[Adephylo-commits] r116 - in pkg/inst/doc: . figs
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 17 18:20:24 CET 2008
Author: jombart
Date: 2008-12-17 18:20:24 +0100 (Wed, 17 Dec 2008)
New Revision: 116
Modified:
pkg/inst/doc/adephylo.Rnw
pkg/inst/doc/adephylo.pdf
pkg/inst/doc/figs/adephylo-012.pdf
pkg/inst/doc/figs/adephylo-phylo4d.pdf
Log:
VIgnette finally fixed.
Modified: pkg/inst/doc/adephylo.Rnw
===================================================================
--- pkg/inst/doc/adephylo.Rnw 2008-12-17 16:35:12 UTC (rev 115)
+++ pkg/inst/doc/adephylo.Rnw 2008-12-17 17:20:24 UTC (rev 116)
@@ -430,17 +430,17 @@
This job is achieved by the function \code{treePart}.
Here is an example using a small simulated tree:
<<fig=TRUE>>=
-youpla <- as(rcoal(5), "phylo4")
-plot(youpla, show.node=TRUE)
-partX <- treePart(youpla)
-partX
-x <- youpla
+x <- as(rtree(5),"phylo4")
+plot(x,show.n=TRUE)
@
+<<>>=
+x.part <- treePart(x)
+x.part
+@
\noindent The obtained partition can also be plotted:
<<fig=TRUE>>=
-partX
-temp <- phylo4d(x, partX)
+temp <- phylo4d(x, x.part)
table.phylo4d(temp, cent=FALSE, scale=FALSE)
@
@@ -643,7 +643,7 @@
data(maples)
traits <- apply(maples$tab, 2, f1)
pca1 <- dudi.pca(traits, scannf=FALSE, nf=1)
-barplot(map.pca1$eig, main="PCA eigenvalues")
+barplot(pca1$eig, main="PCA eigenvalues")
@
\noindent One axis shall be retained.
Modified: pkg/inst/doc/adephylo.pdf
===================================================================
--- pkg/inst/doc/adephylo.pdf 2008-12-17 16:35:12 UTC (rev 115)
+++ pkg/inst/doc/adephylo.pdf 2008-12-17 17:20:24 UTC (rev 116)
@@ -115,19 +115,21 @@
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[TRUNCATED]
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svnlook diff /svnroot/adephylo -r 116
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