net_dis_indi {mina} | R Documentation |
Calculate the network distance of bootstrap and permutation when appliable.
Calculate the network distance of bootstrap and permutation when appliable.
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 = "./", ... )
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'. |
y The 'mina' object with 'dis_bs', 'dis_pm' and 'dis_stat'.
y The 'mina' object with 'dis_bs', 'dis_pm' and 'dis_stat'.
## 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)