mp_cal_divergence-methods: calculate the divergence with MPSE or tbl_mpse

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

calculate the divergence with MPSE or tbl_mpse

Description

calculate the divergence with MPSE or tbl_mpse

Usage

mp_cal_divergence(
  .data,
  .abundance,
  .name = "divergence",
  reference = "mean",
  distFUN = vegan::vegdist,
  method = "bray",
  action = "add",
  ...
)

## S4 method for signature 'MPSE'
mp_cal_divergence(
  .data,
  .abundance,
  .name = "divergence",
  reference = "mean",
  distFUN = vegan::vegdist,
  method = "bray",
  action = "add",
  ...
)

## S4 method for signature 'tbl_mpse'
mp_cal_divergence(
  .data,
  .abundance,
  .name = "divergence",
  reference = "mean",
  distFUN = vegan::vegdist,
  method = "bray",
  action = "add",
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_cal_divergence(
  .data,
  .abundance,
  .name = "divergence",
  reference = "mean",
  distFUN = vegan::vegdist,
  method = "bray",
  action = "add",
  ...
)

Arguments

.data	MPSE or tbl_mpse object
.abundance	The column name of OTU abundance column to be calculate.
.name	the colname name of the divergence results, default is 'divergence'.
reference	a no-empty character, either 'median' or 'mean' or the sample name, or a numeric vector which has length equal to the number of features, default is 'mean'.
distFUN	the function to calculate the distance between the reference and samples, default is 'vegan::vegdist'.
method	the method to calculate the distance, which will pass to the function that is specified in 'distFUN', default is 'bray'.
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.
...	additional arguments, see also the arguments of 'distFUN' function.

Value

update object or other (refer to action)

Author(s)

Shuangbin Xu

See Also

[mp_plot_alpha()]

Examples

## Not run: 
# example(mp_cal_divergence, run.dontrun = TRUE) to run the example.
data(mouse.time.mpse)
mouse.time.mpse %>% 
  mp_cal_divergence(
    .abundance = Abundance,
    .name = 'divergence.mean',
    distFUN = vegan::vegdist,
    method = 'bray'
  ) %>% 
  mp_plot_alpha(
    .alpha = divergence.mean,
    .group = time,
  )

## End(Not run)

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