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NEWS
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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