net_dis,mina,ANY-method {mina} | R Documentation |
Calculate the network distance of 'multi' and test the significance when 'perm' is defined.
## 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, ... )
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. |
x The same 'mina' object with 'net_dis' defined.
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")