backbone (version 2.1.0)

backbone.extract: Extracts a backbone network from a backbone object

Description

backbone.extract returns a binary or signed adjacency matrix containing the backbone that retains only the significant edges.

Usage

backbone.extract(
  bb.object,
  signed = FALSE,
  alpha = 0.05,
  mtc = "none",
  class = "matrix"
)

Value

backbone graph: Binary or signed backbone graph of class given in parameter class.

Arguments

bb.object

backbone: backbone S3 class object.

signed

Boolean: TRUE for a signed backbone, FALSE for a binary backbone (see details)

alpha

Real: significance level of hypothesis test(s)

mtc

string: type of Multiple Test Correction to be applied; can be any method allowed by p.adjust.

class

string: the class of the returned backbone graph, one of c("matrix", "sparseMatrix", "igraph", "edgelist"), converted via tomatrix.

Details

The "backbone" S3 class object is composed of three matrices (the weighted graph, edges' upper-tail p-values, edges' lower-tail p-values), and a string indicating the null model used to compute p-values.

When signed = FALSE, a one-tailed test (is the weight stronger) is performed for each edge with a non-zero weight. It yields a backbone that perserves edges whose weights are significantly stronger than expected in the chosen null model. When signed = TRUE, a two-tailed test (is the weight stronger or weaker) is performed for each every pair of nodes. It yields a backbone that contains positive edges for edges whose weights are significantly stronger, and negative edges for edges whose weights are significantly weaker, than expected in the chosen null model. NOTE: Before v2.0.0, all significance tests were two-tailed and zero-weight edges were evaluated.

Examples

#A binary bipartite network of 30 agents & 75 artifacts; agents form three communities
B <- rbind(cbind(matrix(rbinom(250,1,.8),10),
                 matrix(rbinom(250,1,.2),10),
                 matrix(rbinom(250,1,.2),10)),
           cbind(matrix(rbinom(250,1,.2),10),
                 matrix(rbinom(250,1,.8),10),
                 matrix(rbinom(250,1,.2),10)),
           cbind(matrix(rbinom(250,1,.2),10),
                 matrix(rbinom(250,1,.2),10),
                 matrix(rbinom(250,1,.8),10)))

backbone.object <- fixedrow(B, alpha = NULL)
bb <- backbone.extract(backbone.object, alpha = 0.05)