(c(4,1), c(4,5), c(5,2), c(5,3)), tip.label=c("speciesA", "speciesB", "speciesC"), edge.length=c(1, .2, .8, .8))
+mytree <- phylo4(edge=rbind(c(4,1), c(4,5), c(5,2), c(5,3), c(NA,4)),
+tip.label=c("speciesA", "speciesB", "speciesC"), edge.length=c(1, .2,
+.8, .8, NA))
plot(mytree)
}
\keyword{classes}
Modified: pkg/man/phylo4d.Rd
===================================================================
--- pkg/man/phylo4d.Rd 2008-12-20 01:01:10 UTC (rev 361)
+++ pkg/man/phylo4d.Rd 2008-12-20 01:30:38 UTC (rev 362)
@@ -121,9 +121,9 @@
merge.tip.node = FALSE))
### Example with 'all.data'
-nodeLabels(geoTree) <- as.character(nodeNumbers(geoTree))
+nodeLabels(geoTree) <- as.character(nodeId(geoTree))
rAllData <- data.frame(randomTrait = rnorm(nTips(geoTree) + nNodes(geoTree)),
-row.names = c(labels(geoTree),nodeNumbers(geoTree)))
+row.names = c(labels(geoTree),nodeId(geoTree)))
exGeo5 <- phylo4d(geoTree, all.data = rAllData)
Modified: pkg/man/phyloXXYY.Rd
===================================================================
--- pkg/man/phyloXXYY.Rd 2008-12-20 01:01:10 UTC (rev 361)
+++ pkg/man/phyloXXYY.Rd 2008-12-20 01:30:38 UTC (rev 362)
@@ -1,13 +1,11 @@
\name{phyloXXYY}
\alias{phyloXXYY}
-%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Calculate node x and y coordinates }
\description{
Calculates the node x and y locations for plotting a phylogenetic tree.}
\usage{
phyloXXYY(phy, tip.order = NULL)
}
-%- maybe also 'usage' for other objects documented here.
\arguments{
\item{phy}{ A \code{phylo4} or \code{phylo4d} object. }
\item{tip.order}{ Unused. A character vector indicating the ordering of tip nodes}
@@ -23,7 +21,6 @@
\item{phy.orig}{The original \code{phylo4} or \code{phylo4d} object}
}
-% \references{ ~put references to the literature/web site here ~ }
\author{Peter Cowan \email{pdc at berkeley.edu}}
\seealso{\code{\link{segs}}, \code{treePlot}, \code{\link{tree.plot}}}
@@ -31,7 +28,8 @@
data(geospiza)
coor <- phyloXXYY(geospiza)
-plot(coor$xx, coor$yy, pch = 20)
+## na.omit is temporary hack
+plot(coor$xx, na.omit(coor$yy), pch = 20)
}
\keyword{methods}
Modified: pkg/man/tree.plot.Rd
===================================================================
--- pkg/man/tree.plot.Rd 2008-12-20 01:01:10 UTC (rev 361)
+++ pkg/man/tree.plot.Rd 2008-12-20 01:30:38 UTC (rev 362)
@@ -1,6 +1,5 @@
\name{tree.plot}
\alias{tree.plot}
-%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Plot a phylo4 object }
\description{
Plots the phylogenetic tree contained in a \code{phylo4} or \code{phylo4d} object.
Modified: pkg/man/treePlot-methods.Rd
===================================================================
--- pkg/man/treePlot-methods.Rd 2008-12-20 01:01:10 UTC (rev 361)
+++ pkg/man/treePlot-methods.Rd 2008-12-20 01:30:38 UTC (rev 362)
@@ -1,5 +1,8 @@
\name{treePlot-methods}
\docType{methods}
+\alias{treePlot}
+\alias{plot,pdata,missing-method}
+\alias{plot,phylo4,missing-method}
\alias{treePlot-method}
\alias{treePlot,phylo4,phylo4d-method}
\title{ Phylogeny plotting }
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