News
=====

###### 14/04/2026
* Add S3 method for `confint()` with `deconv` objects to allow calculation of
confidence intervals.
* Add `max_similarity()` for calculating maximum similarity between cell types.
* Add CV of lambda in `deconvolute()` [experimental].
* Use `$opt` element to store call arguments in `deconvolute()`.
* Refine vignette.

###### 19/03/2026
* Improved `plot_comp()` and `plot_path()` with option to show cell percentages.

# cellGeometry 0.6.2
###### 26/02/2026
* Improved error checks in `deconvolute()` to help with issue #20.

## New features

* Add measurement of bias and variance to `tune_deconv()`.
* Add `plot_tunevar()` to compare MSE, bias^2 and variance.
* Add S3 method for `kappa()` to compute the condition number of the spillover 
matrix.
* Add `plot_path()` to show how the coefficient paths vary with compensation for 
either a single bulk sample or a cell subclass.
* Add `plot_pred()` as an alternative to `plot_set()` for viewing predicted vs 
observed results from simulations in a single correlation plot.
* Add `zero_fraction` argument to `generate_samples()`.

# cellGeometry 0.6.1
###### 13/01/2026
* Fix subtle division by near 0 issue in `nest_output`

## New features

* Massive speed up of `deconvolute()`.
* Add ridge parameter `lambda` to `deconvolute()` [experimental].
* Add `resvar` metric to `tune_deconv()` to examine residual variance of bulk 
gene expression.

## Important change

* `deconvolute()` no longer returns `se` and `hat` in the `subclass` list 
element. Standard errors can be obtained with the new function `se()`.
* `cores` argument has been removed from `deconvolute()`

## Important bugfix

* R 4.5.2 for macOS arm64 (Apple M* Macs) has switched to using a faster BLAS
(vecLib?) by default, which causes errors with parallelisation in `mclapply()`.
The problem is isolated to R 4.5.2 arm64 for macOS on M* Macs; or any version of
R for macOS including intel, if vecLib BLAS is being used via a symlink. The
solution is to use `cores = 1` with `deconvolute()` and `tune_deconv()` whenever
vecLib BLAS is in use.
* Removed use of `pbmcapply::pbmclapply()` as this caused problems with R 4.5.2 
for macOS arm64 (Apple M* Macs) even with `cores=1`. This fixes indefinite 
hanging in `tune_deconv()` associated with vecLib BLAS.

# cellGeometry 0.5.7
###### 11/12/2025
* Change `log` argument in `deconvolute()` to `logged_bulk`. NB. this is a 
change of logic.

# cellGeometry 0.5.6
###### 07/10/2025
* Add `residuals.deconv()` to allow recalculation of full residuals matrix.

# cellGeometry 0.5.5
###### 10/09/2025
* Fix bug in `mergeMarkers()` if cellMarkers object has no cell grouping vector.

# cellGeometry 0.5.4
###### 09/09/2025
* Fix CRAN checks
* Switch from using `cat()` to `message()`

# cellGeometry 0.5.3
###### 26/08/2025
* Massive speed up (4-5x) in compensation optimisation

# cellGeometry 0.5.2
###### 30/07/2025

* Expanded to 3 methods for identifying outlier genes (var.e, Cook's distance,
Studentized residuals)
* Improved (nested) parallelisation of `tune_deconv()`
* Rewrite weights code (faster)

# cellGeometry 0.5.0
###### 14/07/2025

* Calculation of SE
* Detection and multipass removal of problematic genes with extreme residuals

# cellGeometry 0.2.0
###### 24/01/2025

* This is the initial build of cellGeometry
