# AllenH: Phylogenetic Entropy of a Community In entropart: Entropy Partitioning to Measure Diversity

## Description

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

## Usage

 `1` ```AllenH(Ps, q = 1, PhyloTree, Normalize = TRUE, Prune = FALSE, CheckArguments = TRUE) ```

## Arguments

 `Ps` A probability vector, summing to 1. `q` A number: the order of entropy. Default is 1. `PhyloTree` An object of class `hclust`, `phylo`, `phylog` or `PPtree`. The tree is not necessarily ultrametric. `Normalize` If `TRUE` (default), diversity is not affected by the height of the tree. If `FALSE`, it is proportional to the height of the tree. `Prune` What to do when somes species are in the tree but not in `Ps`? If `TRUE`, the tree is pruned to keep species of `Ps` only. The height of the tree may be changed if a pruned branch is related to the root. If `FALSE` (default), species with probability 0 are added in `Ps`. `CheckArguments` Logical; if `TRUE`, the function arguments are verified. Should be set to `FALSE` to save time when the arguments have been checked elsewhere.

## Details

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.

## Value

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

## Author(s)

Eric Marcon <[email protected]>

## References

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.

`PhyloEntropy`, `ChaoPD`

## Examples

 ``` 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) ```

### Example output

```    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
```

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