backbone.extract {backbone}

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 = bb.object$class,
  narrative = FALSE
)

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.

narrative

boolean: TRUE if suggested text & citations should be displayed.

Details

The "backbone" S3 class object is composed of (1) the weighted graph as a matrix, (2) upper-tail p-values as a matrix, (3, if signed = TRUE) lower-tail p-values as a matrix, (4, if present) node attributes as a dataframe, and (5) several properties of the original graph and backbone model

When signed = FALSE, a one-tailed test (is the weight stronger?) is performed for each edge. The resulting backbone contains edges whose weights are significantly stronger than expected in the null model. When signed = TRUE, a two-tailed test (is the weight stronger or weaker?) is performed for each edge. The resulting backbone contains positive edges for those whose weights are significantly stronger, and negative edges for those whose weights are significantly weaker, than expected in the null model.

Value

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

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)