[Adephylo-commits] r113 - in pkg/inst/doc: . figs

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Dec 16 11:55:41 CET 2008 

Author: jombart
Date: 2008-12-16 11:55:40 +0100 (Tue, 16 Dec 2008)
New Revision: 113

Modified:
   pkg/inst/doc/adephylo.Rnw
   pkg/inst/doc/adephylo.pdf
   pkg/inst/doc/figs/adephylo-012.pdf
   pkg/inst/doc/figs/adephylo-017.pdf
   pkg/inst/doc/figs/adephylo-phylo4d.pdf
   pkg/inst/doc/figs/adephylo-treePart.pdf
Log:
pdf instruction is fucked up when partitioning the screen and using table.phylo4d. Need to fix that (try R-2.8.1 in pre-release) before goind further (vignette does not show figures right).


Modified: pkg/inst/doc/adephylo.Rnw
===================================================================
--- pkg/inst/doc/adephylo.Rnw	2008-12-16 10:25:50 UTC (rev 112)
+++ pkg/inst/doc/adephylo.Rnw	2008-12-16 10:55:40 UTC (rev 113)
@@ -13,12 +13,6 @@
 \author{Thibaut Jombart}
 \date{\today}
 
-\definecolor{Soutput}{rgb}{0,0,0.56}
-\definecolor{Sinput}{rgb}{0.56,0,0}
-\DefineVerbatimEnvironment{Sinput}{Verbatim}
-{formatcom={\color{Sinput}},fontsize=\footnotesize, baselinestretch=0.75}
-\DefineVerbatimEnvironment{Soutput}{Verbatim}
-{formatcom={\color{Soutput}},fontsize=\footnotesize, baselinestretch=0.75}
 
 
 
@@ -27,6 +21,16 @@
 
 
 \begin{document}
+
+
+
+\definecolor{Soutput}{rgb}{0,0,0.56}
+\definecolor{Sinput}{rgb}{0.56,0,0}
+\DefineVerbatimEnvironment{Sinput}{Verbatim}
+{formatcom={\color{Sinput}},fontsize=\footnotesize, baselinestretch=0.75}
+\DefineVerbatimEnvironment{Soutput}{Verbatim}
+{formatcom={\color{Soutput}},fontsize=\footnotesize, baselinestretch=0.75}
+
 \color{black}
 
 \maketitle
@@ -512,24 +516,30 @@
 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>>=
+<<figFourBas, fig=TRUE,include=FALSE, print=FALSE>>=
 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)
+lapply(ung.listBas, table.phylo4d, repVar=1:5, cex.sym=.7, show.tip.label=FALSE, show.node=FALSE)
 @
 
+\includegraphics[width=.8\textwidth]{figs/adephylo-figFourBas}
+
 \noindent In this case, the first Moran's eigenvectors are all very
 similar.
-In other cases, the orthobases built from different proximities can be
+In other cases, however, the orthobases built from different proximities can be
 quite different.
+\\
 
 
 
+
+
+
+
 %%%%%%%%%%%%%%%%%%%%%
 \subsection{Using multivariate analyses}
 %%%%%%%%%%%%%%%%%%%%%

Modified: pkg/inst/doc/adephylo.pdf
===================================================================
--- pkg/inst/doc/adephylo.pdf	2008-12-16 10:25:50 UTC (rev 112)
+++ pkg/inst/doc/adephylo.pdf	2008-12-16 10:55:40 UTC (rev 113)
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adephylo -r 113

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