mp_adonis {MicrobiotaProcess} | R Documentation

## 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 'adonis' 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")

[Package MicrobiotaProcess version 1.4.4 Index]