c_net_stability: Evaluate the stability of a network

In MetaNet: Network Analysis for Omics Data

Evaluate the stability of a network

Description

Vi=\frac{E-Ei}{E}

E is the global efficiency and Ei is the global efficiency after the removal of the node i and its entire links.

Usage

c_net_stability(
  go_ls,
  mode = "robust_test",
  partial = 0.5,
  step = 10,
  reps = 9,
  threads = 1,
  verbose = TRUE,
  keystone = FALSE
)

robust_test(
  go_ls,
  partial = 0.5,
  step = 10,
  reps = 9,
  threads = 1,
  verbose = TRUE
)

vulnerability(go_ls, threads = 1, verbose = TRUE)

robustness(go_ls, keystone = FALSE, reps = 9, threads = 1, verbose = TRUE)

Arguments

go_ls	an igraph object or igraph list.
mode	"robust_test", "vulnerability", "robustness"
partial	how much percent vertexes be removed in total (default: 0.5, only for robust_test)
step	how many nodes be removed each time? (default: 10, only for robust_test)
reps	simulation number (default: 9)
threads	threads
verbose	verbose
keystone	remove 70%% keystones instead of remove 50%% nodes (default: False, only for robustness)

Value

a data.frame

data.frame (robustness class)

a vector

Examples

data("c_net")
if (requireNamespace("ggpmisc")) {
  c_net_stability(co_net, mode = "robust_test", step = 20, reps = 9) -> robust_res
  plot(robust_res, index = "Average_degree", mode = 2)
}

c_net_stability(co_net, mode = "vulnerability") -> vulnerability_res
plot(vulnerability_res)

robustness(co_net) -> robustness_res
plot(robustness_res)

module_detect(co_net) -> co_net_modu
zp_analyse(co_net_modu, mode = 2) -> co_net_modu

c_net_stability(co_net_modu, mode = "robustness", keystone = TRUE) -> robustness_res
plot(robustness_res)

MetaNet documentation built on May 29, 2024, 1:21 a.m.