net_dis,mina,ANY-method {mina} | R Documentation

## Calculate the network distance of 'multi' and test the significance when 'perm' is defined.

### Description

Calculate the network distance of 'multi' and test the significance when 'perm' is defined.

### Usage

    ## S4 method for signature 'mina,ANY'
    net_dis(
      x,
      method,
      evk = 100,
      egv = TRUE,
      dir = "./",
      sig = TRUE,
      skip = TRUE,
      ...
    )

    ## S4 method for signature 'mina,character'
    net_dis(
      x,
      method,
      evk = 100,
      egv = TRUE,
      dir = "./",
      sig = TRUE,
      skip = TRUE,
      ...
    )

### Arguments

`x` | An object of class 'mina' with 'multi' (and 'perm' if sig is TRUE) defined.
`method` | The distance to be calculated, "spectra" and "Jaccard" are available.
`evk` | The first 'evk' eigenvalues will be used for 'spectra' distance, the default is 100.
`egv` | Wheather to output the eigenvectors for Spectral distance, the defult is TRUE, only validate when 'method == "spectra"'.
`dir` | The folder to output the eigenvectors, only validate when 'egv == TRUE'.
`sig` | Whether to test the significance, if TRUE (by default), 'perm' is needed.
`skip` | Whether to skip the comparison when the dimenstion of adjacency matrix is smaller than setted 'evk'.
`...` | Additional parameters.

### Value

x The same 'mina' object with 'net_dis' defined.

### Examples

    maize <- new("mina", tab = maize_asv2, des = maize_des2)
    maize <- norm_tab(maize, method = "raref")
    maize <- fit_tabs(maize)
    maize <- bs_pm(maize, group = "Compartment")
    maize <- net_dis(maize, method = "Jaccard")

[Package mina version 1.2.0 Index]