Description Usage Arguments Details Value Author(s) References See Also Examples

Calculates the phylogenetic diversity of order *q* of a probability vector.

1 |

`Ps` |
A probability vector, summing to 1. |

`q` |
A number: the order of diversity. Default is 1. |

`PhyloTree` |
An object of class |

`Normalize` |
If |

`Prune` |
What to do when somes species are in the tree but not in |

`CheckArguments` |
Logical; if |

The phylogenetic diversity is calculated following Chao *et al.* (2010). The result is identical to the total diversity calculated by `PhyloDiversity`

but it is much faster. A single value is returned instead of a `PhyloDiversity`

object, and no bias correction is available.

The `Normalize`

arguments allows calculating either *^{q}\bar{D}(T)* (if `TRUE`

) or *^{q}PD(T)* if `FALSE`

.

Diversity can be calculated for non ultrametric trees following Chao *et al.* (2010) even though the meaning of the result is not so clear (Leinster and Cobold, 2011).

A named number equal the diversity of the community. The name is "None" to recall that no bias correction is available.

Eric Marcon <[email protected]>

Chao, A., Chiu, C.-H. and Jost, L. (2010). Phylogenetic diversity measures based on Hill numbers. *Philosophical Transactions of the Royal Society B* 365(1558): 3599-609.

Leinster, T. and Cobbold, C. (2011). Measuring diversity: the importance of species similarity. *Ecology* 93(3): 477-489.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest
# and their taxonomy)
data(Paracou618)
# Ps is the vector of probabilities
Ps <- Paracou618.MC$Ps
# Calculate the phylogenetic Simpson diversity of the plot
(ChaoPD(Paracou618.MC$Ps, 2, Paracou618.Taxonomy, Normalize=TRUE))
# Calculate it using PhyloDiversity
# (more powerful but much slower if the tree has many periods)
PhyloDiversity(Paracou618.MC$Ps, 2, Paracou618.Taxonomy, Normalize=TRUE) -> phyD
summary(phyD)
``` |

entropart documentation built on Feb. 6, 2018, 1:04 a.m.

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