mp_decostand {MicrobiotaProcess} | R Documentation

## This Function Provideds Several Standardization Methods for Community Data

### Description

This Function Provideds Several Standardization Methods for Community Data

### Usage

    mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)

    ## S4 method for signature 'data.frame'
    mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)

    ## S4 method for signature 'MPSE'
    mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)

    ## S4 method for signature 'tbl_mpse'
    mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)

    ## S4 method for signature 'grouped_df_mpse'
    mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)

### Arguments

`.data` | MPSE or tbl_mpse object
`.abundance` | the names of otu abundance to be applied standardization.
`method` | character the name of standardization method, it can one of 'total', 'max', 'frequency', 'normalize', 'range', 'rank', 'rrank', 'standardize' 'pa', 'chi.square', 'hellinger' and 'log', see also `decostand`
`logbase` | numeric The logarithm base used in 'method=log', default is 2.
`...` | additional parameters, see also `decostand`

### Value

update object

### Author(s)

Shuangbin Xu

### Source

mp_decostand for data.frame object is a wrapper method of vegan::decostand from the vegan package

### See Also

[mp_extract_assays()] and [mp_rrarefy()]

decostand

### Examples

    data(mouse.time.mpse)
    mouse.time.mpse %>%
    mp_decostand(.abundance=Abundance, method="hellinger")

[Package MicrobiotaProcess version 1.4.4 Index]