Nothing
## tree.nodf.one ==>> internal function ##
treeNodfOne<-function(comm, tree, order){
sites <- nrow(comm)
spp <- ncol(comm)
tree <- as.phylo(tree)
pds <- pd(comm, tree)$PD
if(order==TRUE){
ord <- order(pds, decreasing=TRUE)
comm <- comm[ord, ]
pds <- pd(comm, tree)$PD
}
tree.nodf.dist <- matrix(NA, sites, sites) ## To store dist. results
rownames(tree.nodf.dist) <- rownames(comm)
colnames(tree.nodf.dist) <- rownames(comm)
s.fraction.dist<-tree.nodf.dist
for(i in 1:(sites - 1)) {
pd.set <- pds[i]
for(j in (i + 1):sites) {
pd.subset <- pds[j]
if(pd.subset >= pd.set) {
one.tree.nodf.par <- 0
one.s.fraction.par <- 0
} else{
comb <- colSums(comm[c(i,j), ])
s.shared <- sum(comb > 1)
one.s.fraction.par <- s.shared / sum(comm[j, ])
comb <- ifelse(comb > 0, 1, 0)
comb <- matrix(comb, 1)
colnames(comb) <- colnames(comm)
pd.comb <- pd(comb, tree)$PD
pd.shared <- pd.set + pd.subset - pd.comb
one.tree.nodf.par <- pd.shared/pd.subset
}#closes else
tree.nodf.dist[j, i] <- one.tree.nodf.par
s.fraction.dist[j, i] <- one.s.fraction.par
}# closes for j
}# closes for i
tree.nodf.dist <- as.dist(tree.nodf.dist * 100)
s.fraction.dist <- as.dist(s.fraction.dist * 100)
return(list(tree.nodf.dist=tree.nodf.dist, s.fraction.dist=s.fraction.dist))
}
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