[Adephylo-commits] r102 - in pkg: . inst inst/doc

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2008-12-14 18:17:42 +0100 (Sun, 14 Dec 2008)
New Revision: 102

Added:
   pkg/inst/doc/
   pkg/inst/doc/adephylo.Rnw
Modified:
   pkg/DESCRIPTION
   pkg/TITLE
   pkg/inst/CITATION
Log:
Added a vignette, started it.


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-12-14 17:02:23 UTC (rev 101)
+++ pkg/DESCRIPTION	2008-12-14 17:17:42 UTC (rev 102)
@@ -1,7 +1,7 @@
 Package: adephylo
 Version: 1.0-0
 Date: 2008/11/20
-Title: adephylo: multivariate analysis for the comparative method.
+Title: adephylo: exploratory analyses for the phylogenetic comparative method.
 Author: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>, Stephane Dray <dray at biomserv.univ-lyon1.fr>
 Maintainer: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>
 Suggests: 

Modified: pkg/TITLE
===================================================================
--- pkg/TITLE	2008-12-14 17:02:23 UTC (rev 101)
+++ pkg/TITLE	2008-12-14 17:17:42 UTC (rev 102)
@@ -1 +1 @@
-adephylo: multivariate analysis for the comparative method.
\ No newline at end of file
+adephylo: exploratory analyses for the phylogenetic comparative method.
\ No newline at end of file

Modified: pkg/inst/CITATION
===================================================================
--- pkg/inst/CITATION	2008-12-14 17:02:23 UTC (rev 101)
+++ pkg/inst/CITATION	2008-12-14 17:17:42 UTC (rev 102)
@@ -1,13 +1,13 @@
-citHeader("To cite the adegenet package:")
+citHeader("To cite the adephylo package:")
 
 citEntry(
 entry="Article",
-title = "adegenet: a R package for the multivariate analysis of genetic markers",
-journal= "Bioinformatics",
+title = "adephylo: exploratory analyses for the phylogenetic comparative method.",
+journal= "",
 year = "2008",
-author = "T. Jombart",
-volume = "24",
-pages = "1403-1405",
-doi = "10.1093/bioinformatics/btn129",
-textVersion = "Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405. doi: 10.1093/bioinformatics/btn129"
+author = "T. Jombart, S. Dray",
+volume = "",
+pages = "",
+doi = "",
+textVersion = "Jombart T., Dray S. (2008) adephylo: exploratory analyses for the phylogenetic comparative method."
 )

Added: pkg/inst/doc/adephylo.Rnw
===================================================================
--- pkg/inst/doc/adephylo.Rnw	                        (rev 0)
+++ pkg/inst/doc/adephylo.Rnw	2008-12-14 17:17:42 UTC (rev 102)
@@ -0,0 +1,36 @@
+\documentclass{article}
+%\VignettePackage{adephylo}
+% \VignetteIndexEntry{adephylo: exploratory analyses for the
+% phylogenetic comparative method}
+\usepackage{graphicx}
+\usepackage[colorlinks=true,urlcolor=blue]{hyperref}
+\usepackage{array}
+\usepackage{color}
+
+\usepackage[utf8]{inputenc} % for UTF-8/single quotes from sQuote()
+\newcommand{\code}[1]{{{\tt #1}}}
+\title{The \code{adephylo} package}
+\author{Thibaut Jombart}
+\date{\today}
+\begin{document}
+\maketitle
+\tableofcontents
+
+\section{Introduction}
+
+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
+taxa whose phylogeny is also provided.
+Procedures implemented in this package rely on exploratory data
+analysis.
+They include data visualization and manipulation, tests for phylogenetic
+autocorrelation, multivariate analysis, computation of phylogenetic
+proximities and distances, and modelling phylogenetic signal using
+orthonormal bases.
+
+These methods can be used to visualize, test, remove or investigate
+the phylogenetic signal in comparative data.
+The purpose of this document is to present the main functionalities of \code{adephylo}.
+
+\end{document}