get_pd_beta: calculate pairwise beta phylogenetic diversity

In daijiang/dli55: Functions collected/wrote by Daijiang Li

Description

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

Usage

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, ...)

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
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?

Value

a data frame

daijiang/dli55 documentation built on Jan. 9, 2020, 3:30 p.m.