Running examples in 'adephylo-Ex.R' failed
The error most likely occurred in:

> ### Name: ppca
> ### Title: Phylogenetic principal component analysis
> ### Aliases: ppca print.ppca summary.ppca scatter.ppca screeplot.ppca
> ###   plot.ppca
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> data(lizards)
> 
> if(require(ape) && require(phylobase)){
+ 
+ #### ORIGINAL EXAMPLE FROM JOMBART ET AL 2010 ####
+ 
+ 
+ ## BUILD A TREE AND A PHYLO4D OBJECT
+ liz.tre <- read.tree(tex=lizards$hprA)
+ liz.4d <- phylo4d(liz.tre, lizards$traits)
+ par(mar=rep(.1,4))
+ table.phylo4d(liz.4d,var.lab=c(names(lizards$traits),
+    "ACP 1\n(\"size effect\")"),show.node=FALSE, cex.lab=1.2)
+ 
+ 
+ ## REMOVE DUPLICATED POPULATIONS
+ liz.4d <- prune(liz.4d, c(7,14))
+ table.phylo4d(liz.4d)
+ 
+ 
+ ## CORRECT LABELS
+ lab <- c("Pa", "Ph", "Ll", "Lmca", "Lmcy", "Phha", "Pha",
+    "Pb", "Pm", "Ae", "Tt", "Ts", "Lviv", "La", "Ls", "Lvir")
+ tipLabels(liz.4d) <- lab
+ 
+ 
+ ## REMOVE SIZE EFFECT
+ dat <- tdata(liz.4d, type="tip")
+ dat <- log(dat)
+ newdat <- data.frame(lapply(dat, function(v) residuals(lm(v~dat$mean.L))))
+ rownames(newdat) <- rownames(dat)
+ tdata(liz.4d, type="tip") <- newdat[,-1] # replace data in the phylo4d object
+ 
+ 
+ ## pPCA
+ liz.ppca <- ppca(liz.4d,scale=FALSE,scannf=FALSE,nfposi=1,nfnega=1, method="Abouheif")
+ liz.ppca
+ tempcol <- rep("grey",7)
+ tempcol[c(1,7)] <- "black"
+ barplot(liz.ppca$eig,main='pPCA eigenvalues',cex.main=1.8,col=tempcol)
+ 
+ par(mar=rep(.1,4))
+ plot(liz.ppca,ratio.tree=.7)
+ 
+ 
+ ## CONTRIBUTIONS TO PC (LOADINGS) (viewed as dotcharts)
+ dotchart(liz.ppca$c1[,1],lab=rownames(liz.ppca$c1),main="Global principal
+ component 1")
+ abline(v=0,lty=2)
+ 
+ dotchart(liz.ppca$c1[,2],lab=rownames(liz.ppca$c1),main="Local principal
+ component 1")
+ abline(v=0,lty=2)
+ 
+ 
+ ## REPRODUCE FIGURES FROM THE PAPER
+ obj.ppca <- liz.4d
+ tdata(obj.ppca, type="tip") <- liz.ppca$li
+ myLab <- paste(" ",rownames(liz.ppca$li), sep="")
+ 
+ ## FIGURE 1
+ par(mar=c(.1,2.4,2.1,1))
+ table.phylo4d(obj.ppca, ratio=.7, var.lab=c("1st global PC", "1st local
+    PC"), tip.label=myLab,box=FALSE,cex.lab=1.4, cex.sym=1.2, show.node.label=TRUE)
+ add.scatter.eig(liz.ppca$eig,1,1,1,csub=1.2, posi="topleft", ratio=.23)
+ 
+ 
+ ## FIGURE 2
+ s.arrow(liz.ppca$c1,xlim=c(-1,1),clab=1.3,cgrid=1.3)
+ 
+ 
+ 
+ #### ANOTHER EXAMPLE - INCLUDING NA REPLACEMENT ####
+ ## LOAD THE DATA
+ data(maples)
+ tre <- read.tree(text=maples$tre)
+ x <- phylo4d(tre, maples$tab)
+ omar <- par("mar")
+ par(mar=rep(.1,4))
+ table.phylo4d(x, cex.lab=.5, cex.sym=.6, ratio=.1) # note NAs in last trait ('x')
+ 
+ ## FUNCTION TO REPLACE NAS
+ f1 <- function(vec){
+ if(any(is.na(vec))){
+ m <- mean(vec, na.rm=TRUE)
+ vec[is.na(vec)] <- m
+ }
+ return(vec)
+ }
+ 
+ 
+ ## PERFORM THE PPCA
+ dat <- apply(maples$tab,2,f1) # replace NAs
+ x.noNA <- phylo4d(tre, as.data.frame(dat))
+ map.ppca <- ppca(x.noNA, scannf=FALSE, method="Abouheif")
+ map.ppca
+ 
+ 
+ ## SOME GRAPHICS
+ screeplot(map.ppca)
+ scatter(map.ppca, useLag=TRUE)
+ plot(map.ppca, useLag=TRUE)
+ 
+ 
+ ## MOST STRUCTURED TRAITS
+ a <- map.ppca$c1[,1] # loadings on PC 1
+ names(a) <- row.names(map.ppca$c1)
+ highContrib <- a[a< quantile(a,0.1) | a>quantile(a,0.9)]
+ datSel <- cbind.data.frame(dat[, names(highContrib)], map.ppca$li)
+ temp <- phylo4d(tre, datSel)
+ table.phylo4d(temp) # plot of most structured traits
+ 
+ 
+ ## PHYLOGENETIC AUTOCORRELATION TESTS FOR THESE TRAITS
+ prox <- proxTips(tre, method="Abouheif")
+ abouheif.moran(dat[, names(highContrib)], prox)
+ 
+ }
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges

Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
Calls: ppca -> dudi.pca -> as.dudi
Execution halted