mp_cal_pd_metric-methods: Calculating related phylogenetic alpha metric with MPSE or...

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 with MPSE or tbl_mpse object

Description

Calculating related phylogenetic alpha metric with MPSE or tbl_mpse object

Usage

mp_cal_pd_metric(
  .data,
  .abundance,
  action = "add",
  metric = c("PAE", "NRI", "NTI", "PD", "HAED", "EAED", "all"),
  abundance.weighted = FALSE,
  force = FALSE,
  seed = 123,
  ...
)

## S4 method for signature 'MPSE'
mp_cal_pd_metric(
  .data,
  .abundance,
  action = "add",
  metric = c("PAE", "NRI", "NTI", "PD", "HAED", "EAED", "IAC", "all"),
  abundance.weighted = FALSE,
  force = FALSE,
  seed = 123,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_cal_pd_metric(
  .data,
  .abundance,
  action = "add",
  metric = c("PAE", "NRI", "NTI", "PD", "HAED", "EAED", "all"),
  abundance.weighted = TRUE,
  force = FALSE,
  seed = 123,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_cal_pd_metric(
  .data,
  .abundance,
  action = "add",
  metric = c("PAE", "NRI", "NTI", "PD", "HAED", "EAED", "all"),
  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.
metric	the related phylogenetic metric, options is 'NRI', 'NTI', 'PD', 'PAE', 'HAED', 'EAED', 'IAC', 'all', default is 'PAE', 'all' 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 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

References

Cadotte, M.W., Jonathan Davies, T., Regetz, J., Kembel, S.W., Cleland, E. and Oakley, T.H. (2010), Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecology Letters, 13: 96-105. https://doi.org/10.1111/j.1461-0248.2009.01405.x.

Webb, C. O. (2000). Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. The American Naturalist, 156(2), 145-155. https://doi.org/10.1086/303378.

Examples

## Not run: 
  suppressPackageStartupMessages(library(curatedMetagenomicData))
  xx <- curatedMetagenomicData('ZellerG_2014.relative_abundance', dryrun=F)
  xx[[1]] %>% as.mpse -> mpse
  mpse %<>% 
    mp_cal_pd_metric(
      .abundance = Abundance, 
      force = TRUE,
      metric = 'PAE'
    )
  mpse %>% 
    mp_plot_alpha(
      .alpha = PAE,
      .group = disease
  )

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on July 26, 2024, 4:21 a.m.