[Phylobase-commits] r683 - in pkg: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 30 01:44:29 CEST 2009
Author: pdc
Date: 2009-09-30 01:44:29 +0200 (Wed, 30 Sep 2009)
New Revision: 683
Modified:
pkg/R/class-multiphylo4.R
pkg/man/multiPhylo-class.Rd
Log:
Disable the functionality (basically nonexistent) of mutliPhylo4(d) objects. This commit causes a helpful error to be issued anytime one attempts to make such and object and leaves the help as a note about possible future versions. We plan on implementing this, so I'll leave the files in place, hopefully as a useful guide
addresses bug #607, which I will move to a feature request
Modified: pkg/R/class-multiphylo4.R
===================================================================
--- pkg/R/class-multiphylo4.R 2009-09-29 23:11:00 UTC (rev 682)
+++ pkg/R/class-multiphylo4.R 2009-09-29 23:44:29 UTC (rev 683)
@@ -6,3 +6,8 @@
setClass("multiPhylo4d", representation(tip.data = "data.frame"),
contains = "multiPhylo4")
+
+setMethod("initialize", "multiPhylo4", function(.Object, ...) {
+ stop('multiPhylo and multiphylo4d not yet implemented.
+ Try using a list of phylo4(d) objects and lapply()')
+})
Modified: pkg/man/multiPhylo-class.Rd
===================================================================
--- pkg/man/multiPhylo-class.Rd 2009-09-29 23:11:00 UTC (rev 682)
+++ pkg/man/multiPhylo-class.Rd 2009-09-29 23:44:29 UTC (rev 683)
@@ -5,62 +5,62 @@
\alias{multiPhylo4d-class}
\alias{tbind}
\title{multiPhylo4 and extended classes}
-\description{Classes for lists of phylogenetic trees
-(FIXME: passes check but very incomplete)}
-\section{Objects from the Class}{
- Objects can be created by calls of the form \code{new("phylo4", ...)}
- Translation from other phylogenetic packages ...
- }
-\section{Slots}{
- \describe{
- \item{\code{phylo}:}{Matrix of edges}
- \item{\code{edge.length}:}{Numeric vector of edge lengths}
- \item{\code{Nnode}:}{Integer: number of nodes}
- \item{\code{tip.label}:}{Character vector of tip labels}
- \item{\code{root.edge}:}{Integer: root edge (NA if none)}
- \item{\code{phylolist}:}{(multiPhylo4) list of phylogenetic trees (each of which
- may be of type \code{phylo4d}, containing node and/or edge data)}
-}
-}
-\section{Methods}{
- \describe{
- \item{\$}{\code{signature(x = "phylo4")}: extract a slot}
- \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 slots names}
-}
-}
-% commented to eliminate Note: on build
-%\usage{
-% }
- \arguments{
- \item{x}{a phylo4 object}
- \item{printlen}{Maximum number of tip labels to print}
- \item{quiet}{a logical stating whether the results of the summary
- should be printed to the screen (FALSE, default) or not (TRUE)}
- \item{\dots}{additional arguments (for generic consistency)}
- }
- \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
- - \code{mean.el}: mean of edge lengths \cr
- - \code{var.el}: variance of edge lengths (estimate for population) \cr
- - \code{sumry.el}: summary (i.e. range and quartiles) of the edge
- lengths \cr
+\description{Classes for lists of phylogenetic trees. These classes and methods are planned for a future version of \code{phylobase}.}
- The \code{names} method returns a vector of characters corresponding
- to the names of the slots.
- }
- \author{Ben Bolker, Thibaut Jombart}
-\examples{
-### An extract from Sibley and Ahlquist (1990)
-cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);", file = "ex.tre", sep = "\n")
-tree.owls <- read.tree("ex.tre", keep.multi = TRUE)
-tree.owls
-(as(tree.owls, "multiPhylo4"))
-}
+% \section{Objects from the Class}{
+% Objects can be created by calls of the form \code{new("phylo4", ...)}
+% Translation from other phylogenetic packages ...
+% }
+% \section{Slots}{
+% \describe{
+% \item{\code{phylo}:}{Matrix of edges}
+% \item{\code{edge.length}:}{Numeric vector of edge lengths}
+% \item{\code{Nnode}:}{Integer: number of nodes}
+% \item{\code{tip.label}:}{Character vector of tip labels}
+% \item{\code{root.edge}:}{Integer: root edge (NA if none)}
+% \item{\code{phylolist}:}{(multiPhylo4) list of phylogenetic trees (each of which
+% may be of type \code{phylo4d}, containing node and/or edge data)}
+% }
+% }
+% \section{Methods}{
+% \describe{
+% \item{\$}{\code{signature(x = "phylo4")}: extract a slot}
+% \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 slots names}
+% }
+% }
+% % commented to eliminate Note: on build
+% %\usage{
+% % }
+% \arguments{
+% \item{x}{a phylo4 object}
+% \item{printlen}{Maximum number of tip labels to print}
+% \item{quiet}{a logical stating whether the results of the summary
+% should be printed to the screen (FALSE, default) or not (TRUE)}
+% \item{\dots}{additional arguments (for generic consistency)}
+% }
+% \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
+% - \code{mean.el}: mean of edge lengths \cr
+% - \code{var.el}: variance of edge lengths (estimate for population) \cr
+% - \code{sumry.el}: summary (i.e. range and quartiles) of the edge
+% lengths \cr
+%
+% The \code{names} method returns a vector of characters corresponding
+% to the names of the slots.
+% }
+% \author{Ben Bolker, Thibaut Jombart}
+% \examples{
+% ### An extract from Sibley and Ahlquist (1990)
+% cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);", file = "ex.tre", sep = "\n")
+% tree.owls <- read.tree("ex.tre", keep.multi = TRUE)
+% tree.owls
+% (as(tree.owls, "multiPhylo4"))
+% }
\keyword{classes}
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