[Adephylo-commits] r133 - in pkg: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 5 14:12:13 CET 2009
Author: jombart
Date: 2009-11-05 14:12:12 +0100 (Thu, 05 Nov 2009)
New Revision: 133
Modified:
pkg/R/ppca.R
pkg/man/abouheif.Rd
pkg/man/adephylo.package.Rd
pkg/man/distRoot.Rd
pkg/man/distTips.Rd
pkg/man/listDD.Rd
pkg/man/listTips.Rd
pkg/man/miscUtils.Rd
pkg/man/moranIdx.Rd
pkg/man/orthobasis.Rd
pkg/man/orthogram.Rd
pkg/man/ppca.Rd
pkg/man/proxTips.Rd
pkg/man/sp.tips.Rd
pkg/man/table.phylo4d.Rd
pkg/man/treePart.Rd
Log:
updated my email address
Modified: pkg/R/ppca.R
===================================================================
--- pkg/R/ppca.R 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/R/ppca.R 2009-11-05 13:12:12 UTC (rev 133)
@@ -1,7 +1,7 @@
####
#### Phylogenetic ordination tools
####
-#### Thibaut Jombart 2008 (jombart at biomserv.univ-lyon1.fr)
+#### Thibaut Jombart 2008 (tjombart at imperial.ac.uk)
################
# Function ppca
Modified: pkg/man/abouheif.Rd
===================================================================
--- pkg/man/abouheif.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/abouheif.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -60,11 +60,11 @@
\emph{Environmental and Ecological Statistics}, \bold{2}, 1--14.
}
\author{Original code from ade4 (gearymoran function) by Sébastien Ollier\cr
- Adapted and maintained by Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>.
+ Adapted and maintained by Thibaut Jombart <tjombart at imperial.ac.uk>.
}
\seealso{
- - \code{\link[pkg:ade4]{gearymoran}} from the ade4 package\cr
- - \code{\link[pkg:ape]{Moran.I}} from the ape package for the
+ - \code{\link[ade4]{gearymoran}} from the ade4 package\cr
+ - \code{\link[ape]{Moran.I}} from the ape package for the
classical Moran's I test. \cr
}
\examples{
Modified: pkg/man/adephylo.package.Rd
===================================================================
--- pkg/man/adephylo.package.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/adephylo.package.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -12,7 +12,7 @@
Comparative data (phylogeny+traits) are handled as
\linkS4class{phylo4d} objects, a canonical class implemented by the
- \code{phylobase} package. Trees are handled as \code{\link[pkg:ape]{phylo}}
+ \code{phylobase} package. Trees are handled as \code{\link[ape]{phylo}}
objects (from the \code{ape} package) or as \linkS4class{phylo4}
objects (\code{phylobase}'s extension of \code{phylo} objects).\cr
@@ -136,7 +136,7 @@
}
}
\author{
- Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>\cr
+ Thibaut Jombart <tjombart at imperial.ac.uk>\cr
with contributions Stéphane Dray <dray at biomserv.univ-lyon1.fr>. \cr
Parts of former code from \code{ade4} by Daniel Chessel and Sébastien Ollier.
}
Modified: pkg/man/distRoot.Rd
===================================================================
--- pkg/man/distRoot.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/distRoot.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -9,7 +9,7 @@
distRoot(x, tips, method=c("patristic","nNodes","Abouheif","sumDD"))
}
\arguments{
- \item{x}{a tree of class \code{\link[pkg:ape]{phylo}},
+ \item{x}{a tree of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.}
\item{tips}{A vector of integers identifying tips by their numbers, or
a vector of characters identifying tips by their names.}
@@ -38,7 +38,7 @@
computing the product of all terms in DDP, this distance computes the
sum of all terms in DDP.
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\references{
Pavoine, S.; Ollier, S.; Pontier, D. & Chessel, D. (2008) Testing for
phylogenetic signal in life history variable: Abouheif's test
Modified: pkg/man/distTips.Rd
===================================================================
--- pkg/man/distTips.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/distTips.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -13,7 +13,7 @@
distTips(x, tips, method=c("patristic","nNodes","Abouheif","sumDD"))
}
\arguments{
- \item{x}{a tree of class \code{\link[pkg:ape]{phylo}},
+ \item{x}{a tree of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.}
\item{tips}{A vector of integers identifying tips by their numbers, or
a vector of characters identifying tips by their names. Distances
@@ -43,7 +43,7 @@
computing the product of all terms in DDP, this distance computes the
sum of all terms in DDP.
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\seealso{\code{\link{distTips}} which computes several phylogenetic
distances between tips.
}
Modified: pkg/man/listDD.Rd
===================================================================
--- pkg/man/listDD.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/listDD.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -3,14 +3,14 @@
\title{List direct descendants for all nodes of a tree}
\description{
The function \code{listDD} lists the direct descendants from each node
- of a tree. The tree can be of class \code{\link[pkg:ape]{phylo}},
+ of a tree. The tree can be of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.
}
\usage{
listDD(x, nameBy=c("label","number"))
}
\arguments{
- \item{x}{A tree of class \code{\link[pkg:ape]{phylo}},
+ \item{x}{A tree of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.}
\item{nameBy}{a character string indicating whether the returned list
must be named by node labels ("label") or by node numbers ("number").}
@@ -19,7 +19,7 @@
A list whose components are vectors of named nodes (or tips) for a
given internal node.
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\seealso{\code{\link{listTips}} which lists the tips descending from
each node. \cr
Modified: pkg/man/listTips.Rd
===================================================================
--- pkg/man/listTips.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/listTips.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -3,20 +3,20 @@
\title{List tips descendings from all nodes of a tree}
\description{
The function \code{listTips} lists the tips descending from each node
- of a tree. The tree can be of class \code{\link[pkg:ape]{phylo}},
+ of a tree. The tree can be of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.
}
\usage{
listTips(x)
}
\arguments{
- \item{x}{A tree of class \code{\link[pkg:ape]{phylo}},
+ \item{x}{A tree of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.}
}
\value{
A list whose components are vectors of named tips for a given node.
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\seealso{\code{\link{listDD}} which lists the direct descendants for
each node. \cr
Modified: pkg/man/miscUtils.Rd
===================================================================
--- pkg/man/miscUtils.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/miscUtils.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -27,7 +27,7 @@
\value{
\code{.tipToRoot}: a vector of named integers identifying nodes.\cr
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\examples{
if(require(ape) & require(phylobase)){
## make a tree
Modified: pkg/man/moranIdx.Rd
===================================================================
--- pkg/man/moranIdx.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/moranIdx.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -21,7 +21,7 @@
\value{
The numeric value of Moran's index.
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\references{
Moran, P.A.P. (1948) The interpretation of statistical
maps. \emph{Journal of the Royal Statistical Society, B}
Modified: pkg/man/orthobasis.Rd
===================================================================
--- pkg/man/orthobasis.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/orthobasis.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -25,7 +25,7 @@
orthobasis.phylo(x=NULL, prox=NULL, method=c("patristic","nNodes","oriAbouheif","Abouheif","sumDD"), a=1)
}
\arguments{
- \item{x}{A tree of class \code{\link[pkg:ape]{phylo}},
+ \item{x}{A tree of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.}
\item{prox}{a matrix of phylogenetic proximities as returned by \code{\link{proxTips}}.}
\item{method}{a character string (full or abbreviated without
@@ -48,7 +48,7 @@
- attr(...,"weights"): weights of tips; current implementation uses
only uniform weights
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\references{
Peres-Neto, P. (2006) A unified strategy for estimating and controlling
spatial, temporal and phylogenetic autocorrelation in ecological models
Modified: pkg/man/orthogram.Rd
===================================================================
--- pkg/man/orthogram.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/orthogram.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -25,7 +25,7 @@
}
\arguments{
\item{x}{a numeric vector corresponding to the quantitative variable}
- \item{tre}{a tree of class \code{\link[pkg:ape]{phylo}},
+ \item{tre}{a tree of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.}
\item{orthobas}{an object of class \code{'orthobasis'}}
\item{prox}{a matrix of phylogenetic proximities as returned by \code{\link{proxTips}}.}
Modified: pkg/man/ppca.Rd
===================================================================
--- pkg/man/ppca.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/ppca.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -85,7 +85,7 @@
The phylogenetic Principal Component Analysis (pPCA, Jombart et al.,
in prep) is derived from the spatial Principal Component Analysis
(spca, Jombart et al. 2008), implemented in the adegenet package (see
- \code{\link[pkg:adegenet]{spca}}).\cr
+ \code{\link[adegenet]{spca}}).\cr
pPCA is designed to investigate phylogenetic patterns in the variability of a set of
traits. The analysis returns principal components maximizing the
@@ -139,10 +139,10 @@
of Moran's I and Geary's c. \emph{Geographical Analysis}, \bold{16}, 17--24.
}
-\seealso{The implementation of \code{\link[pkg:adegenet]{spca}} in the
- adegenet package (\code{\link[pkg:adegenet]{adegenet}}) \cr
+\seealso{The implementation of \code{\link[adegenet]{spca}} in the
+ adegenet package (\code{\link[adegenet]{adegenet}}) \cr
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\examples{
## build an look at data
data(maples)
Modified: pkg/man/proxTips.Rd
===================================================================
--- pkg/man/proxTips.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/proxTips.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -40,7 +40,7 @@
a=1, normalize=c("row","col","none"), symmetric=TRUE)
}
\arguments{
- \item{x}{a tree of class \code{\link[pkg:ape]{phylo}},
+ \item{x}{a tree of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.}
\item{tips}{A vector of integers identifying tips by their numbers, or
a vector of characters identifying tips by their names. Distances
@@ -92,7 +92,7 @@
inverse of the sum of all terms in DDP. This matrix was denoted 'M' in
Pavoine \emph{et al.} (2008), who reported that it is related to May's index (May, 1990).
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\seealso{\code{\link{distTips}} which computes several phylogenetic
distances between tips.
}
Modified: pkg/man/sp.tips.Rd
===================================================================
--- pkg/man/sp.tips.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/sp.tips.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -4,14 +4,14 @@
\description{
The function \code{sp.tips} finds the shortest path between tips of a
tree, identified as \code{tip1} and \code{tip2}.
- This function applies to trees with the class \code{\link[pkg:ape]{phylo}}, \linkS4class{phylo4} or
+ This function applies to trees with the class \code{\link[ape]{phylo}}, \linkS4class{phylo4} or
\linkS4class{phylo4d}. Several tips can be provided at a time.
}
\usage{
sp.tips(x, tip1, tip2, useTipNames=FALSE, quiet=FALSE, include.mrca=TRUE)
}
\arguments{
- \item{x}{A tree of class \code{\link[pkg:ape]{phylo}},
+ \item{x}{A tree of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.}
\item{tip1}{A vector of integers identifying tips by their numbers, or
a vector of characters identifying tips by their names. Recycled if needed.}
@@ -34,8 +34,8 @@
same. These cases are deleted when detected, issuing a warning (unless
\code{quiet} is set to TRUE).
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
-\seealso{\code{\link[pkg:phylobase]{shortestPath}} which does the same
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
+\seealso{\code{\link[phylobase]{shortestPath}} which does the same
thing as \code{sp.tips}, for any node (internal or tip), but much more
slowly. \cr
}
Modified: pkg/man/table.phylo4d.Rd
===================================================================
--- pkg/man/table.phylo4d.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/table.phylo4d.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -8,9 +8,9 @@
allows plotting of a tree and one or more quantitative traits
(possibly containing missing data, represented by an 'x').\cr
- The plot of phylogenies is performed by a call to \code{\link[pkg:ape]{plot.phylo}}
+ The plot of phylogenies is performed by a call to \code{\link[ape]{plot.phylo}}
from the \code{ape} package. Hence, many of the arguments of
- \code{\link[pkg:ape]{plot.phylo}} can be passed to \code{table.phylo4d},
+ \code{\link[ape]{plot.phylo}} can be passed to \code{table.phylo4d},
through the \dots argument, but their names must be complete.
}
\usage{
@@ -55,23 +55,23 @@
indicating the lower-left position of the legend. Can be set to
\code{locator(1) to position the legend interactively.}}
\item{\dots}{further arguments to be passed to plot methods from
- \code{ape}. See \code{\link[pkg:ape]{plot.phylo}}.}
+ \code{ape}. See \code{\link[ape]{plot.phylo}}.}
}
\seealso{The \linkS4class{phylo4d} class for storing \code{phylogeny+data}.\cr
- \code{\link[pkg:ape]{plot.phylo}} from the \code{ape} package.\cr
+ \code{\link[ape]{plot.phylo}} from the \code{ape} package.\cr
An alternative (deprecated) representation is available from
- \code{\link[pkg:ade4]{dotchart.phylog}}.
+ \code{\link[ade4]{dotchart.phylog}}.
}
\details{
The function \code{table.phylo4d} is based on former plot method for
\linkS4class{phylo4d} objects from the \code{phylobase} package.
It replaces the deprecated \code{ade4} functions
- \code{\link[pkg:ade4]{symbols.phylog}} and
- \code{\link[pkg:ade4]{table.phylog}}.
+ \code{\link[ade4]{symbols.phylog}} and
+ \code{\link[ade4]{table.phylog}}.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}}
+\author{Thibaut Jombart \email{tjombart at imperial.ac.uk}}
\examples{
if(require(ape) & require(phylobase) & require(ade4)){
Modified: pkg/man/treePart.Rd
===================================================================
--- pkg/man/treePart.Rd 2009-11-05 13:00:22 UTC (rev 132)
+++ pkg/man/treePart.Rd 2009-11-05 13:12:12 UTC (rev 133)
@@ -16,7 +16,7 @@
treePart(x, result=c("dummy", "orthobasis"))
}
\arguments{
- \item{x}{a tree of class \code{\link[pkg:ape]{phylo}},
+ \item{x}{a tree of class \code{\link[ape]{phylo}},
\linkS4class{phylo4} or \linkS4class{phylo4d}.}
\item{result}{a character string specifying the type of result: either
a basis of dummy vectors (\code{dummy}), or an orthobasis derived from these dummy vectors (\code{orthobasis}).}
@@ -25,7 +25,7 @@
A matrix of numeric vectors (in columns) having one value for each
tip (rows).
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\references{
Ollier, S., Chessel, D. and Couteron, P. (2005) Orthonormal Transform to Decompose the Variance of a Life-History Trait across a Phylogenetic Tree. \emph{Biometrics}, \bold{62}, 471--477.
}
@@ -37,7 +37,7 @@
}
\details{
Orthobasis produced by this function are identical to those stored in
- the \$Bscores component of deprecated \link[pkg:ade4]{phylog} objects,
+ the \$Bscores component of deprecated \link[ade4]{phylog} objects,
from the ade4 package.
}
\examples{
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