[Adephylo-commits] r111 - in pkg: R inst/doc inst/doc/figs

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Dec 15 22:48:14 CET 2008 

Author: jombart
Date: 2008-12-15 22:48:14 +0100 (Mon, 15 Dec 2008)
New Revision: 111

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
Log:
advances in vignette.


Modified: pkg/R/table.phylo4d.R
===================================================================
--- pkg/R/table.phylo4d.R	2008-12-15 18:46:43 UTC (rev 110)
+++ pkg/R/table.phylo4d.R	2008-12-15 21:48:14 UTC (rev 111)
@@ -45,6 +45,7 @@
     isNum <- sapply(clas, function(e) e %in% c("integer","numeric"))
     ## keep only numeric data
     dat <- dat[isNum]
+    var.label <- var.label[repVar]
     var.label <- var.label[isNum]
     ## order data like tips
     E <- edges(x)

Modified: pkg/inst/doc/adephylo.Rnw
===================================================================
--- pkg/inst/doc/adephylo.Rnw	2008-12-15 18:46:43 UTC (rev 110)
+++ pkg/inst/doc/adephylo.Rnw	2008-12-15 21:48:14 UTC (rev 111)
@@ -450,17 +450,37 @@
 table.phylo4d(temp)
 @
 
-\noindent And here is the orthonormal basis for our dataset of ungulates:
+\noindent And here are the first 10 vectors of the orthonormal basis
+for the ungulate dataset:
 <<fig=TRUE>>=
 temp <- phylo4d(myTree, treePart(myTree, result="orthobasis") )
-table.phylo4d(temp, repVar=1:10)
+par(mar=rep(.1,4))
+table.phylo4d(temp, repVar=1:8)
 @
 
+The decomposition of variance achieved by projecting a trait onto this
+orthonormal basis gives rise to several test statistics, that are
+performed by the function \code{orthogram}.
+Like the \code{abouheif.moran} function, \code{orthogram} outputs a
+\code{krandtest} object:
+<<orthogram, plot=TRUE>>=
+afbw.ortgTest <- orthogram(afbw, myTree)
+afbw.ortgTest
+@
 
+\noindent Here again, \code{afbw} does not seem to be phylogenetically structured.
+
+
+
 %%%%%%%%%%%%%%%%%%%%%
 \subsection{Modelling phylogenetic signal}
 %%%%%%%%%%%%%%%%%%%%%
 
+~\\
+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.
 
 
 %%%%%%%%%%%%%%%%%%%%%

Modified: pkg/inst/doc/figs/adephylo-012.pdf
===================================================================
--- pkg/inst/doc/figs/adephylo-012.pdf	2008-12-15 18:46:43 UTC (rev 110)
+++ pkg/inst/doc/figs/adephylo-012.pdf	2008-12-15 21:48:14 UTC (rev 111)
@@ -2,8 +2,8 @@
 %âãÏÓ\r
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-/CreationDate (D:20081215194216)
-/ModDate (D:20081215194216)
+/CreationDate (D:20081215224730)
+/ModDate (D:20081215224730)
 /Title (R Graphics Output)
 /Producer (R 2.8.0)
 /Creator (R)
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+61.91 226.12 17.50 12.22 re B
+304.08 130.79 17.50 12.22 re B
+310.12 182.79 17.50 12.22 re B
+341.71 321.45 17.50 12.22 re B
 BT
 0.000 0.000 0.000 rg
-/F2 1 Tf 12.00 0.00 -0.00 12.00 64.07 145.23 Tm (N1) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 64.07 227.56 Tm (N1) Tj
 ET
 BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 275.23 210.23 Tm (N2) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 306.24 132.23 Tm (N2) Tj
 ET
 BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 345.82 270.89 Tm (N3) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 312.28 184.23 Tm (N3) Tj
 ET
 BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 347.16 322.89 Tm (N4) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 343.87 322.89 Tm (N4) Tj
 ET
 Q
 endstream

Modified: pkg/inst/doc/figs/adephylo-treePart.png
===================================================================
(Binary files differ)

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