# News

All notable changes will be documented in this file.

## [0.3] - 2020-09-19

### Added

- Add support for
`glmGamPoi`

as method to estimate the model parameters; thanks @yuhanH for his pull request
- Add option to use
`theta.md`

, `theta.mm`

or`theta.ml`

to estimate theta when `method = 'poisson'`

- Add a
`poisson_fast`

method for parameter estimation that uses the `speedglm`

package and `theta.mm`

by default
- Add ability to plot overdispersion factor in
`plot_model_pars`

- Add and return time stamps at various steps in the
`vst`

function
- Add functions to calculate grouped arithmetic and geometric mean per row for sparse matrices (
`dgCMatrix`

) - might come in handy some time

### Changed

- Default theta regularization is now based on overdispersion factor (
`1 + m / theta`

where m is the geometric mean of the observed counts) not `log10(theta)`

; old behavior available via `theta_regularization`

parameter
- Refactored model fitting code - is now more efficient when using parallel processing
- Changed how message and progress bar output is controlled; integer
`verbosity`

parameter controls all output: 0 for no output, 1 for only messages, 2 for messages and progress bars
- Increased default bin size (genes being processed simultaneously) from 256 to 500
- Better input checking for cell attributes; more efficient calculation of missing ones

### Fixed

- Some non-regularized model parameters were not plotted

## [0.2.1] - 2019-12-17

### Added

- Add function to generate data given the output of a vst run
- Add cpp support for dense integer matrices
- Minimum variance parameter added to vst function

## [0.2.0] - 2019-04-12

### Added

- Rcpp versions of utility functions
- Helper functions to get corrected UMI and variance of pearson residuals for large UMI matrices

### Changed