mp_anosim {MicrobiotaProcess} | R Documentation

## Analysis of Similarities (ANOSIM) with MPSE or tbl_mpse object

### Description

Analysis of Similarities (ANOSIM) with MPSE or tbl_mpse object

### Usage

    mp_anosim(
      .data,
      .abundance,
      .group,
      distmethod = "bray",
      action = "add",
      permutations = 999,
      seed = 123,
      ...
    )

    ## S4 method for signature 'MPSE'
    mp_anosim(
      .data,
      .abundance,
      .group,
      distmethod = "bray",
      action = "add",
      permutations = 999,
      seed = 123,
      ...
    )

    ## S4 method for signature 'tbl_mpse'
    mp_anosim(
      .data,
      .abundance,
      .group,
      distmethod = "bray",
      action = "add",
      permutations = 999,
      seed = 123,
      ...
    )

    ## S4 method for signature 'grouped_df_mpse'
    mp_anosim(
      .data,
      .abundance,
      .group,
      distmethod = "bray",
      action = "add",
      permutations = 999,
      seed = 123,
      ...
    )

### Arguments

`.data` | MPSE or tbl_mpse object
`.abundance` | the name of abundance to be calculated.
`.group` | The name of the column of the sample group information.
`distmethod` | character the method to calculate pairwise distances, default is 'bray'.
`action` | character "add" joins the ANOSIM result to internal attribute of the object, "only" and "get" return 'anosim' 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 ANOSIM analysis reproducible, default is 123.
`...` | additional parameters see also 'anosim' of vegan.

### Value

update object according action argument

### Author(s)

Shuangbin Xu

### Examples

    data(mouse.time.mpse)
    mouse.time.mpse %<>%
      mp_decostand(.abundance=Abundance)
    # action = "get" will return a anosim object
    mouse.time.mpse %>%
      mp_anosim(.abundance=hellinger, .group=time, action="get")
    # action = "only" will return a tbl_df that can be as the input of ggplot2.
    library(ggplot2)
    tbl <- mouse.time.mpse %>%
           mp_anosim(.abundance=hellinger,
                     .group=time,
                     permutations=999, # for more robust, set it to 9999
                     action="only")
    tbl
    tbl %>%
    ggplot(aes(x=class, y=rank, fill=class)) +
    geom_boxplot(notch=TRUE, varwidth = TRUE)

[Package MicrobiotaProcess version 1.4.4 Index]