Changes in Version 1.11.6 (2020-07-18)
=====================================

* Fixed a bug in the initialization of beta_j.
* Fixed a bug in zinbsurf.
* Changed zinbwave default to `K=2`.
* Fix bug in the initialization of W.

Changes in Version 1.7.5 (2019-10-08)
=====================================

* Changed default of `zinbwave` to `observationalWeights=FALSE` to speed up
  computations when weights are not needed.
* Added argument `zeroinflation = TRUE`: when set to FALSE a negative binomial
  model is fit.
* Removed dependence on the `copula` package to avoid depending on `gsl`.

Changes in Version 1.5.3 (2019-04-19)
=====================================

* Updated vignette to reflect new way of interacting with Seurat.
* Illustrate the use of approximate `zinbsurf` function.

Changes in Version 1.4.2 (2019-03-11)
=====================================

* Fix bug in computeObservationalWeights.

Changes in Version 1.3.1 (2018-05-09)
=====================================

* New `zinbsurf` function implements approximate method for large matrices.
* New option `which_genes` in `zinbwave` to specify which genes to use to
  compute `W`.


Changes in Version 1.1.6 (2018-04-17)
=====================================

* `zinbwave` now uses `counts` assay by default.
* Users can now specify which assay to use to fit the zinb model.

Changes in Version 1.1.5 (2018-02-15)
=====================================

* Computational weights are computed in `zinbwave` as saved as assay.
* Modified vignette to include example of Differential Expression.
* Improved documentation for `zinbwave`.

Changes in Version 0.99.10 (2017-10-23)
=====================================

* Added AIC and BIC to decide number of factors
* Added function to compute observational weights for DE

Changes in Version 0.99.7 (2017-07-17)
=====================================

* `zinbwave()` now returns a `SingleCellExperiment` object.

Changes in Version 0.99.6 (2017-07-05)
=====================================

* Fixed bug in zinb.loglik.matrix to avoid Inf values

Changes in Version 0.99.5 (2017-07-03)
=====================================

* Added function computeDevianceResiduals() to compute residuals
* Added function imputeZeros() to use the model to impute technical zeros
* Added function zinbwave() to perform dimensionality reduction
* Changed vignette to illustrate new functions

Changes in Version 0.99.4 (2017-06-08)
=====================================

* Switch from parallel to BiocParallel
* Improvements to code efficiency, e.g., avoid copying ZinbModel objects

Changes in Version 0.99.3 (2017-05-31)
=====================================

* More informative Description: field
* Improved documentation
* Added getAlpha, getBeta, and getGamma accessor functions
* Improved show() method
* Vectorized code in zinbSim()
* Fixed bug that introduced an error when initializing an object with empty X or V
* Added tests on numerical correctness

Changes in Version 0.99.2 (2017-05-12)
=====================================

* New formula interface for SummarizedExperiment
* Add t-SNE example to vignette

Changes in Version 0.99.0 (2017-05-09)
=====================================

* Bumped version for submission to Bioconductor
* Minor changes to compile vignette
* Required R version 3.4

Changes in Version 0.1.4 (2017-04-10)
=====================================

* Improved documentation
* zinbSim now produces matrix of J x n dimension
* Removed unnecessary dependency on clusterExperiment
* Additional tests
* Better default for epsilon

Changes in Version 0.1.2 (2017-03-29)
=====================================

* New vignette
* Change name to zinbwave

Changes in Version 0.1.0 (2016-09-23)
=====================================

* Introducing S4 class zinbModel
* Major restructuring of the initialization and optimization (see vignette)
* Method zinbFit to fit a model
* Many other methods, including zinbInitialize, zinbOptimize, zinbSim

