get_pd_beta: calculate pairwise beta phylogenetic diversity

Description Usage Arguments Value

View source: R/pd.R

Description

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

Usage

1
2
3
4
5
6
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. 28, 2018, 3:48 a.m.