sparsify.with.hypergeometric: Extract Goldberg and Roth's (2003) Hypergeometric backbone

In backbone: Extracts the Backbone from Graphs

Extract Goldberg and Roth's (2003) Hypergeometric backbone

Description

sparsify.with.hypergeometric is a wrapper for sparsify() that extracts the hypergeometric backbone described by Goldberg and Roth (2003). It is equivalent to sparsify(escore = "hypergeometric", normalize = "none", filter = "threshold", umst = FALSE).

Usage

sparsify.with.hypergeometric(U, s, class = "original", narrative = FALSE)

Arguments

U	An unweighted unipartite graph, as: (1) an adjacency matrix in the form of a matrix or sparse Matrix; (2) an edgelist in the form of a two-column dataframe; (3) an igraph object.
s	numeric: Sparsificiation threshold, 0 < s < 1; smaller values yield sparser graphs
class	string: the class of the returned backbone graph, one of c("original", "matrix", "Matrix", "igraph", "edgelist"). If "original", the backbone graph returned is of the same class as U.
narrative	boolean: TRUE if suggested text & citations should be displayed.

Value

An unweighted, undirected, unipartite graph of class class.

References

package: Neal, Z. P. (2022). backbone: An R Package to Extract Network Backbones. PLOS ONE, 17, e0269137. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1371/journal.pone.0269137")}

model: Goldberg, D. S., & Roth, F. P. (2003). Assessing experimentally derived interactions in a small world. Proceedings of the National Academy of Sciences, 100, 4372-4376. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1073/pnas.0735871100")}

Examples

U <- igraph::sample_sbm(60, matrix(c(.75,.25,.25,.25,.75,.25,.25,.25,.75),3,3), c(20,20,20))
plot(U) #A hairball
sparse <- sparsify.with.hypergeometric(U, s = 0.3, narrative = TRUE)
plot(sparse) #Clearly visible communities

backbone documentation built on May 29, 2024, 8:03 a.m.