net_dis-mina: Calculate the network distance of 'multi' and test the...

In Guan06/mina: Microbial community dIversity and Network Analysis

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")

Guan06/mina documentation built on Feb. 21, 2022, 11:56 a.m.