R/weighted.faith.R

In NGSwenson/lefse_0.5: Phylogenetic and Functional Analyses for Ecology

weighted.faith <-
function(my.phylo, my.sample){

weighted.faith.function = function(my.sub.sample){
		
			## extract the names of species in a community with an abundance greater than zero and use that information to make a pruned phylogeny for that community.
		tmp.tree = treedata(my.phylo, my.sub.sample[my.sub.sample > 0],warnings=F)$phy

	
			## Create empty branches matrix
		branches = matrix(NA, nrow = nrow(tmp.tree$edge), ncol = 4)

			## Fill first two columns of the matrix with node numbers defining each edge.
		branches[,1:2] = tmp.tree$edge

			## Fill the third column with the length of each branch
		branches[,3] = tmp.tree$edge.length
	
				get.leaves<-function(x){
					leaves.node<-tips(tmp.tree,x[2])
				}
		
				## Apply the get.leaves() function to each row in the branches object. This will retrieve species names subtended by each branch (i.e. ## row) in the branches matrix
		leaves = apply(branches, MARGIN = 1, get.leaves)
	
					## Now quickly loop through each set of leaves to ## calculate the mean abundance (Ai) for those species.
				for(i in 1:length(leaves)){
					branches[i,4] = mean(my.sub.sample[leaves[[i]]], na.rm = T) 

				}

			## Lastly calculated the Weighted Faith’s Index
		nrow(tmp.tree$edge) * ((sum(branches[,3] * branches[,4])) / sum(branches[,4]))


	}
outt = apply(my.sample, MARGIN = 1, weighted.faith.function)
outt

}