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#'
#' @title W index value for a single topology.
#'
#' @description This function assigns the weight according to the ramification patterns
#' (see Van-Wright et al., 1981).
#' The input tree is reordered in post order.
#' Returns a vector with weights.
#'
#' @param tree is a single tree with n terminals, an ape phylo object.
#'
#' @examples
#' library(jrich)
#' data(tree)
#' plot(tree)
#' indexw <- IndexW(tree)
#' newTree <- tree
#' newTree$tip.label <- indexw
#' plot(newTree)
#'
#'
#'
#'@author Miranda-Esquivel Daniel R.
#'
#'
IndexW <- function (tree=tree) {
## masked functions
Ancestor <- function (tree=tree,node=node) {
ancestro <- tree$edge[(tree$edge[,2] == node)][1]
return(ancestro)
}
node.Matrix <- matrix(0,nrow=1,ncol=(length(tree$tip.label)*2-1))
tree <- reorder.phylo(tree,order="postorder")
raiz <-length(tree$tip.label)+1
node.Matrix[1,raiz] <- 1
hijos <- Children(tree=tree,node=raiz)
node.Matrix[1,hijos] <- node.Matrix[1,raiz]
for (i in (((length(tree$tip.label)+2)):(length(tree$tip.label)+tree$Nnode))){
node.Matrix[1,i] <- node.Matrix[1,Ancestor(tree=tree,node=i)]+1
hijos <- Children(tree=tree,node=i)
node.Matrix[1,hijos] <- node.Matrix[1,i]
}
node.Matrix <- node.Matrix[1,1:length(tree$tip.label)]
node.Matrix <- sum(node.Matrix)/node.Matrix
node.Matrix <- node.Matrix/min(node.Matrix)
return(node.Matrix)
}
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