[Adephylo-commits] r101 - in pkg: . man

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

Author: jombart
Date: 2008-12-14 18:02:23 +0100 (Sun, 14 Dec 2008)
New Revision: 101

Modified:
   pkg/DESCRIPTION
   pkg/man/carni70.Rd
   pkg/man/lizards.Rd
   pkg/man/orthobasis.Rd
   pkg/man/orthogram.Rd
   pkg/man/ungulates.Rd
Log:
Fixed dependencies pb and version conflict with ade4's orthogram.


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-12-14 15:52:39 UTC (rev 100)
+++ pkg/DESCRIPTION	2008-12-14 17:02:23 UTC (rev 101)
@@ -4,8 +4,8 @@
 Title: adephylo: multivariate analysis for the 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: ade4
-Depends: methods, phylobase, ape
+Suggests: 
+Depends: methods, phylobase, ape, ade4
 Description: Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
 License: GPL (>=2)
 LazyLoad: yes

Modified: pkg/man/carni70.Rd
===================================================================
--- pkg/man/carni70.Rd	2008-12-14 15:52:39 UTC (rev 100)
+++ pkg/man/carni70.Rd	2008-12-14 17:02:23 UTC (rev 101)
@@ -30,6 +30,7 @@
 par(mar=rep(.1,4))
 s.phylo4d(x,cex.lab=.5, show.n=FALSE, ratio=.5)
 
+
 ## transform size in log and test for a phylogenetic signal
 size <- log(carni70$tab)[,1]
 names(size) <- row.names(carni70$tab)
@@ -39,5 +40,6 @@
 yrange <- scalewt(carni70$tab)[,2]
 names(yrange) <- row.names(carni70$tab)
 orthogram(yrange, tre)
+
 }
 \keyword{datasets}

Modified: pkg/man/lizards.Rd
===================================================================
--- pkg/man/lizards.Rd	2008-12-14 15:52:39 UTC (rev 100)
+++ pkg/man/lizards.Rd	2008-12-14 17:02:23 UTC (rev 101)
@@ -32,17 +32,15 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
-data(lizards)
-
 ## see data
 data(lizards)
 liz.tr <- read.tree(tex=lizards$hprA) # make a tree
-liz <- phylo4d(liz.tr, traits) # make a phylo4d object
+liz <- phylo4d(liz.tr, lizards$traits) # make a phylo4d object
 s.phylo4d(liz)
 
 ## compute and plot principal components
 if(require(ade4)){
-liz.pca1 <- dudi.pca(traits, cent=TRUE, scale=TRUE, scannf=FALSE, nf=2) # PCA of traits
+liz.pca1 <- dudi.pca(lizards$traits, cent=TRUE, scale=TRUE, scannf=FALSE, nf=2) # PCA of traits
 myPC <- phylo4d(liz.tr, liz.pca1$li) # store PC in a phylo4d object
 varlab <- paste("Principal \ncomponent", 1:2) # make labels for PCs
 s.phylo4d(myPC, ratio=.8, var.lab=varlab) # plot the PCs

Modified: pkg/man/orthobasis.Rd
===================================================================
--- pkg/man/orthobasis.Rd	2008-12-14 15:52:39 UTC (rev 100)
+++ pkg/man/orthobasis.Rd	2008-12-14 17:02:23 UTC (rev 101)
@@ -58,7 +58,7 @@
 
 }
 \examples{
-if(require(ape) & require(ade4)){
+
 ## make a tree
 x <- rtree(50)
 
@@ -72,7 +72,8 @@
 
 
 ## removing phylogenetic autocorrelation in a model ##
-example(ungulates)
+example(ungulates, package="adephylo")
+
 lm1
 resid1 <- residuals(lm1)
 orthogram(resid1, tre) # residuals are autocorrelated
@@ -87,5 +88,4 @@
 s.phylo4d(phylo4d(tre, cbind.data.frame(resid1, resid2)))
 
 }
-}
 \keyword{manip}

Modified: pkg/man/orthogram.Rd
===================================================================
--- pkg/man/orthogram.Rd	2008-12-14 15:52:39 UTC (rev 100)
+++ pkg/man/orthogram.Rd	2008-12-14 17:02:23 UTC (rev 101)
@@ -69,6 +69,13 @@
 \seealso{
   \code{\link{orthobasis.phylo}}
 }
+\note{
+  This function replaces the former version from the ade4 package, which
+  is deprecated. Note that if ade4 is not loaded BEFORE adephylo, then
+  the version from ade4 will erase that of adephylo, which will still be
+  available from adephylo::orthogram. In practice, though, this should
+  never happen, since ade4 is loaded as a dependence by adephylo.
+}
 \examples{
 ## a phylogenetic example
 data(ungulates)

Modified: pkg/man/ungulates.Rd
===================================================================
--- pkg/man/ungulates.Rd	2008-12-14 15:52:39 UTC (rev 100)
+++ pkg/man/ungulates.Rd	2008-12-14 17:02:23 UTC (rev 101)
@@ -46,7 +46,7 @@
 x <- phylo4d(tre, cbind.data.frame(afbw, neonatw)) # traits on the phylogeny
 
 ## test phylogenetic inertia in residuals
+orthogram(residuals(lm1), x) 
 
-orthogram(residuals(lm1), x)
 }
 \keyword{datasets}