Description Usage Arguments Details Value References Examples

View source: R/phylodiv_expected.R

Calculates the expected Phylogenetic Diversity (PD) of multiple samples simultaneously based on probabilities of occurrence (or extinction) for each combination of species and site. Note that this function uses that version of PD that always includes the path to the root of the tree.

1 | ```
phylodiv.expected(x, phy, occur = TRUE)
``` |

`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 |

`occur` |
is a |

`phylodiv.expected`

takes probability data and a phylogenetic
tree (rooted and with branch lengths) and calculates the expected
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). Expected PD is the summed branch length
expected for each site given the probability of occurrence (or extinction)
of species (and ancestral branches) at that site (Witting & Loeschcke 1995;
Faith 2013). 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.

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

.

Faith DP. 1992. Conservation evaluation and phylogenetic diversity.

*Biological Conservation*61: 1-10.Faith DP. 2013. Biodiversity and evolutionary history: useful extensions of the PD phylogenetic diversity assessment framework.

*Annals of the New York Academy of Sciences*1289: 69–89.Witting L. & Loeschcke V. 1995. The optimization of biodiversity conservation.

*Biological Conservation*71: 205–207.

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