PDFD {entropart} | R Documentation |

## Phylogenetic Diversity / Functional Diversity of a Community

### Description

Calculates Faith's PD / Petchey and Gaston' FD of a community described by a probability vector and a phylogenetic / functional tree.

### Usage

```
PDFD(Ps, Tree, CheckArguments = TRUE)
```

### Arguments

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

`Tree` |
An object of class |

`CheckArguments` |
Logical; if |

### Details

PD and FD are defined as the total legth of the branches of the tree.

The probability vector is used to select branches: branches with probability 0 are eliminated.

Bias correction requires the number of individuals to estimate sample `Coverage`

.

Use `bcPhyloDiversity`

`(Ps, 0, Tree)`

and choose the `Correction`

.

### Value

A named number equal to the calculated diversity. The name is that of the bias correction used.

### References

Faith, D. P. (1992). Conservation evaluation and phylogenetic diversity. *Biological Conservation* 61(1): 1-10.

Petchey, O. L. and Gaston, K. J. (2002). Functional diversity (FD), species richness and community composition. *Ecology Letters* 5: 402-411.

### See Also

### Examples

```
# 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 Shannon diversity of the plot
PDFD(Ps, Paracou618.Taxonomy)
```

*entropart*version 1.6-13 Index]