mp_adonis-methods: Permutational Multivariate Analysis of Variance Using...

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

Permutational Multivariate Analysis of Variance Using Distance Matrices for MPSE or tbl_mpse object

Description

Permutational Multivariate Analysis of Variance Using Distance Matrices for MPSE or tbl_mpse object

Usage

mp_adonis(
  .data,
  .abundance,
  .formula,
  distmethod = "bray",
  action = "get",
  permutations = 999,
  seed = 123,
  ...
)

## S4 method for signature 'MPSE'
mp_adonis(
  .data,
  .abundance,
  .formula,
  distmethod = "bray",
  action = "get",
  permutations = 999,
  seed = 123,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_adonis(
  .data,
  .abundance,
  .formula,
  distmethod = "bray",
  action = "get",
  permutations = 999,
  seed = 123,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_adonis(
  .data,
  .abundance,
  .formula,
  distmethod = "bray",
  action = "get",
  permutations = 999,
  seed = 123,
  ...
)

Arguments

.data	MPSE or tbl_mpse object
.abundance	the name of abundance to be calculated.
.formula	Model formula right hand side gives the continuous variables or factors, and keep left empty, such as ~ group, it is required.
distmethod	character the method to calculate pairwise distances, default is 'bray'.
action	character "add" joins the cca result to the object, "only" return a non-redundant tibble with the cca result. "get" return 'cca' object can be analyzed using the related vegan funtion.
permutations	the number of permutations required, default is 999.
seed	a random seed to make the adonis analysis reproducible, default is 123.
...	additional parameters see also 'adonis2' of vegan.

Value

update object according action argument

Author(s)

Shuangbin Xu

Examples

data(mouse.time.mpse)
mouse.time.mpse %>%
  mp_decostand(
     .abundance=Abundance, 
     method="hellinger") %>%
  mp_adonis(.abundance=hellinger, 
            .formula=~time, 
            distmethod="bray", 
            permutations=999, # for more robust, set it to 9999. 
            action="get")

xiangpin/MicrobiotaProcess documentation built on Nov. 12, 2024, 2:05 p.m.