R: Calculate phylogenetic diversity

calcPhyDv {treeman} | R Documentation

## Calculate phylogenetic diversity

### Description

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

    library(treeman)
    tree <- randTree(10)
    calcPhyDv(tree, tree['tips'])

[Package treeman version 1.1.4 Index]