Remove alternateAnalyze.R functions?

[meowcat]

Are the functions in alternateAnalyze.R in active use? Those were originally implemented by ermueller 8 years ago and small touches were done by treutler later.

L167 references an occurrenceMatrix that doesn't point to anything I know.

analyzeMsMs.formula.optimized is used by analyzeMsMs.optimized is used by newStep2WorkFlow is used in validateMassBank.R -> .unitTestRMB2. This is not called from anywhere currently, and other than that I am not aware of any use of newStep2WorkFlow. Unless there is a maintainer who takes over alternateAnalyze and figures out what occurrenceMatrix is, I would advocate to remove the functionality (despite probably being more efficient than the original implementation).

@sneumann @tsufz @schymane ?

RMassBank/R/alternateAnalyze.R

Line 167 in 3db8775

newfragData <- fragData[-which(apply(occurrenceMatrix[,rAtoms,drop=FALSE], 1, any)),]

[tsufz]

In my patchy memory, I can remember that ermueller worked also on the unit tests. Hence, it is not surprising that the functions are used in .unitTestRMB2. I suggest to deprecate the functions.