[Adephylo-commits] r112 - in pkg: R inst/doc inst/doc/figs man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Dec 16 11:25:51 CET 2008 

Author: jombart
Date: 2008-12-16 11:25:50 +0100 (Tue, 16 Dec 2008)
New Revision: 112

Modified:
   pkg/R/table.phylo4d.R
   pkg/inst/doc/adephylo.Rnw
   pkg/inst/doc/figs/adephylo-012.pdf
   pkg/inst/doc/figs/adephylo-012.png
   pkg/inst/doc/figs/adephylo-017.pdf
   pkg/inst/doc/figs/adephylo-017.png
   pkg/inst/doc/figs/adephylo-phylo4d.pdf
   pkg/inst/doc/figs/adephylo-treePart.pdf
   pkg/inst/doc/figs/adephylo-treePart.png
   pkg/man/orthobasis.Rd
Log:
Some fixes to table.phylo4d (bug for 1 trait).
Advances in vignette.


Modified: pkg/R/table.phylo4d.R
===================================================================
--- pkg/R/table.phylo4d.R	2008-12-15 21:48:14 UTC (rev 111)
+++ pkg/R/table.phylo4d.R	2008-12-16 10:25:50 UTC (rev 112)
@@ -40,7 +40,7 @@
 #### data handling
     ## retrieve data
     dat <- tdata(x, which="tip")
-    dat <- dat[, repVar]
+    dat <- dat[, repVar, drop=FALSE]
     clas <- lapply(dat,class)
     isNum <- sapply(clas, function(e) e %in% c("integer","numeric"))
     ## keep only numeric data

Modified: pkg/inst/doc/adephylo.Rnw
===================================================================
--- pkg/inst/doc/adephylo.Rnw	2008-12-15 21:48:14 UTC (rev 111)
+++ pkg/inst/doc/adephylo.Rnw	2008-12-16 10:25:50 UTC (rev 112)
@@ -22,6 +22,10 @@
 
 
 
+\sloppy
+\hyphenpenalty 10000
+
+
 \begin{document}
 \color{black}
 
@@ -472,17 +476,60 @@
 
 
 
+
+
 %%%%%%%%%%%%%%%%%%%%%
 \subsection{Modelling phylogenetic signal}
 %%%%%%%%%%%%%%%%%%%%%
 
-~\\
+% % % % % % % % % % %
+\subsubsection{Using orthonormal bases}
+% % % % % % % % % % %
+
+In fact, the previous section describing the 'orthogram' has already
+shown that testing phylogenetic signal can (often) underlie modelling
+phylogenetic signal.
+In the case of the orthogram, several tests are linked to the
+decomposition of the variance of a trait onto a particular basis describing tree topology.
 In fact, it is possible to extend the principle of the 'orthogram' to
 any orthonormal basis modelling phylogenetic topology.
 Another example of such bases is offered by Moran's eigenvectors,
-which model different observable phylogenetic structures.
+which can be used to model different observable phylogenetic
+structures (see references in \code{me.phylo}).
 
+Moran's phylogenetic eigenvectors are implemented by the function
+\code{me.phylo} (also nicknamed \code{orthobasis.phylo}).
+The returned object is a data.frame with the class \code{orthobasis}
+defined in \code{ade4}; columns of this object are Moran's eigenvectors.
+An \code{orthobasis} be coerced to a regular data.frame or to a matrix
+using \code{as.data.frame} and \code{as.matrix}.
+<<>>=
+me.phylo(myTree.withBrLe)
+@
 
+\noindent Moran's eigenvectors are constructed from a matrix of
+phylogenetic proximities between tips.
+While any proximity can be used (argument \code{prox}), 5 proximities
+implemented by the \code{proxTips} function can be used, giving rise
+to different orthobases:
+<<fig=TRUE>>=
+ung.listBas <- list()
+ung.listBas[[1]] <- phylo4d(myTree, as.data.frame(me.phylo(myTree.withBrLe, method="patristic")))
+ung.listBas[[2]] <- phylo4d(myTree, as.data.frame(me.phylo(myTree, method="nNodes")))
+ung.listBas[[3]]<- phylo4d(myTree, as.data.frame(me.phylo(myTree, method="Abouheif")))
+ung.listBas[[4]] <- phylo4d(myTree, as.data.frame(me.phylo(myTree, method="sumDD")))
+par(mar=rep(.1,4), mfrow=c(2,2))
+lapply(ung.listBas, table.phylo4d, repVar=1:5, cex.sym=.7,
+show.tip.label=FALSE, show.node=FALSE)
+@
+
+\noindent In this case, the first Moran's eigenvectors are all very
+similar.
+In other cases, the orthobases built from different proximities can be
+quite different.
+
+
+
 %%%%%%%%%%%%%%%%%%%%%
 \subsection{Using multivariate analyses}
 %%%%%%%%%%%%%%%%%%%%%

Modified: pkg/inst/doc/figs/adephylo-012.pdf
===================================================================
--- pkg/inst/doc/figs/adephylo-012.pdf	2008-12-15 21:48:14 UTC (rev 111)
+++ pkg/inst/doc/figs/adephylo-012.pdf	2008-12-16 10:25:50 UTC (rev 112)
@@ -2,8 +2,8 @@
 %âãÏÓ\r
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+/CreationDate (D:20081216112518)
+/ModDate (D:20081216112518)
 /Title (R Graphics Output)
 /Producer (R 2.8.0)
 /Creator (R)
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Modified: pkg/inst/doc/figs/adephylo-017.png
===================================================================
(Binary files differ)

Modified: pkg/inst/doc/figs/adephylo-phylo4d.pdf
===================================================================
--- pkg/inst/doc/figs/adephylo-phylo4d.pdf	2008-12-15 21:48:14 UTC (rev 111)
+++ pkg/inst/doc/figs/adephylo-phylo4d.pdf	2008-12-16 10:25:50 UTC (rev 112)
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Modified: pkg/inst/doc/figs/adephylo-treePart.pdf
===================================================================
--- pkg/inst/doc/figs/adephylo-treePart.pdf	2008-12-15 21:48:14 UTC (rev 111)
+++ pkg/inst/doc/figs/adephylo-treePart.pdf	2008-12-16 10:25:50 UTC (rev 112)
@@ -2,8 +2,8 @@
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@@ -37,51 +37,51 @@
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+/F4 1 Tf 12.00 0.00 -0.00 12.00 378.04 149.69 Tm (t1) Tj
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+/F2 1 Tf 12.00 0.00 -0.00 12.00 345.26 270.89 Tm (N3) Tj
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Modified: pkg/inst/doc/figs/adephylo-treePart.png
===================================================================
(Binary files differ)

Modified: pkg/man/orthobasis.Rd
===================================================================
--- pkg/man/orthobasis.Rd	2008-12-15 21:48:14 UTC (rev 111)
+++ pkg/man/orthobasis.Rd	2008-12-16 10:25:50 UTC (rev 112)
@@ -49,6 +49,20 @@
   only uniform weights
 }
 \author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\references{
+Peres-Neto, P. (2006) A unified strategy for estimating and controlling
+spatial, temporal and phylogenetic autocorrelation in ecological models
+\emph{Oecologica Brasiliensis} \bold{10}: 105-119.\cr
+
+Dray, S.; Legendre, P. \& Peres-Neto, P. (2006) Spatial modelling: a
+  comprehensive framework for principal coordinate analysis of
+  neighbours matrices (PCNM) \emph{Ecological Modelling} \bold{196}:
+  483-493.\cr
+
+Griffith, D. \& Peres-Neto, P. (2006) Spatial modeling in ecology: the
+flexibility of eigenfunction spatial analyses \emph{Ecology} \bold{87}:
+2603-2613.\cr
+}
 \seealso{
   - \code{\link{proxTips}} which computes phylogenetic proximities
   between tips.\cr

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