NEWS

backbone 3.0.3

• Updated/added generic print(), summary() and plot() functions for backbone objects
• Corrected p-values in asymmetric marginal likelihood filter (h/t @florian-huber)

backbone 3.0.2

• minor updates to unit tests

backbone 3.0.1

• remove deprecated functions from manual
• replace all remaining %*% with (t)crossprod()
• include backbone details as graph attributes when input is an igraph object
• add backbone() wrapper function for all input network types
• speed-ups to .fixedfill() null model
• specifying backbone_only = FALSE returns a backbone-class object that can be described using print()

backbone 3.0.0

• all functions re-written to be modular, to facilitate future extensions
• streamlined functions to focus on input network type, rather than backbone model
• keep attributes of retained edges in igraph objects
• functions renamed in snake_case, to match naming conventions in igraph
• eliminated support for edgelist inputs, because they can be ambiguous
• eliminated ordinal stochastic degree sequence model (oSDSM) for bipartite projections, because it has limited applications and has not been formally validated
• all functions have associated unit tests

backbone 2.1.4

• updated depricated igraph functions
• ensure row/column labels are included in p-value matrices

backbone 2.1.3

• added support for structural 0s and 1s in sdsm() via the logit() function
• vectorized and added additional options to sparsify()
• implemented Marginal Likelihood Filter in mlf()
• implemented Locally Adaptive Network Sparsification in lans()
• added missing.as.zero option to statistical models

backbone 2.1.2

• speedups in pb() and sdsm()
• fixed minor bugs introduced by igraph 1.4.0

backbone 2.1.1

• speedups in sparsify() and all statistical backbone functions
• eliminated hyperg() as alternate name for fixedrow(), eliminated universal() as alternate name for global()
• empty & full rows/cols no longer need to be removed from bipartite inputs
• replaced testthat with tinytest; expanded unit tests
• backbone object includes node attributes, if present

backbone 2.1.0

• eliminated dependency on PoissonBinomial; sdsm() and fixedcol() now use an efficient implementation of the Refined Normal Approximation in base R
• eliminated dependency on MASS; osdsm() now uses glm() in base R to implement the conditional logistic regression method described by Neal (2017)
• eliminated dependency on network and support for network objects, which can easily be converted to matrix objects
• removed bipartite generative functions bipartite.from.probability(), bipartite.from.sequence(), bipartite.from.distribution(), and bipartite.add.blocks(). These are now part of the incidentally package
• speed improvements to bicm()
• updated the information provided in the narrative text when narrative = TRUE
• when the original graph is supplied as an igraph object with vertex attributes, the attributes are preserved in the backbone
• added links to new tutorial: Neal, Z. P. 2022. backbone: An R Package to Extract Network Backbones. PLOS ONE, 17, e0269137. https://doi.org/10.1371/journal.pone.0269137

backbone 2.0.3

• fixed bug in fastball() so it will work with R < 4.1.0

backbone 2.0.2

• fixed bug in fastball() so it will work with R < 4.1.0

backbone 2.0.1

• minor bug fixes
• faster implementation of fastball() algorithm
• set alpha = 0.05 as default in all statistical models
• renamed fwer (familywise error rate) parameter as mtc (multiple test correction)

backbone 2.0.0

• remove davis example data; add examples using synthetic data
• add support for unweighted graphs: sparsify()
• add support for weighted bipartite graphs: osdsm()
• add support for non-projection weighted graphs: disparity()
• new vignette illustrating all functions
• add implementation of fastball() algorithm for marginal-preserving matrix randomization
• re-add testthat tests
• allow backbone functions to directly output a backbone, eliminating the need for the backbone.extract() function
• add support for any p.adjust() method of correcting for familywise error rates
• Minor bug fixes

backbone 1.5.1

• removed testthat tests due to unknown MKL error; will be restored in a future version

backbone 1.5.0

• add four functions to generate random bipartite graphs: bipartite.from.probability(), bipartite.from.sequence(), bipartite.from.distribution(), and bipartite.add.blocks()
• set diagonal in positive and negative backbone object matrices to NA
• corrected p-value computation in fixedfill()
• remove running time from backbone object summary dataframe
• update documentation, readme, vignette

backbone 1.4.0

• add fixedcol() function - null model where column degrees are fixed and row sums are allowed to vary
• add fixedfill() function - null model where the number of 1’s in the matrix (number of edges in the graph) are fixed
• replace class.convert() with tomatrix() and frommatrix()
• use updated Poisson binomial calculations (more accurate approximation)
• hyperg() now called fixedrow()
• remove bipartite.null function
• update documentation, readme, vignette
• include logo

backbone 1.3.1

• speedups to sdsm

backbone 1.3.0

• update sdsm to use the bicm model - a new, fast, approximation of the probabilities
• remove all other models from sdsm
• if an older model is called in sdsm, show warning that model has changed
• add new function bipartite.null which lets the user pick if they want rows/cols to be fixed or vary
• update fwer m parameter

backbone 1.2.2

• fix fdsm to accept all graph inputs
• rename sdsm “chi2” model to “rcn”
• universal function can now return weighted projection
• universal function now has a narrative parameter
• class.convert now drops (with warning) rows and columns with zero sum before sending output to universal, sdsm, fdsm, or hyperg.
• update citations

backbone 1.2.1

• add narrative parameter to backbone.extract for suggested manuscript text
• add scobit model to sdsm
• add time unit to runtime calculation
• minor spelling and comment fixes

backbone 1.2.0

• add support for sparse matrix, igraph, network, and edgelist objects (see ‘class.convert’)
• add family-wise error rate test corrections (see ‘backbone.extract’)
• sdsm: add multiple methods for computing initial probabilities (see ‘sdsm’ details) one of which uses convex optimization (see ‘polytope’)
• sdsm: update poisson binomial computation method to increase speed (see ‘sdsm’ and ‘rna’)
• add more descriptives to summary dataframe output of backbone object
• update documentation of functions
• update vignette to reflect package changes
• bug fixes for R 4.0.0

backbone 1.1.0

• add support for sparse matrices
• add support for speedglm in sdsm
• add poisson binomial approx. in sdsm
• add summary output to sdsm, fdsm, hyperg, universal
• update vignette to reflect package changes
• bug fixes

backbone 1.0.0

• initial release