AllenH {entropart} | R Documentation |
Calculates the phylogenetic diversity of order q
of a probability vector.
AllenH(Ps, q = 1, PhyloTree, Normalize = TRUE, Prune = FALSE, CheckArguments = TRUE)
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 |
The phylogenetic entropy is calculated following Allen et al. (2009) for order q=1
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.
A named number equal the entropy of the community. The name is "None" to recall that no bias correction is available.
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.
# 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)