# ChemoSpecUtils 1.0.5 2025-04-12
## Misc.
* ChemoSpec2D no longer exports .unstack (as of a few days ago), so a copy of .unstack was added to `sampleDist.Spectra2D.R`.  Self-inflicted error!

# ChemoSpecUtils 1.0.4 2024-01-31
## Misc.
* At CRAN's request, updated a few small documentation issues.

# ChemoSpecUtils 1.0.3 2023-05-28
## Misc.
* At CRAN's request, made examples and test conditional on any packages in Suggests:.
* Replaced uses of `@template` with inline functions (`@template` has been deprecated).

# ChemoSpecUtils 1.0.1 2022-12-04
## Misc.
* Rewrote `.drawEllipse` and `.scorePlot` to avoid use of the `plyr` package which is retired.
* Behind the scene updates to CI and rename master branch to main.

# ChemoSpecUtils 1.0.0 2021-10-09
## Significant Changes
* Thanks to GSOC and Tejasvi Gupta, a number of functions in `ChemoSpec` and `ChemoSpec2D` gain the ability to produce `ggplot2` and/or `plotly` graphics, which required changes here in `ChemoSpecUtils`.  See the news files for `ChemoSpec` and `ChemoSpec2D` for more details.

# ChemoSpecUtils 0.4.96 2021-03-15
## Misc.
* Checked against `R` r80087.

## Documentation
* Documentation of `...` in `sumSpectra` corrected to show how to pass `tol` to `check4Gaps`.  Affects `ChemoSpec` only at this time.

## New Features
* A colorblind-friendly option, `Col7` added to the color options.

# ChemoSpecUtils 0.4.51 2020-04-20
## Bug Fixes
* Function `rowDist`, which supports a number of functions, was overhauled to address confusion in the documentation, and in my head, about distances vs. similarities.  Also, different definitions found in the literature were documented more clearly.  The Minkowski distance option was removed (ask if you want it back), code was cleaned up, documentation greatly improved, an example was added and unit tests were added.  Plot scales were also corrected as necessary.  Depending upon which distance option is chosen, this change affects `hcaSpectra`, `plotSpectraDist`, `sampleDist` and `hcaScores` in package `ChemoSpec` as well as `hats_alignSpectra2D` and `hcaScores` in package `ChemoSpec2D`.

## Misc.
* Function `.shrinkLeaf` now shrinks the size of leaf labels more aggressively as the number of samples increases.

# ChemoSpecUtils 0.4.38 2020-01-22
## New Features
* New color and symbol schemes are now provided to support new color assignment options in `ChemoSpec` and `ChemoSpec2D`.
* `removeFreq.Spectra` now accepts a formula for `rem.freq`.
* New functions `sampleDist`, `distPlot`, `sampleDist.Spectra` and `sampleDist.Spectra2D`; `sampleDist.Spectra` moved here from `ChemoSpec` or created anew, with changes to the plot details for consistency between the two classes.

# ChemoSpecUtils 0.3.60 2019-12-06
## Bug Fixes
* `.getLimits` now knows how to handle negative values in the formulas.
* `sumSpectra.Spectra` now respects/accepts the `...` argument, used to pass `tol`.  This was accidentally disabled.
## Misc.
* Some issues involving class(es) of matrices and class-checking in general, fixed to conform to new defaults in R 4.x series, coming soon, at the request of CRAN folks.
* Built and checked against R 4.x development version.

# ChemoSpecUtils 0.3.39 2019-06-24
## Improvements
* `chkSpectra` methods now check for duplicated sample names.
* `plotScores` now accepts user supplied values for `xlim` and/or `ylim`; the default calculation is still available.

## Misc.
* Unit test framework converted to `tinytest`.
* `rowDist(..., method = "cosine")` now has a unit test.
* Removed `dontrun` sections in examples, needed for last submission.

# ChemoSpecUtils 0.3.20 2019-06-09
## Improvements
* Internal changes to the handling of PCA results were made to accommodate the introduction of additional PCA options.  Some of these are listed below.
* New function `getVarExplained` handles this common task for all data reduction methods.
* Function `plotScree.mia` was eliminated via the introduction of `.getVarExplained` and small changes to `plotScree.default`.
* NAMESPACE cleaned up a bit.
* Miscellaneous polishing of functions and documentation.

## Misc.
* `conColScheme` was moved from `ChemoSpec` to `ChemoSpecUtils` so it could be readily available for `Spectra2D` objects.  It was also re-written in the style of `updateGroups` for consistency and user-friendliness.
* Documentation `colorSymbol` was moved from `ChemoSpec` to `ChemoSpecUtils`.

## Bug Fixes
* An issue with the setting of x and y limits in `plotScores` was fixed.  This was a long standing bug that somehow escaped notice (dating to the first few months of `ChemoSpec`!).
* `.getVarExplained` was returning the eigenvalues, not the percent variance explained, for `class(mia)`.  This affected scree plots for `class(mia)` in `ChemoSpec2D`.
* `plotScores` was no longer including the percent variance explained in score plots, if `xlab` and/or `ylab` were not provided.  Fixed.

# ChemoSpecUtils 0.2.211 2019-02-28
## Bug Fixes
* `chkSpectra.Spectra2D` would fail if there was only one sample when checking to see if NAs were present in the same positions across all data sets.  Fixed.
* Replaced code for cosine distance calculation in `rowDist`.  The previous version was giving slightly wrong answers.

# ChemoSpecUtils 0.2.204 2018-12-19
## Bug Fixes
* `updateGroups` now reports the old groups if `new.grps = NULL`, as intended and claimed in the documentation.

## Bug Fixes
* `plotScree` now knows what to do with class `princomp`.

# ChemoSpecUtils 0.2.197 2018-12-02
## Bug Fixes
* More changes to `.chkArgs` since errors were introduced via the most recent "fix"!  Updated unit tests for the function, but even more work should be done there.  Using `HandyStuff::examplePage` to look for errors and warnings.  None found.

# ChemoSpecUtils 0.2.170 2018-11-28
## Bug Fixes
* Fixed a problem in `.chkArgs(mode = 13)` that was giving an error in `ChemoSpec::r_pcaSpectra`.

# ChemoSpecUtils 0.2.163 2018-11-28
## Improvements
* Added function `updateGroups`.

# ChemoSpecUtils 0.2.160 2018-11-23
## Bug Fixes
* Fixed a problem with color assignment in `.groupNcolor` (the problem seems to have been present from the very first version of `ChemoSpec`).  Reported by Reinhard Kerschner (many thanks!).

## Improvements
* Made `check4Gaps` gap checking more robust, with better examples and documentation.  If no gap found, a data frame with one row is returned.  In turn, this required changes over in `.binData` and `binSpectra` which are in `ChemoSpec`.  In addition, while `check4Gaps` still accepts an argument `tol` no other functions are using it, and a much more suitable default value is computed in `check4Gaps` rather than being computed in another function and passed here.

# ChemoSpecUtils 0.2.142 2018-11-09
## Improvements
* Consistent argument checking introduced via `.chkArgs`.

# ChemoSpecUtils 0.2.23 2018-10-28
## Improvements
* Improved `sumSpectra` output format.
* `removeGroup` and `removeSample` go full S3 dispatch for consistency among the three packages.
* Unit tests moved from `ChemoSpec2D`.
* `hcaScores` moved from `ChemoSpec` and converted to S3 dispatch.

## New Features
* New function `chkArgs` and associated unit tests added, but it is not yet used in any of the other functions.

## Misc.
Seems to work correctly on behalf of `ChemoSpec` and `ChemoSpec2D` devel versions.

# ChemoSpecUtils 0.1.62 2018-10-12
## Misc.
* S3 generics created for `chkSpectra`, `removeFreq`, `sumSpectra`, `sumGroups`.
* Removed Additional_repositories field from DESCRIPTION (I was using it incorrectly).
* Removed Rd cross references to `ChemoSpec2D` for CRAN, temporarily.

# ChemoSpecUtils 0.1.52 2018-10-08
## Misc.
* Additional_repositories added to DESCRIPTION.
* Added dependency on `ChemoSpec` >= 5.0.

# ChemoSpecUtils 0.1.44 2018-10-08
## Misc.
* ORCID added to DESCRIPTION.

# ChemoSpecUtils 0.1.43 2018-10-08
## Misc.
* `.groupNcolor` added with argument mode.
* README.md added.

# ChemoSpecUtils 0.1.38 2018-10-06
## Misc.
* General polishing and documentation improvements.

# ChemoSpecUtils 0.1.12 2018-10-01
## Misc.
* Seems to be fully functional with the 5.0 series of ChemoSpec.

# ChemoSpecUtils 0.1.1 2018-09-27
## Misc.
* `addLegend` gets an example.

# ChemoSpecUtils 0.1.1 2018-09-27
## Misc.
* Package framework & first set of functions.
