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, ...)

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

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.

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 <- 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)
maize <- norm_tab(maize, method = "raref")
maize <- fit_tabs(maize)
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 1.0.0 Index]