NEWS.md

In ChemoSpecUtils: Functions Supporting Packages ChemoSpec and ChemoSpec2D

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.

ChemoSpecUtils documentation built on May 29, 2024, 3:12 a.m.