get_NRI_NTI {MicrobiotaProcess}R Documentation

NRI (Nearest Relative Index) and NTI (Nearest Taxon Index)

Description

calculate NRT and NTI of sample. It is a wrapper method of picante::ses.mpd and picante::ses.mntd

Usage

get_NRI_NTI(obj, ...)

## S4 method for signature 'matrix'
get_NRI_NTI(
  obj,
  mindepth,
  sampleda,
  tree,
  abundance.weighted = TRUE,
  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 see also "ses.mpd" and "ses.mntd" of "picante".

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.

abundance.weighted

logical, whether calculate mean nearest taxon distances for each species weighted by species abundance, default is TRUE.

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


[Package MicrobiotaProcess version 1.6.0 Index]