wrote by Daijiang Li

A function to calculate a bunch of phylo diversity: Faith's PD, MPD, VPD (variance of pairwise distance), MNTD, PSV/PSE. Results of MPD/MNTD from PhyloMeasures are equal with those from Phylocom/Picante with abundance.weight = FALSE Results of PD from PhyloMeasures are unrooted; PD from Phylocom are rooted.

get_pd_alpha(samp_wide, tree, samp_long, null.model.pd.root = FALSE,
  null.model.phylomeasures = TRUE, null.model.phylocom = FALSE,
  null.type.phylomeasures = "uniform", null.type.phylocom = 0,
  null.type.picante = "taxa.labels", n.item = 999, abund.weight = FALSE,
  verbose = TRUE, vpd = FALSE, ...)

`samp_wide`	wide version of samp_long, row.names are sites, colnames are species
`tree`	a phylogeny with class of 'phylo'
`samp_long`	a 3-column data frame, site, freq, sp
`null.model.pd.root`	whether to run null models for rooted PD?
`null.type.phylomeasures`	if null.model is TRUE, which null model to use for PhyloMeasure?
`null.type.phylocom`	if null.model is TRUE, which null model to use for Phylocom? - 0: phylogeny shuffle. - 1: maintain site richness and draw from species actually observed in sites. - 2: maintain site richness and draw from the phylogeny - 3: independent swap. See ?phylocomr::ph_comstruct for details
`null.type.picante`	if null.model is TRUE, which null model to use for Picante? Not used yet.
`n.item`	the number of randomization
`abund.weight`	should abundance information used when calculating pd with Phylocom/Picante? Default is FALSE
`verbose`	do you want to see relevant information?
`vpd`	to calculate vpd (varance of pairwise distance) or not?