backbone.extract {backbone} R Documentation

## 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"
)


### 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.

### 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)


[Package backbone version 2.1.0 Index]