High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)

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Documentation for package ‘BiRewire’ version 3.40.0

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BiRewire-package The BiRewire package
BiRewire The BiRewire package
birewire.analysis.bipartite Analysis of Jaccard similarity trends across switching steps.
birewire.analysis.dsg Analysis of Jaccard similarity trends across switching steps.
birewire.analysis.undirected Analysis of Jaccard similarity trends across switching steps.
birewire.bipartite.from.incidence Converts an incidence matrix into a bipartite graph.
birewire.build.dsg Transform a dsg object in a SIF file.
birewire.induced.bipartite Transform a SIF data frame into a dsg object (a list of positive and negative incidence matrix).
birewire.load.dsg Read a SIF file from a given path
birewire.rewire.bipartite Efficient rewiring of bipartite graphs
birewire.rewire.bipartite.and.projections Analysis and rewiring function processing a bipartite graphs and its two projections
birewire.rewire.dsg Efficient rewiring of directed signed graphs
birewire.rewire.undirected Efficient rewiring of undirected graphs
birewire.sampler.bipartite Efficient generation of a null model for a given bipartite graph
birewire.sampler.dsg Efficient generation of a null model for a given dsg.
birewire.sampler.undirected Efficient generation of a null model for a given undirected graph
birewire.similarity Compute the Jaccard similarity index between two binary matrices with the same number of non-null entries and the sam row- and column-wise sums.
birewire.similarity.dsg Compute the Jaccard similarity index between dsg.
birewire.slum.to.sparseMatrix The function transforms a triplet sparse matrix from slum package to a Matrix sparse matrix.
birewire.visual.monitoring.bipartite Visual monitoring of the Markov chain underlying the SA for directed graphs.
birewire.visual.monitoring.dsg Visual monitoring of the Markov chain underlying the SA for dsgs.
birewire.visual.monitoring.undirected Visual monitoring of the Markov chain underlying the SA for undirected graphs.
BRCA_binary_matrix TCGA Brest Cancer data
test_dsg Tool example of dsg