net_dis_indi {mina} | R Documentation

## Calculate the network distance of bootstrap and permutation when appliable.

### Description

Calculate the network distance of bootstrap and permutation when appliable.

Calculate the network distance of bootstrap and permutation when appliable.

### Usage

    net_dis_indi(x, method, ...)

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

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

### Arguments

`x` | The folder store the network inference results. defined.
`method` | The distance to be calculated, "spectra" and "Jaccard" are available.
`...` | Additional parameters.
`evk` | The first 'evk' eigenvalues will be used for 'spectra' distance, the default is 100.
`sig` | Whether to test the significance, if TRUE (by default), permutation results should be included in the folder 'x'.
`skip` | Whether to skip the comparison when the dimenstion of adjacency matrix is smaller than setted 'evk', default TRUE.
`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'.

### Value

y The 'mina' object with 'dis_bs', 'dis_pm' and 'dis_stat'.

y The 'mina' object with 'dis_bs', 'dis_pm' and 'dis_stat'.

### Examples

    ## Not run:
    data(maize)
    maize <- norm_tab(maize, method = "raref")
    maize <- fit_tabs(maize)
    maize <- get_rep(maize, top = 5)
    maize <- bs_pm(maize, group = "Compartment", individual = TRUE, out_dir =
    "./individual_bs_pm/")
    maize_stat1 <- net_dis_indi(x = "./individual_bs_pm/", method = "spectra")
    maize_stat2 <- net_dis_indi(x = "./individual_bs_pm/", method = "Jaccard")
    maize_stat3 <- net_dis_indi(x = "./individual_bs_pm/", method = "spectra",
    evk = 100, skip = TRUE)

    ## End(Not run)
    ## Not run:
    data(maize)
    norm(maize) <- maize_asv2
    maize <- fit_tabs(maize)
    maize <- get_rep(maize, top= 5)
    maize <- bs_pm(maize, group = "Compartment", individual = TRUE, out_dir =
    "./individual_bs_pm/")
    maize_stat1 <- net_dis_indi("./individual_bs_pm/", method = "spectra")
    maize_stat2 <- net_dis_indi("./individual_bs_pm/", method = "Jaccard")
    maize_stat3 <- net_dis_indi("./individual_bs_pm/", method = "spectra",
    evk = 100, skip = TRUE)

    ## End(Not run)

[Package mina version 1.2.0 Index]