Description Usage Arguments Details Value References

Calculates the Phylogenetic Diversity (PD) of multiple samples simultaneously. Note that this function uses that version of PD that always includes the path to the root of the tree.

1 | ```
phylodiv(x, phy)
``` |

`x` |
is the community data given as a |

`phy` |
is a rooted phylogenetic tree with branch lengths stored as a
phylo object (as in the |

`phylodiv`

takes community data and a phylogenetic tree (rooted
and with branch lengths) and calculates the Phylogenetic Diversity (PD) of
all samples/sites. PD is defined as the total length of all branches
spanning a set of terminal taxa representing an ecological sample (Faith,
1992). Please note that, if the common ancestor (node) of the set of taxa
of a sample is not the root of the tree, then the set of branches
connecting this node to the root are also included in the calculation.
Calculations are achieved using the efficient matrix algebra solution of
Rodrigues & Gaston (2002).

A vector of Phylogenetic Diversity (PD) values for each sample/site
in `x`

.

Faith DP. 1992. Conservation evaluation and phylogenetic diversity.

*Biological Conservation*61: 1-10.Rodrigues A & Gaston KJ. 2002. Maximising phylogenetic diversity in the selection of networks of conservation areas.

*Biological Conservation*105: 103-111.

davidnipperess/PDcalc documentation built on July 1, 2018, 3:59 p.m.

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