qDT {adiv} | R Documentation |
Function qDT
calculates the ^qD(T) index developed by Chao et al. (2010) as the mean diversity of order q over T years in a phylogenetic tree. In function qDT
, the index is computed over the whole tree from root to tips. It uses the formula of the ^qD(T) index extended to non-ultrametric trees (where the distance from tip to root varies) (Chao et al. 2010, equation 4.5) .
qDT(phyl, comm, q = 2, tol = 1e-08)
phyl |
an object inheriting the class |
comm |
a data frame or a matrix typically with communities as rows, species as columns and abundance as entry. Species should be labeled as in the phylogenetic tree where they are the tips. |
q |
a vector with nonnegative value(s) for parameter |
tol |
numeric tolerance threshold: values between - |
If only one value of q
is given, a vector with the phylogenetic diversity of each community is returned.
If more than one value of q
is given, a list of two objects is returned:
q |
the vector of values for |
div |
a data frame with the phylogenetic diversity of each community calculated for all values of |
The results of function plot.qDT
are of class "evodivparam"
. As such, function plot.evodivparam
allows to plot the results of function qDT
.
Sandrine Pavoine sandrine.pavoine@mnhn.fr
Chao, A., Chiu, C.-H., Jost, L. (2010) Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society London Series B, 365, 3599–3609.
## Not run: if(require(ape)){ data(batcomm) phy <- read.tree(text=batcomm$tre) ab <- batcomm$ab[, phy$tip.label] plot(qDT(phy, ab)) plot(qDT(phy, ab, q=seq(0, 10, length=20))) } ## End(Not run)