get_NRI_NTI-methods: calculating related phylogenetic alpha metric

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

calculating related phylogenetic alpha metric

Description

calculating related phylogenetic alpha metric

Usage

get_NRI_NTI(obj, ...)

## S4 method for signature 'matrix'
get_NRI_NTI(
  obj,
  mindepth,
  sampleda,
  tree,
  metric = c("PAE", "NRI", "NTI", "PD", "HAED", "EAED", "IAC", "all"),
  abundance.weighted = FALSE,
  force = FALSE,
  seed = 123,
  ...
)

## S4 method for signature 'data.frame'
get_NRI_NTI(obj, mindepth, sampleda, tree, abundance.weighted = TRUE, ...)

## S4 method for signature 'phyloseq'
get_NRI_NTI(obj, mindepth, abundance.weighted = TRUE, ...)

Arguments

obj	object, data.frame of (nrow sample * ncol taxonomy(feature)) or phyloseq.
...	additional arguments, meaningless now.
mindepth	numeric, Subsample size for rarefying community.
sampleda	data.frame, sample information, row sample * column factors.
tree	tree object, it can be phylo object or treedata object.
metric	the related phylogenetic metric, options is 'NRI', 'NTI', 'PD', 'PAE', 'HAED', 'EAED', 'IAC', 'all', default is 'PAE', meaning all the metrics ('NRI', 'NTI', 'PD', 'PAE', 'HAED', 'EAED', 'IAC').
abundance.weighted	logical, whether calculate mean nearest taxon distances for each species weighted by species abundance, default is FALSE.
force	logical whether calculate the index even the count of otu is not rarefied, default is FALSE. If it is TRUE, meaning the rarefaction is not be performed automatically.
seed	integer a random seed to make the result reproducible, default is 123.

Value

alphasample object contained NRT and NTI.

Author(s)

Shuangbin Xu

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.