ChaoPD {entropart} | R Documentation |
Calculates the phylogenetic diversity of order q
of a probability vector.
ChaoPD(Ps, q = 1, PhyloTree, Normalize = TRUE, Prune = FALSE, CheckArguments = TRUE)
Ps |
A probability vector, summing to 1. |
q |
A number: the order of diversity. 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 diversity is calculated following Chao et al. (2010). The result is identical to the total diversity calculated by PhyloDiversity
but it is much faster. A single value is returned instead of a PhyloDiversity
object, and no bias correction is available.
The Normalize
arguments allows calculating either ^{q}\bar{D}(T)
(if TRUE
) or ^{q}PD(T)
if FALSE
.
Diversity can be calculated for non ultrametric trees following Chao et al. (2010) even though the meaning of the result is not so clear (Leinster and Cobold, 2011).
A named number equal the diversity of the community. The name is "None" to recall that no bias correction is available.
Chao, A., Chiu, C.-H. and Jost, L. (2010). Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society B 365(1558): 3599-609.
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 <- Paracou618.MC$Ps
# Calculate the phylogenetic Simpson diversity of the plot
(ChaoPD(Paracou618.MC$Ps, 2, Paracou618.Taxonomy, Normalize=TRUE))
# Calculate it using PhyloDiversity
# (more powerful but much slower if the tree has many periods)
PhyloDiversity(Paracou618.MC$Ps, 2, Paracou618.Taxonomy, Normalize=TRUE) -> phyD
summary(phyD)