[Adephylo-commits] r105 - in pkg: inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 15 15:21:07 CET 2008
Author: jombart
Date: 2008-12-15 15:21:07 +0100 (Mon, 15 Dec 2008)
New Revision: 105
Modified:
pkg/inst/doc/adephylo.Rnw
pkg/man/adephylo.package.Rd
pkg/man/table.phylo4d.Rd
Log:
Finished the doc of ?adephylo.
Modified: pkg/inst/doc/adephylo.Rnw
===================================================================
--- pkg/inst/doc/adephylo.Rnw 2008-12-15 13:25:58 UTC (rev 104)
+++ pkg/inst/doc/adephylo.Rnw 2008-12-15 14:21:07 UTC (rev 105)
@@ -20,7 +20,7 @@
This document describes the \code{adephylo} package for the R software.
\code{adephylo} aims at implementing exploratory methods for the
-analysis of phylogenetic comparative data, i.e. traits measured for
+analysis of phylogenetic comparative data, i.e. biological traits measured for
taxa whose phylogeny is also provided.
Procedures implemented in this package rely on exploratory data
analysis.
Modified: pkg/man/adephylo.package.Rd
===================================================================
--- pkg/man/adephylo.package.Rd 2008-12-15 13:25:58 UTC (rev 104)
+++ pkg/man/adephylo.package.Rd 2008-12-15 14:21:07 UTC (rev 105)
@@ -6,24 +6,123 @@
\title{The adephylo package}
\description{This package is devoted to exploratory analysis of
- phylogenetic comparative data.
+ phylogenetic comparative data. It re-implements and extends
+ phylogenetic procedures from the \code{ade4} package (which are now
+ deprecated).\cr
+
+ 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}}
+ objects (from the \code{ape} package) or as \linkS4class{phylo4}
+ objects (\code{phylobase}'s extension of \code{phylo} objects).\cr
+
+ Main functionalities of \code{adephylo} are summarized below.\cr
+
+ === TOPOLOGICAL INFORMATION ===\cr
+ Several functions allow one to retrieve topological information from
+ a tree; such information can be used, for instance, as a basis to
+ compute distances or proximities between tips.\cr
+
+ - \code{\link{listDD}}: lists the direct descendants from each node
+ of a tree.\cr
+
+ - \code{\link{listTips}}: lists the tips descending from each node
+ of a tree.\cr
+
+ - \code{\link{.tipToRoot}}: finds the set of nodes between a tip and the root of
+ a tree.\cr
+
+ - \code{\link{sp.tips}}: finds the shortest path between tips of a
+ tree.\cr
+
+ - \code{\link{treePart}}: defines partitions of tips reflecting the
+ topology of a tree. This function can output non-independent dummy
+ vectors, or alternatively an orthonormal basis used by the orthogram procedure.\cr
+
+
+ === PHYLOGENETIC PROXIMITIES/DISTANCES ===\cr
+ Several phylogenetic proximities and distances are
+ implemented. Auxiliary function easing the computation of other
+ distances/proximities are also provided:\cr
+
+ - \code{\link{distRoot}}: computes different distances of a set of tips to the
+ root.\cr
+ - \code{\link{distTips}}: computes different pairwise distances in a set of tips.\cr
+ - \code{\link{proxTips}}: computes different proximities between a
+ set of tips.\cr
+
+
+ === MEASURES/TESTS OF PHYLOGENETIC AUTOCORRELATION ===\cr
+ Several procedures allow one to measure, and/or test phylogenetic
+ signal in biological traits:\cr
- === MANIPULATING DATA ===\cr
- Several functions allow one to manipulate \linkS4class{genind} or
- \linkS4class{genpop} objects\cr
- - \code{\link{}}: convert a \linkS4class{genind} object
- to a \linkS4class{genpop} \cr
-
+ - \code{\link{abouheif.moran}}: performs Abouheif's test, designed to detect phylogenetic
+ autocorrelation in a quantitative trait. This implementation is not
+ based on original heuristic procedure, but on the exact formulation
+ proposed by Pavoine et al. (2008), showing that the test is in fact a
+ Moran's index test. This implementation further extends the procedure
+ by allowing any measure of phylogenetic proximity (5 are proposed).\cr
- === ANALYZING DATA ===\cr
- :\cr
- - \code{\link{}}: performs HWE test for all
-
+ - \code{\link{orthogram}}: performs the orthonormal decomposition of
+ variance of a quantitative variable on an orthonormal basis as in
+ Ollier et al. (2005). It also returns the results of five non
+ parametric tests associated to the variance decomposition.\cr
+
+ - \code{\link{moran.idx}}: computes Moran's index of autocorrelation given a
+ variable and a matrix of proximities among observations (no test).\cr
+
+ === MODELLING/INVESTIGATION OF PHYLOGENETIC SIGNAL ===\cr
+ Rather than testing or measuring phylogenetic autocorrelation, these
+ procedures can be used for further investigation of phylogenetic
+ signal. Some, like \code{\link{me.phylo}}, can be used to remove
+ phylogenetic autocorrelation. Others can be used to understand the
+ nature of this autocorrelation (i.e., to ascertain which traits and
+ tips are concerned by phylogenetic non-independence).\cr
+
+ - \code{\link{me.phylo}}/\code{\link{orthobasis.phylo}}: these
+ synonymous functions compute Moran's eigenvectors (ME) associated to
+ a tree. These vectors model different observable phylogenetic
+ signals. They can be used as covariables to remove phylogenetic
+ autocorrelation from data.\cr
+
+ - \code{\link{orthogram}}: the orthogram mentionned above also
+ provides a description of how biological variability is structured
+ on a phylogeny.\cr
+
+ - \code{\link{ppca}}: performs a phylogenetic principal
+ component analysis (pPCA, Jombart et al. in prep). This multivariate
+ method investigates phylogenetic patterns in a set of quantitative
+ traits.\cr
+
+
+ === GRAPHICS ===\cr
+ Some plotting functions are proposed, most of them being devoted to
+ representing phylogeny and a quantitative information at the same
+ time.\cr
+
+ - \code{\link{table.phylo4d}}: fairly customisable way of
+ representing traits onto the tips of a phylogeny. Several traits can
+ be plotted in a single graphic.\cr
+
+ - \code{\link{scatter.ppca}}, \code{\link{screeplot.ppca}},
+ \code{\link{plot.ppca}}: several plots associated to a phylogenetic
+ principal component analysis (see \code{\link{ppca}}).\cr
+
+
+ === DATASETS ===\cr
+ Several datasets are also proposed. Some of these datasets
+ replace former version from \code{ade4}, which are now deprecated.
+ Here is a list of available datasets: \code{\link{carni19}},
+ \code{\link{carni70}}, \code{\link{lizards}}, \code{\link{maples}},
+ \code{\link{mjrochet}}, \code{\link{palm}}, \code{\link{procella}},
+ \code{\link{tithonia}}, and \code{\link{ungulates}}.\cr
+
+
To cite adephylo, please use the reference given by
\code{citation("adephylo")}.
}
@@ -32,12 +131,15 @@
Package: \tab adephylo\cr
Type: \tab Package\cr
Version: \tab 1.0-0\cr
- Date: \tab 2008-12-30 \cr
+ Date: \tab 2008-12-24 \cr
License: \tab GPL (>=2)
}
}
-\author{Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>\cr
-with contributions Stéphane Dray}
+\author{
+ Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>\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.
+}
\keyword{manip}
\keyword{multivariate}
-\seealso{The \code{ade4} package for multivariate analysis}
+\seealso{The \code{ade4} package for multivariate analysis.}
Modified: pkg/man/table.phylo4d.Rd
===================================================================
--- pkg/man/table.phylo4d.Rd 2008-12-15 13:25:58 UTC (rev 104)
+++ pkg/man/table.phylo4d.Rd 2008-12-15 14:21:07 UTC (rev 105)
@@ -1,8 +1,8 @@
\name{table.phylo4d}
\alias{table.phylo4d}
-\title{scatterplot for a phylogeny and traits}
+\title{Graphical display of phylogeny and traits}
\description{
- This function displays scatterplots of traits provided for the tips of
+ This function represents traits onto the tips of
a phylogeny. Plotted objects must be valid \linkS4class{phylo4d}
objects (implemented by the \code{phylobase} package). Current version
allows plotting of a tree and one or more quantitative traits
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