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

## Calculate the adjacency matrix of 'norm' by correlation with 'mina' class object as input.

### Description

Calculate the adjacency matrix of 'norm' by correlation with 'mina' class object as input.

### Usage

    ## S4 method for signature 'mina,ANY'
    adj(x, method, sig = FALSE, threads = 80, nblocks = 400, ...)

    ## S4 method for signature 'mina,character'
    adj(x, method, sig = FALSE, threads = 80, nblocks = 400, ...)

### Arguments

`x` | An object of the class mina with 'norm' defined or a 'norm' matrix.
`method` | The correlation coeffient used for adjacacency matrix.
`sig` | The asymtotic P-values, only applicable for Pearson and Spearman methods, FALSE by default.
`threads` | The number of threads used for parallel running, 80 by default.
`nblocks` | The number of row/column for splitting sub-matrix, 400 by default.
`...` | Additional parameters.

### Value

x The same 'mina' object with 'adj' added.

### Examples

    maize <- new("mina", tab = maize_asv2, des = maize_des2)
    maize <- norm_tab(maize, method = "raref")
    maize <- fit_tabs(maize)
    maize <- adj(maize, method = "spearman", sig = FALSE)

[Package mina version 1.2.0 Index]