---
title: "NEWS"
output: html_document
---
## backbone 3.0.4

* perform parameter/input checks inside each `backbone_from_` function
* updated citation

## 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
