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 entropy. 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 entropy is calculated following Allen *et al.* (2009) for order *q=1* and Leinster and Cobold (2011) for other orders.The result is identical to the total entropy calculated by `PhyloEntropy`

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

object, and no bias correction is available.

The `Normalize`

argument allows normalizing entropy by the height of the tree, similarly to `ChaoPD`

.

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

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

Eric Marcon <[email protected]>

Allen, B., Kon, M. and Bar-Yam, Y. (2009). A New Phylogenetic Diversity Measure Generalizing the Shannon Index and Its Application to Phyllostomid Bats. *American Naturalist* 174(2): 236-243.

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 | ```
# 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 <- as.ProbaVector(Paracou618.MC$Ns)
# Calculate the phylogenetic Shannon diversity of the plot
AllenH(Ps, 1, Paracou618.Taxonomy, Normalize=TRUE)
# Calculate it using PhyloEntropy: more powerful but much slower is the tree has many periods
PhyloEntropy(Ps, 1, Paracou618.Taxonomy, Normalize=TRUE) -> phyE
summary(phyE)
``` |

```
None
3.919941
alpha or gamma phylogenetic or functional entropy of order 1 of distribution Ps
Phylogenetic or functional entropy was calculated according to the tree
Paracou618.Taxonomy
Entropy is normalized
Entropy equals: 3.919941
```

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