pd_from_Cadotte: Calculate phylogenetic diversity
In eliotmiller/ecoPDcorr: Ecologically-informed phylodiversity metrics

Description Usage Arguments Details Value Author(s) References Examples

Calculates PD (phylogenetic diversity) for a phylogeny

  ## S4 method for signature 'phylo4com'
pd(x, method = c("traditional", "polytomy",
    "yule"))
  ## S4 method for signature 'phylo4d'
pd(x, method = c("traditional", "polytomy",
    "yule"), ...)
  ## S4 method for signature 'phylo4'
pd(x, method = c("traditional"))

`x`	A `phylo4com`, `phylo4d`, or `phylo4` object.
`method`	Method for calculating pd.
`...`	additional arguments to be passed to other methods

TODO

When applied to a phylo4 tree, traditional PD is the only option (because the object contains no abundance data in this case).

For phylo4com or phylo4d, a numeric vector of length equal to the number of communities. For phylo4, a single numeric value for the tree.

Jim Regetz (regetz@nceas.ucsb.edu)

TODO

  pd(weeds)

  # traditional pd of the master tree
  pd(phylo4(weeds))

#  minTL(weeds$A) <- getMinTL(weeds$A, genera(weeds$A))
#  pd(weeds$A, "polytomy")
#  pd(weeds$A, "yule")