backbone - Backbone v2.1.3

CRAN release 2.1.3

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Published by zpneal about 2 years ago

backbone - backbone v2.1.2

CRAN release v2.1.2

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Published by zpneal about 3 years ago

backbone - backbone v2.1.1

CRAN release v2.1.1

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Published by zpneal over 3 years ago

backbone - backbone v2.1.0

• 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

- R
Published by zpneal almost 4 years ago

backbone - backbone v2.0.3

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

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Published by zpneal about 4 years ago

backbone - backbone v2.0.0

• 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

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Published by zpneal over 4 years ago

backbone - backbone v1.5.1

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

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Published by zpneal over 4 years ago

backbone - backbone v1.5.0

• 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

- R
Published by domagal9 almost 5 years ago

backbone - backbone v1.4.0

• 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

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Published by domagal9 almost 5 years ago

backbone - backbone v1.3.1

• speedups to sdsm
• minor corrections

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Published by domagal9 about 5 years ago

backbone - backbone v1.3.0

• 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

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Published by domagal9 about 5 years ago

backbone - backbone v1.2.2

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

- R
Published by domagal9 over 5 years ago

backbone - backbone v1.2.1

• 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

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Published by domagal9 over 5 years ago

backbone - backbone v1.2.0

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Published by domagal9 almost 6 years ago

backbone - backbone 1.1.0

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Published by domagal9 over 6 years ago