PDFD {entropart} | R Documentation |
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)
Ps |
A probability vector, summing to 1. |
Tree |
An object of class |
CheckArguments |
Logical; if |
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
.
A named number equal to the calculated diversity. The name is that of the bias correction used.
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.
# 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)