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#' @title Make fossil species on a phylogeny
#' @description This function takes an object of class \code{'phylo'} and
#' randomly changes the lengths of the leaves.
#' @usage makeFossil(tree,p=0.5,ex=0.5)
#' @param tree a phylogenetic tree. The tree needs not to be ultrametric and
#' fully dichotomous.
#' @param p the proportion of tips involved. By default it is half of the number
#' of tips.
#' @param ex the multiplying parameter to change the leaf lengths. It is set at
#' 0.5 by default.
#' @export
#' @return The function produces a phylogeny having the same backbone of the
#' original one.
#' @author Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro
#' Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco
#' Carotenuto
#' @examples
#' data("DataApes")
#' DataApes$Tstage->Tstage
#'
#' makeFossil(tree=Tstage)
makeFossil<-function(tree,
p=0.5,
ex=0.5){
#require(ape)
which(tree$edge[,2]<(Ntip(tree)+1))->leaves
Ntip(tree)*p->prop
sample(leaves,prop)->ext.leaves
tree$edge.length[ext.leaves]*ex->tree$edge.length[ext.leaves]
return(tree)
}
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