Update to backbonePhylo methods to permit multiple clades to have the same label

I have just added a feature to the functions phylo.toBackbone and plot.backbonePhylo to permit multiple clades to have the same names. This could be handy to plot (for instance) a phylogeographic tree in which multiple subtrees come from the same region. The way that I did this is by creating a unique clade ID for each subtree independent of the clade label.

Here is a simulated case just to illustrate the point. Remember we can make this object using an interactive mode.

library(phytools)

## Loading required package: ape

## Loading required package: maps

## 
##  # maps v3.1: updated 'world': all lakes moved to separate new #
##  # 'lakes' database. Type '?world' or 'news(package="maps")'.  #

## now let's create our backbone tree
tree<-phytools:::lambdaTree(pbtree(n=10),lambda=0.5)

## create a translation table
## leaving a couple of single-taxon clades for fun
tip.label<-sample(tree$tip.label,8)
clade.label<-sample(c("Puerto Rico","Vieques","Virgin Islands"),8,
    replace=TRUE)
N<-ceiling(runif(n=8,min=1,max=20))
## set crown node depth to 1/2 the maximum depth
depth<-sapply(tip.label,function(x,y) 
    0.5*y$edge.length[which(tree$edge[,2]==which(y$tip.label==
    x))],y=tree)
trans<-data.frame(tip.label,clade.label,N,depth)
rownames(trans)<-NULL
rm(tip.label,clade.label,N,depth)
## this is what our translation table looks like for NON-interactive mode
trans

##   tip.label    clade.label  N     depth
## 1        t1    Puerto Rico  7 0.7765093
## 2        t6    Puerto Rico  5 0.5923332
## 3        t7    Puerto Rico  6 0.5611997
## 4        t2    Puerto Rico 10 0.7693265
## 5       t10        Vieques 11 0.5050155
## 6        t3        Vieques  8 0.7459787
## 7        t4 Virgin Islands  5 0.7459787
## 8        t5    Puerto Rico  8 0.5923332

## convert to "backbonePhylo" object
obj<-phylo.toBackbone(tree,trans)
## just to see, here are the clade labels & the unique clade IDs
sapply(obj$tip.clade,function(x) x$label)

##  [1] "Vieques"        "Virgin Islands" "t9"             "Vieques"       
##  [5] "Puerto Rico"    "Puerto Rico"    "Puerto Rico"    "t8"            
##  [9] "Puerto Rico"    "Puerto Rico"

sapply(obj$tip.clade,function(x) x$id)

##  [1] "IDGhhL" "1VY7KJ" "28HUn7" "DDSSM8" "41RQvF" "Ip26tj" "XxOFYs"
##  [8] "jOJTgb" "XRlU1x" "pBtF6T"

## plot
cols<-setNames(c("white","blue","red"),
    c("Vieques","Puerto Rico","Virgin Islands"))
plot(obj,col=cols,fixed.height=TRUE,print.clade.size=TRUE)

This update can be obtained by getting the latest development version of phytools from GitHub.