Returns the phylogenetic diversity of a tree for the tips specified.
Arguments
- tree
TreeMan
object- tids
tip ids
- parallel
logical, make parallel?
- progress
name of the progress bar to use, see
create_progress_bar
Details
Faith's phylogenetic diversity is calculated as the sum of all connected
branches for specified tips in a tree. It can be used to investigate how biodviersity
as measured by the phylogeny changes. Parallelizable.
The function uses getCnntdNds()
.
References
Faith, D. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.
Examples
tree <- randTree(10)
calcPhyDv(tree, tree["tips"])
#> [1] 8.28878