wrote by Daijiang Li

A function to calculate a bunch of pairwise beta phylo diversity: unifraction, MPD, MNTD, PCD

get_pd_beta(samp_wide, tree, samp_long, get.unif = TRUE, get.mpd = TRUE,
  get.mntd = TRUE, get.pcd = TRUE, null.model.phylocom = TRUE,
  null.type.phylocom = 0, n.item = 999, abund.weight = FALSE,
  null.model.mpd.phylomeasures = TRUE,
  null.model.mntd.phylomeasures = FALSE, verbose = TRUE,
  verbose.mntd.null = 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
`get.unif`	whether to calculate pairwise UniFrac
`get.mpd`	whether to calculate pairwise mpd_beta
`get.mntd`	whether to calculate pairwise mntd_beta
`get.pcd`	calculate PCD or not? Can be time consuming.
`null.model.phylocom`	whether to run null models for MPD and MNTD with Phylocom?
`null.type.phylocom`	if null.model.phylocom is TRUE, which null model to use? See ?phylocomr::ph_comstruct for details
`n.item`	the number of randomization with Phylocom
`abund.weight`	should abundance information used when calculating MPD/MNTD with Phylocom? Note: mntd_beta with Phylocom seems not reliable.
`null.model.mpd.phylomeasures`	whether to run null models for MPD with PhyloMeasures?
`null.model.mntd.phylomeasures`	whether to run null models for MNTD with PhyloMeasures?
`verbose`	do you want to see relevant information?
`verbose.mntd.null`	do you want to see relevant information about null models of MNTD with PhyloMeasures?