wrote by Daijiang Li

get_pd_alpha

R Documentation

Calculate alpha phylogenetic diversity

Description

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.

Usage

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,
  ...
)

Arguments

`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.model.phylomeasures`	Whether to run null models using PhyloMeasures package?
`null.model.phylocom`	Whether to run null models using phylocomr package?
`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?
`...`	Additional arguments.