AllenH {entropart} | R Documentation |
Phylogenetic Entropy of a Community
Description
Calculates the phylogenetic diversity of order of a probability vector.
Usage
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 |
Normalize |
If |
Prune |
What to do when somes species are in the tree but not in |
CheckArguments |
Logical; if |
Details
The phylogenetic entropy is calculated following Allen et al. (2009) for order 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.
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.
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 <- 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)