Phylogenetic Diversity / Functional Diversity of a Community

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

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.

See also

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)
#> None 
#>  395