Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.
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.rowDist. The previous version was giving slightly wrong answers.updateGroups now reports the old groups if new.grps = NULL, as intended and claimed in the documentation.plotScree now knows what to do with class princomp..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..chkArgs(mode = 13) that was giving an error in ChemoSpec::r_pcaSpectra.updateGroups..groupNcolor (the problem seems to have been present from the very first version of ChemoSpec). Reported by Reinhard Kerschner (many thanks!).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..chkArgs.sumSpectra output format.removeGroup and removeSample go full S3 dispatch for consistency among the three packages.ChemoSpec2D.hcaScores moved from ChemoSpec and converted to S3 dispatch.chkArgs and associated unit tests added, but it is not yet used in any of the other functions.Seems to work correctly on behalf of ChemoSpec and ChemoSpec2D devel versions.
chkSpectra, removeFreq, sumSpectra, sumGroups.ChemoSpec2D for CRAN, temporarily.ChemoSpec >= 5.0..groupNcolor added with argument mode.addLegend gets an example.