[Adephylo-commits] r196 - in pkg: . man vignettes vignettes/figs

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

Author: jombart
Date: 2013-08-10 11:53:00 +0200 (Sat, 10 Aug 2013)
New Revision: 196

Modified:
   pkg/ChangeLog
   pkg/man/carni19.Rd
   pkg/man/carni70.Rd
   pkg/man/lizards.Rd
   pkg/man/maples.Rd
   pkg/man/mjrochet.Rd
   pkg/man/moranIdx.Rd
   pkg/man/orthobasis.Rd
   pkg/man/orthogram.Rd
   pkg/man/palm.Rd
   pkg/man/ppca.Rd
   pkg/man/procella.Rd
   pkg/man/sp.tips.Rd
   pkg/man/table.phylo4d.Rd
   pkg/man/tithonia.Rd
   pkg/man/treePart.Rd
   pkg/man/ungulates.Rd
   pkg/vignettes/adephylo.pdf
   pkg/vignettes/figs/adephylo-012.pdf
   pkg/vignettes/figs/adephylo-016.pdf
   pkg/vignettes/figs/adephylo-018.pdf
   pkg/vignettes/figs/adephylo-aboutest.pdf
   pkg/vignettes/figs/adephylo-figFourBas.pdf
   pkg/vignettes/figs/adephylo-lm1.pdf
   pkg/vignettes/figs/adephylo-loadings.pdf
   pkg/vignettes/figs/adephylo-orthobas1.pdf
   pkg/vignettes/figs/adephylo-pca1.pdf
   pkg/vignettes/figs/adephylo-pca2.pdf
   pkg/vignettes/figs/adephylo-phylo4d.pdf
   pkg/vignettes/figs/adephylo-resid.pdf
Log:
Changes for the new release 1.1-5

Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/ChangeLog	2013-08-10 09:53:00 UTC (rev 196)
@@ -1,3 +1,15 @@
+			CHANGES IN ADEPHYLO VERSION 1.1-5
+
+FIXES
+	o the new NAMESPACE selectively imports procedures to avoid
+	conflicts between ape, phylobase, and ade4. Thes packages are no
+	longer attached when loading adephylo
+
+	o most dataset examples have been 'dontrun-ed' to save time during
+	checks of the package on CRAN
+
+
+
 			CHANGES IN ADEPHYLO VERSION 1.1-4
 
 

Modified: pkg/man/carni19.Rd
===================================================================
--- pkg/man/carni19.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/carni19.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -23,6 +23,7 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+\dontrun{
 if(require(ape) && require(phylobase)){
 
 data(carni19)
@@ -31,4 +32,5 @@
 table.phylo4d(x, ratio=.5, center=FALSE)
 }
 }
+}
 \keyword{datasets}

Modified: pkg/man/carni70.Rd
===================================================================
--- pkg/man/carni70.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/carni70.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -26,6 +26,7 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+\dontrun{
 if(require(ape) && require(phylobase)){
 
 data(carni70)
@@ -49,4 +50,5 @@
 orthogram(yrange, tre)
 }
 }
+}
 \keyword{datasets}

Modified: pkg/man/lizards.Rd
===================================================================
--- pkg/man/lizards.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/lizards.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -33,6 +33,7 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+\dontrun{
 if(require(ape) && require(phylobase)){
 
 ## see data
@@ -65,4 +66,5 @@
 }
 }
 }
+}
 \keyword{datasets}

Modified: pkg/man/maples.Rd
===================================================================
--- pkg/man/maples.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/maples.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -27,6 +27,7 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+\dontrun{
 if(require(ape) && require(phylobase)){
 
 data(maples)
@@ -54,4 +55,5 @@
 cor.test(pic.bif, pic.dom) # correlation is no longer significant
 }
 }
+}
 \keyword{datasets}

Modified: pkg/man/mjrochet.Rd
===================================================================
--- pkg/man/mjrochet.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/mjrochet.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -44,6 +44,7 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+\dontrun{
 if(require(ape) && require(phylobase)){
 
 data(mjrochet)
@@ -62,4 +63,5 @@
 
 }
 }
+}
 \keyword{datasets}

Modified: pkg/man/moranIdx.Rd
===================================================================
--- pkg/man/moranIdx.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/moranIdx.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -37,9 +37,14 @@
   between tips of a phylogeny.
 }
 \examples{
+\dontrun{
 ## use maples dataset
-example(maples)
+data(maples)
+tre <- read.tree(text=maples$tre)
+dom <- maples$tab$Dom
+bif <- maples$tab$Bif
 
+
 ## get a proximity matrix between tips 
 W <- proxTips(tre, met="Abouheif")
 
@@ -60,4 +65,5 @@
 abline(v=sim[1], col="red", lwd=3)
 
 }
+}
 \keyword{manip}

Modified: pkg/man/orthobasis.Rd
===================================================================
--- pkg/man/orthobasis.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/orthobasis.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -76,6 +76,7 @@
 \examples{
 if(require(ape) && require(phylobase)){
 
+## SIMPLE EXAMPLE ##
 ## make a tree
 x <- rtree(50)
 
@@ -88,9 +89,22 @@
 table.phylo4d(obj, cex.sym=.7, cex.lab=.7)
 
 
-## removing phylogenetic autocorrelation in a model ##
-example(ungulates, package="adephylo")
+\dontrun{
+## REMOVING PHYLOGENETIC AUTOCORRELATION IN A MODEL ##
+## use example in ungulates dataset
+data(ungulates)
+tre <- read.tree(text=ungulates$tre)
+plot(tre)
 
+## look at two traits
+afbw <- log(ungulates$tab[,1])
+neonatw <- log((ungulates$tab[,2]+ungulates$tab[,3])/2)
+names(afbw) <- tre$tip.label
+names(neonatw) <- tre$tip.label
+plot(afbw, neonatw) # relationship between traits
+lm1 <- lm(neonatw~afbw)
+abline(lm1)
+
 lm1
 resid1 <- residuals(lm1)
 orthogram(resid1, tre) # residuals are autocorrelated
@@ -105,4 +119,5 @@
 table.phylo4d(phylo4d(tre, cbind.data.frame(resid1, resid2)))
 }
 }
+}
 \keyword{manip}

Modified: pkg/man/orthogram.Rd
===================================================================
--- pkg/man/orthogram.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/orthogram.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -103,6 +103,7 @@
   never happen, since ade4 is loaded as a dependence by adephylo.
 }
 \examples{
+\dontrun{
 if(require(ape) && require(phylobase)){
 
 ## a phylogenetic example
@@ -136,3 +137,4 @@
 abouheif.moran(resid, W)
 }
 }
+}

Modified: pkg/man/palm.Rd
===================================================================
--- pkg/man/palm.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/palm.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -34,6 +34,7 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+\dontrun{
 if(require(ape) && require(phylobase)){
 
 ## load data, make a tree and a phylo4d object
@@ -55,4 +56,5 @@
 }
 }
 }
+}
 \keyword{datasets}

Modified: pkg/man/ppca.Rd
===================================================================
--- pkg/man/ppca.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/ppca.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -247,6 +247,7 @@
 prox <- proxTips(tre, method="Abouheif")
 abouheif.moran(dat[, names(highContrib)], prox)
 
+detach("package:ade4")
 }
 }
 \keyword{multivariate}
\ No newline at end of file

Modified: pkg/man/procella.Rd
===================================================================
--- pkg/man/procella.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/procella.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -34,30 +34,16 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+\dontrun{
 if(require(ape) && require(phylobase)){
+
 ## load data, make tree and phylo4d object
 data(procella)
 tre <- read.tree(text=procella$tre)
 x <- phylo4d(tre, procella$traits)
 par(mar=rep(.1,4))
 table.phylo4d(x,cex.lab=.7)
-
-## test phylogenetic autocorrelation in traits
-if(require(ade4)){
-
-f1 <- function(vec){ # to replace missing data
-m <- mean(vec,na.rm=TRUE)
-vec[is.na(vec)] <- m
-return(vec)
 }
-
-traits <- data.frame(lapply(procella$traits, f1))
-prox <- proxTips(tre)
-
-myTests <- gearymoran(prox, traits)
-plot(myTests)
 }
 }
-
-}
 \keyword{datasets}

Modified: pkg/man/sp.tips.Rd
===================================================================
--- pkg/man/sp.tips.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/sp.tips.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -40,6 +40,7 @@
   slowly. \cr
 }
 \examples{
+\dontrun{
 if(require(ape) & require(phylobase)){
 ## make a tree
 x <- as(rtree(20),"phylo4")
@@ -49,4 +50,5 @@
 sp.tips(x, 1, 2:20, TRUE)
 }
 }
+}
 \keyword{manip}

Modified: pkg/man/table.phylo4d.Rd
===================================================================
--- pkg/man/table.phylo4d.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/table.phylo4d.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -121,6 +121,8 @@
 table.phylo4d(myPC, ratio=.8, var.lab=varlab) # plot the PCs
 add.scatter.eig(liz.pca1$eig,2,1,2,posi="topleft", inset=c(0,.15))
 title("Phylogeny and the principal components")
+
+detach("package:ade4")
 }
 }
 \keyword{hplot}

Modified: pkg/man/tithonia.Rd
===================================================================
--- pkg/man/tithonia.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/tithonia.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -39,27 +39,19 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+\dontrun{
 if(require(ape) && require(phylobase)){
 
 data(tithonia)
 tre <- read.tree(text=tithonia$tre)
 traits <- log(tithonia$tab + 1)
+rownames(traits) <- gsub("_", ".", rownames(traits))
 
 ## build a phylo4d object
 x <- phylo4d(tre, traits)
 par(mar=rep(.1,4))
 table.phylo4d(x)
 
-## perform a Geary/Moran test to detect phylogenetic signal in variables
-if(require(ade4)){
-
-## use branch length to define proximities
-prox1 <- proxTips(tre, method="patristic")
-gearymoran(prox1, traits)
-
-## use Abouheif's proximity
-prox2 <- proxTips(tre, method="Abouheif")
-gearymoran(prox2, traits)
 }
 }
 }

Modified: pkg/man/treePart.Rd
===================================================================
--- pkg/man/treePart.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/treePart.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -43,6 +43,8 @@
   from the ade4 package.
 }
 \examples{
+\dontrun{
+
 if(require(ape) & require(phylobase)){
 ## make a tree
 x <- as(rtree(10),"phylo4")
@@ -53,19 +55,6 @@
 temp <- phylo4d(x, partition)
 table.phylo4d(temp, cent=FALSE, scale=FALSE)
 }
-
-if(require(ade4)){
-## former orthobasis in ade4
-data(ungulates)
-ung.Bscores <- newick2phylog(ungulates$tre)$Bscores
-
-## version using treePart
-ung <- read.tree(text=ungulates$tre)
-ung.orthobas <- treePart(ung, res="orthobasis")
-
-## comparison of the first 3 vectors
-cbind(ung.Bscores[,1], ung.orthobas[,1],ung.Bscores[,2],
-   ung.orthobas[,2], ung.Bscores[,3], ung.orthobas[,3])
 }
 }
 \keyword{manip}

Modified: pkg/man/ungulates.Rd
===================================================================
--- pkg/man/ungulates.Rd	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/man/ungulates.Rd	2013-08-10 09:53:00 UTC (rev 196)
@@ -32,6 +32,7 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+\dontrun{
 if(require(ape) && require(phylobase)){
 ## load data
 data(ungulates)
@@ -52,4 +53,5 @@
 orthogram(residuals(lm1), x) 
 }
 }
+}
 \keyword{datasets}

Modified: pkg/vignettes/adephylo.pdf
===================================================================
--- pkg/vignettes/adephylo.pdf	2013-08-09 14:47:49 UTC (rev 195)
+++ pkg/vignettes/adephylo.pdf	2013-08-10 09:53:00 UTC (rev 196)
@@ -106,28 +106,31 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adephylo -r 196