ChemoSpec 5.2.12 2020-01-23
Misc.
- Fixed class-checking issues due to changes coming in R 4.0 coming soon.
- Improved documentation in various places.
- Added documentation for
updateGroups which has been in ChemoSpecUtils for a while but effectively hidden from users of ChemoSpec.
- Fixed the example in
plotSpectraDist which had strange limits.
- Fixed the example in
mclustSpectra which had an error and used data that was not a good illustration.
sampleDistSpectra was renamed sampleDist and moved to ChemoSpecUtils. The internal workings and plot details have changed.
Changes in ChemoSpecUtils that affect ChemoSpec
- New color and symbol schemes are now provided for using during the import process.
removeFreq now accepts a formula for rem.freq. The old syntax remains valid. See the documentation for ChemoSpec2D for examples of how to construct formulas.- New functions
sampleDist, sampleDist.Spectra and sampleDist.Spectra2D.
ChemoSpec 5.1.88 2019-11-14
Improvements
- Documentation for
hypTestScores now shows several ways to look at the results.
files2SpectraObject now will pass the argument SOFC to readJDX if JCAMP-DX files are being processed.
Bug Fixes
- In
hmapSpectra the return values (updated in version 5.1.48) were labeled incorrectly. Noticed by Gabriele Beltrame. The function now returns everything returned by seriation::hmap making it easier for the user to extract the information they desire. Documentation was improved, and additional examples were added illustrating how to pass arguments downstream to customize the plot.
- Fixed a bug in
plotScores3D and plotScoresRGL in which the wrong percent variance was plotted in the axes labels. Reported by Owen Horsfall.
ChemoSpec 5.1.48 2019-07-25
Improvements
plotScoresRGL gains an argument axes which allows one to control the drawing of the reference axes.hmapSpectra now returns the carpet matrix in addition to the sample and frequency rankings.
New Features
- A new vignette, Introduction to PCA, was added.
ChemoSpec 5.1.34 2019-06-23
Improvements
matrix2SpectraObject can now handle multiple input matrices (i.e. argument in.file can be a vector of file names). The function now includes a progress bar, similar to files2SpectraObject.
Bug Fixes
- Fixed a buglet in
hcaSpectra that involved an undesirable cast to data frame, which upset the cosine calculation.
evalClusters was not returning the result in the case of pkg = "NbClust".
Misc.
- Unit test framework shifted to
tinytest.
- Additional unit tests added.
ChemoSpec 5.1.9 2019-06-09
New Features
- Function
s_pcaSpectra which performs sparse PCA added.
- Function
irlba_pcaSpectra which performs IRLBA PCA added.
Improvements
- Numerous internal changes to the handling of PCA results were made to accommodate the introduction of sparse PCA features, and allow for easier future introduction of other PCA methods.
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 from the early days of this package. Note that plotScores is actually in ChemoSpecUtils but is called from ChemoSpec, affecting the results here.
Misc.
- Function
conColScheme moved to package ChemoSpecUtils.
- Documentation
colorSymbol was moved to package ChemoSpecUtils.
- Vignette updated regarding color issues.
ChemoSpec 5.0.229 2019-02-28
Misc.
- Unit tests added for
.cleanArgs.
ChemoSpec 5.0.215 2018-12-06
Improvements
files2SpectraObject can now accept any arguments to list.files or read.table via the … mechanism. Arguments are sanitized more robustly. However, it is possible to pass arguments that may not be of real utility. For instance na.strings can be specified, but any NA in the data imported will trigger warnings and errors.
Misc.
plotScree added to r_pcaSpectra example.
ChemoSpec 5.0.207 2018-11-28
Improvements
files2SpectraObject can now accept optional arguments path and recursive to allow reading through a directory substructure. In addition, a progress bar is now displayed unless debug = TRUE. Both features suggested by Reinhard Kerschner along with preliminary code (thanks!).
ChemoSpec 5.0.193 2018-11-20
Bug Fixes
- Fixed a problem with color assignment in
.groupNcolor (the problem seems to have been present from the very beginning). Reported by Reinhard Kerschner (many thanks!). Note .groupNcolor now resides in ChemoSpecUtils. Reported here for convenience.
Improvements
matrix2SpectraObject now uses tryCatch() to more gracefully fail and offer suggestions to user.files2SpectraObject
Notices