Faith's phylogenetic diversity
Faith's phylogenetic diversity gives the total branch length on a phylogenetic tree that is spanned by a community. The abundance of each species in the community is not considered.
faith_pd(x, tree, x_labels = NULL)
x |
A numeric vector of species counts or proportions, or a logical vector of species presence/absence. |
tree |
A phylogenetic tree object.. |
x_labels |
A character vector of species labels for |
If the vector x is named, the names will be automatically
used to match x with the tree. Missing names are filled in with
zero counts. If x is not named and x_labels is provided,
these labels are used to match the elements of x with the tree.
If x is not named and x_labels is not provided, it is
assumed that x is already in the correct order, and we simply
check that its length matches the number of tips in the tree.
Faith's phylogenetic diversity, PD ≥q 0.
Faith DP. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 1992;61:1–10. doi: 10.1016/0006-3207(92)91201-3.
# Faith's phylogenetic diversity for whole tree is equal to the sum of the
# branch lengths.
sum(faith_tree$edge.length)
faith_pd(c(1, 1, 1, 1, 1), faith_tree)
# Can use named vector or additional argument to match species to tree.
faith_tree$tip.label
faith_pd(c(0, 0, 0, 10, 12), faith_tree)
faith_pd(c(d=10, e=12), faith_tree)
faith_pd(c(10, 12), faith_tree, c("d", "e"))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.