mp_cal_NRI_NTI {MicrobiotaProcess}R Documentation

Calculating NRI (Nearest Relative Index) and NTI (Nearest Taxon Index) with MPSE or tbl_mpse object

Description

Calculating NRI (Nearest Relative Index) and NTI (Nearest Taxon Index) with MPSE or tbl_mpse object

Usage

mp_cal_NRI_NTI(
  .data,
  .abundance,
  action = "add",
  abundance.weighted = TRUE,
  force = FALSE,
  seed = 123,
  ...
)

## S4 method for signature 'MPSE'
mp_cal_NRI_NTI(
  .data,
  .abundance,
  action = "add",
  abundance.weighted = TRUE,
  force = FALSE,
  seed = 123,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_cal_NRI_NTI(
  .data,
  .abundance,
  action = "add",
  abundance.weighted = TRUE,
  force = FALSE,
  seed = 123,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_cal_NRI_NTI(
  .data,
  .abundance,
  action = "add",
  abundance.weighted = TRUE,
  force = FALSE,
  seed = 123,
  ...
)

Arguments

.data

object, MPSE or tbl_mpse object

.abundance

The column name of OTU abundance column to be calculate.

action

character it has three options, "add" joins the new information to the input tbl (default), "only" return a non-redundant tibble with the just new information, ang 'get' return a 'alphasample' 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 alpha index even the '.abundance' is not rarefied, default is FALSE.

seed

integer a random seed to make the result reproducible, default is 123.

...

additional arguments see also "ses.mpd" and "ses.mntd" of "picante".

Value

update object.

Author(s)

Shuangbin Xu


[Package MicrobiotaProcess version 1.6.4 Index]