Calculate phylogenetic diversity

Returns the phylogenetic diversity of a tree for the tips specified.

Usage

calcPhyDv(tree, tids, parallel = FALSE, progress = "none")

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.

See also

calcFrPrp, calcOvrlp, getCnnctdNds, https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

tree <- randTree(10)
calcPhyDv(tree, tree["tips"])
#> [1] 8.28878