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 hclust, phylo, phylog or PPtree. The tree must be ultrametric. 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

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.

bcPhyloDiversity

### 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)


[Package entropart version 1.6-10 Index]