mp_cal_rarecurve {MicrobiotaProcess} | R Documentation

## Calculating the different alpha diversities index with different depth

### Description

Calculating the different alpha diversities index with different depth

### Usage

    mp_cal_rarecurve(
      .data,
      .abundance = NULL,
      action = "add",
      chunks = 400,
      seed = 123,
      force = FALSE,
      ...
    )

    ## S4 method for signature 'MPSE'
    mp_cal_rarecurve(
      .data,
      .abundance = NULL,
      action = "add",
      chunks = 400,
      seed = 123,
      force = FALSE,
      ...
    )

    ## S4 method for signature 'tbl_mpse'
    mp_cal_rarecurve(
      .data,
      .abundance = NULL,
      action = "add",
      chunks = 400,
      seed = 123,
      force = FALSE,
      ...
    )

    ## S4 method for signature 'grouped_df_mpse'
    mp_cal_rarecurve(
      .data,
      .abundance = NULL,
      action = "add",
      chunks = 400,
      seed = 123,
      force = FALSE,
      ...
    )

### Arguments

`.data` | MPSE or tbl_mpse object
`.abundance` | the name of otu abundance to be calculated.
`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 'rarecurve' object.
`chunks` | numeric the split number of each sample to calculate alpha diversity, default is 400. eg. A sample has total 40000 reads, if chunks is 400, it will be split to 100 sub-samples (100, 200, 300,..., 40000), then alpha diversity index was calculated based on the sub-samples.
`seed` | a random seed to make the result reproducible, default is 123.
`force` | logical whether calculate rarecurve forcibly when the '.abundance' is not be rarefied, default is FALSE
`...` | additional parameters.

### Value

update rarecurce calss

### Author(s)

Shuangbin Xu

### See Also

[mp_plot_rarecurve()] and [mp_extract_rarecurve()]

### Examples

    data(mouse.time.mpse)
    mouse.time.mpse %>%
    mp_rrarefy() -> mpse
    mpse
    # larger 'chunks' means more robust, but it will become slower.
    mpse %<>% mp_cal_rarecurve(.abundance=RareAbundance, chunks=100, action="add")
    mpse
    p1 <- mpse %>%
          mp_plot_rarecurve(.rare=RareAbundanceRarecurve, .alpha="Observe")
    p2 <- mpse %>%
          mp_plot_rarecurve(.rare=RareAbundanceRarecurve, .alpha=c("Observe", "ACE"))

[Package MicrobiotaProcess version 1.4.4 Index]