backbone2.1.4 package

Extracts the Backbone from Graphs

fastball

Randomize a binary matrix using the fastball algorithm

fdsm

Extract backbone using the Fixed Degree Sequence Model

fixedcol

Extract backbone using the Fixed Column Model

fixedfill

Extract backbone using the Fixed Fill Model

fixedrow

Extract backbone using the Fixed Row Model

frommatrix

Converts a backbone adjacency matrix to a graph object of specified cl...

backbone.extract

Extracts a backbone network from a backbone object

backbone

backbone: Extracts the Backbone from Graphs

backbone.suggest

Suggest a backbone model

bicm

Bipartite Configuration Model

disparity

Extract backbone using the Disparity Filter

global

Compute global threshold backbone

lans

Extract backbone using Locally Adaptive Network Sparsification

logit

Logit-based probabilities for SDSM

loglikelihood_bicm

Computes the loglikelihood for the bicm function

loglikelihood_hessian_diag_bicm

Computes the loglikelihood hessian for the bicm function

loglikelihood_prime_bicm

Computes the loglikelihood gradient for the bicm function

mlf

Extract backbone using the Marginal Likelihood Filter

osdsm

Extract backbone using the Ordinal Stochastic Degree Sequence Model

pb

Poisson binomial distribution function

sdsm

Extract backbone using the Stochastic Degree Sequence Model

sparsify

Extract the backbone from a network using a sparsification model

sparsify.with.geometric

Extract Goldberg and Roth's (2003) Geometric backbone

sparsify.with.gspar

Extract Satuluri et al's (2011) G-spar backbone

sparsify.with.hypergeometric

Extract Goldberg and Roth's (2003) Hypergeometric backbone

sparsify.with.jaccard

Extract Goldberg and Roth's (2003) Jaccard backbone

tomatrix

Converts an input graph object to an adjacency/incidence matrix and id...

sparsify.with.localdegree

Extract Hamann et al.'s (2016) Local Degree backbone

sparsify.with.lspar

Extract Satuluri et al's (2011) L-spar backbone

sparsify.with.meetmin

Extract Goldberg and Roth's (2003) MeetMin backbone

sparsify.with.quadrilateral

Extract Nocaj et al.'s (2015) Quadrilateral Simmelian backbone

sparsify.with.simmelian

Extract Nick et al's (2013) Simmelian backbone

sparsify.with.skeleton

Extract Karger's (1999) skeleton backbone

trials.needed

Estimate number of monte carlo trials needed to estimate p-value

write.narrative

Generates suggested manuscript text

An implementation of methods for extracting an unweighted unipartite graph (i.e. a backbone) from an unweighted unipartite graph, a weighted unipartite graph, the projection of an unweighted bipartite graph, or the projection of a weighted bipartite graph (Neal, 2022 <doi:10.1371/journal.pone.0269137>).

  • Maintainer: Zachary Neal
  • License: GPL-3
  • Last published: 2024-05-09