[Phylobase-commits] r602 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Aug 27 05:41:01 CEST 2009
Author: francois
Date: 2009-08-27 05:41:01 +0200 (Thu, 27 Aug 2009)
New Revision: 602
Added:
pkg/man/tdata.Rd
Modified:
pkg/man/phylo4-accessors.Rd
pkg/man/phylo4-class.Rd
pkg/man/phylo4d-class.Rd
Log:
created a special man page for tdata, tweaked a few things in documentation
Modified: pkg/man/phylo4-accessors.Rd
===================================================================
--- pkg/man/phylo4-accessors.Rd 2009-08-27 02:17:47 UTC (rev 601)
+++ pkg/man/phylo4-accessors.Rd 2009-08-27 03:41:01 UTC (rev 602)
@@ -50,7 +50,10 @@
\item{nEdges}{\code{signature(object = "phylo4")}: number of edges}
\item{edges}{\code{signature(object = "phylo4")}: returns the edge
- matrix}
+ matrix}
+
+ \item{edgeOrder}{\code{signature(object = "phylo4")}: returns the
+ order in which the edges are stored}
\item{hasEdgeLength}{\code{signature(object = "phylo4")}: whether
tree has edge (branch) lengths}
Modified: pkg/man/phylo4-class.Rd
===================================================================
--- pkg/man/phylo4-class.Rd 2009-08-27 02:17:47 UTC (rev 601)
+++ pkg/man/phylo4-class.Rd 2009-08-27 03:41:01 UTC (rev 602)
@@ -3,14 +3,13 @@
\alias{phylo4_orderings}
\alias{phylo-class}
\alias{phylo4-class}
-\alias{[,phylo4,ANY,missing,missing-method}
\alias{print,phylo4-method}
\alias{show,phylo4-method}
\alias{head,phylo4-method}
\alias{tail,phylo4-method}
\alias{summary,phylo4-method}
\alias{names,phylo4-method}
-\title{phylo4 and extended classes}
+\title{Displaying phylo4 object}
\description{Classes for phylogenetic trees}
\section{Objects from the Class}{
Phylogenetic tree objects can be created by calls to the \code{\link{phylo4}} constructor function.
@@ -33,19 +32,19 @@
}
}
\section{Methods}{
- \describe{
- \item{\$}{\code{signature(x = "phylo4")}: extract a slot}
+ \describe{
\item{print}{\code{signature(x = "phylo4")}: print method}
\item{show}{\code{signature(object = "phylo4")}: show method }
\item{summary}{\code{signature(object = "phylo4")}: summary method}
\item{names}{\code{signature(x = "phylo4")}: gives the slot names}
\item{head}{\code{signature(object = "phylo4")}: show first few
-nodes}
+ nodes}
\item{tail}{\code{signature(object = "phylo4")}: show last few nodes} }
}
\usage{
\S4method{print}{phylo4}(x, edgeOrder = c("pretty", "real"), printall)
\S4method{summary}{phylo4}(object, quiet=FALSE)
+ \S4method{show}{phylo4}(object)
\S4method{names}{phylo4}(x)
}
\arguments{
@@ -79,7 +78,9 @@
to the names of the slots.
}
\seealso{the \code{\link{phylo4}} constructor, the \code{\link{checkPhylo4}}
- function to check the validity of \code{phylo4} objects. See also the \code{\link{phylo4d}} constructor and the \linkS4class{phylo4d} class.}
+ function to check the validity of \code{phylo4} objects. See also the
+ \code{\link{phylo4d}} constructor and the \linkS4class{phylo4d}
+ class.}
\author{Ben Bolker, Thibaut Jombart}
\examples{
Modified: pkg/man/phylo4d-class.Rd
===================================================================
--- pkg/man/phylo4d-class.Rd 2009-08-27 02:17:47 UTC (rev 601)
+++ pkg/man/phylo4d-class.Rd 2009-08-27 03:41:01 UTC (rev 602)
@@ -14,15 +14,9 @@
\alias{hasTipData}
\alias{hasTipData-methods}
\alias{hasTipData,phylo4d-method}
-\alias{tdata}
-\alias{tdata<-}
-\alias{tdata-methods}
-\alias{tdata,phylo4d-method}
-\alias{tdata<-,phylo4d-method}
\alias{addData}
\alias{addData,phylo4-method}
\alias{addData,phylo4d-method}
-\alias{[,phylo4d,ANY,ANY,ANY-method}
\title{phylo4d class}
\description{S4 class for phylogenetic tree and data.}
\section{Objects from the Class}{
@@ -59,21 +53,19 @@
\item{summary}{\code{signature(object = "phylo4d")}: summary method}
\item{names}{\code{signature(x = "phylo4d")}: gives the slots names}
\item{head}{\code{signature(object = "phylo4d")}: show first few
-nodes}
+ nodes}
\item{tail}{\code{signature(object = "phylo4d")}: show last few
-nodes}
- \item{hasNodeData}{\code{signature(object = "phylo4d")}: whether
- tree has internal node data}
- \item{hasTipData}{TODO}
+ nodes}
+ \item{hasNodeData}{\code{signature(object = "phylo4d")}: whether
+ tree has internal node data}
+ \item{hasTipData}{\code{signature(object = "phylo4d")}: whether tree
+ has data associated with its tips}
}
}
\usage{
\S4method{print}{phylo4d}(x, edgeOrder = c("pretty", "real"), printall=TRUE)
- \S4method{summary}{phylo4d}(object)
+ \S4method{summary}{phylo4d}(object, quiet=FALSE)
\S4method{names}{phylo4d}(x)
-\S4method{tdata}{phylo4d}(x, type=c("tip", "internal", "allnode"),
-label.type=c("row.names", "column"), empty.columns=TRUE, \dots)
- \S4method{tdata}{phylo4d}(object, type = "tip", \dots) <- value
}
\arguments{
\item{x}{a phylo4d object}
@@ -81,24 +73,25 @@
\item{edgeOrder}{Character string indicating whether the edges should be printed
as ordered in the tree "real" (e.g. preorder or postorder), or "pretty" printed
with tips collated together}
- \item{type}{TODO}
- \item{label.type}{TODO}
- \item{empty.columns}{TODO}
- \item{\dots}{TODO}
- \item{value}{TODO}
+ \item{quiet}{Should the summary be displayed on screen?}
\item{printall}{If TRUE all tip labels are printed}
}
\value{
The \code{summary} method invisibly returns a list with the
- following components: \cr
- - \code{name}: the name of the object \cr
- - \code{nb.tips}: the number of tips\cr
- - \code{nb.nodes}: the number of nodes \cr
+ following components:
+ - \code{name}: the name of the object
+ - \code{nb.tips}: the number of tips
+ - \code{nb.nodes}: the number of nodes
- The \code{names} method returns a vector of characters corresponding
- to the names of the slots.
+ The \code{names} method returns a vector of characters corresponding
+ to the names of the slots.
}
-\seealso{\code{\link{coerce-methods}} for translation functions. The \code{\link{phylo4d}} constructor and the \code{\link{formatData}} function to check the validity of trees and data. See also the \code{\link{phylo4}} constructor, the \linkS4class{phylo4} class, and the \code{\link{checkPhylo4}} function to check the validity of \code{phylo4} trees. }
+\seealso{\code{\link{coerce-methods}} for translation functions. The
+ \code{\link{phylo4d}} constructor and the \code{\link{formatData}}
+ function to check the validity of trees and data. See also the
+ \code{\link{phylo4}} constructor, the \linkS4class{phylo4} class,
+ and the \code{\link{checkPhylo4}} function to check the validity of
+ \code{phylo4} trees. }
\author{Ben Bolker, Thibaut Jombart}
\examples{
library(ape)
Added: pkg/man/tdata.Rd
===================================================================
--- pkg/man/tdata.Rd (rev 0)
+++ pkg/man/tdata.Rd 2009-08-27 03:41:01 UTC (rev 602)
@@ -0,0 +1,66 @@
+\name{tdata}
+\alias{tdata}
+\alias{tdata-method}
+\alias{tdata,phylo4d-method}
+\alias{tdata<-}
+\alias{tdata<-,phylo4d-method}
+\alias{tdata<-,phylo4d,ANY-method}
+\title{Retrieving or updating tip and node data in phylo4d objects}
+\description{
+ Method to retrieve or update tip, node or all data associated with a
+ phylogenetic tree stored as a phylo4d object
+}
+\usage{
+ \S4method{tdata}{phylo4d}(x, type=c("tip", "internal", "allnode"),
+ label.type=c("row.names", "column"), empty.columns=TRUE, \dots)
+ \S4method{tdata}{phylo4d,ANY}(x, type = "tip", \dots) <- value
+}
+\arguments{
+
+ \item{x}{A \code{phylo4d} object}
+ \item{type}{The type of data to retrieve or update:
+ \code{\dQuote{tip}} for data associated with tips,
+ \code{\dQuote{internal}} for data associated with internal nodes,
+ \code{\dQuote{allnode}} for data associated with tip and internal
+ nodes.}
+
+ \item{label.type}{How the tip/node labels from the tree be
+ returned? \code{\dQuote{row.names}} returns them as row names of
+ the data frame, \code{\dQuote{column}} returns the labels in the
+ first column of the data frame. This options is useful in the case
+ of missing (\code{NA}) or non-unique labels.}
+
+ \item{empty.columns}{Should columns filled with \code{NA} be
+ returned?}
+
+ \item{\dots}{Further arguments similar to those used by
+ \code{phylo4d} (e.g. \code{match.data}), see \link{phylo4d} for
+ more details.}
+
+ \item{value}{a data frame to replace the values associated with the
+ nodes specified by the argument \code{type}}
+
+}
+
+\section{Methods}{
+ \describe{
+ \item{tdata}{\code{signature(object="phylo4d")}: retrieve or update
+ data associated with a tree in a \code{phylo4d} object}
+ }
+}
+
+\value{
+ \code{tdata} returns a data frame
+}
+\seealso{
+ \code{\link{phylo4d}}
+}
+\examples{
+ data(geospiza)
+ tdata(geospiza)
+ tdata(geospiza, "tip") <- 1:nTips(geospiza)
+ tdata(geospiza)
+ \dontshow{data(geospiza)}
+}
+\author{Ben Bolker, Thibaut Jombart, Francois Michonneau}
+\keyword{methods}
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