CHANGES IN VERSION 1.21.2
--------------------------
  o move examples from mzData to mzML after xcms dropped mzData support
    (thx to @sneumann)

CHANGES IN VERSION 1.5.1
--------------------------
  o fix error in plotting to graphic device with too small margins (#53)
    (thx to @sneumann)
    
CHANGES IN VERSION 1.4.0 = 1.5.0
--------------------------
  o Biocondcutor release 3.6

CHANGES IN VERSION 1.3.3
--------------------------
User visible:
  o new `plot`-parameter for `optimizeXcmsSet` and `optimizeRetGroup` to
    control plotting (#51)

CHANGES IN VERSION 1.3.2
--------------------------
  o bug fix #50: correct peaks-matrix, to handle xcms bug (sneumann/xcms#220) 
    for older xcms-versions
  o test order of parameters to optimize


CHANGES IN VERSION 1.3.1
--------------------------
  o bug fix regarding conflict of BPPARAM and nSlaves arguments (thx to @lauzikaite)


CHANGES IN VERSION 1.2.0 = 1.3.0
--------------------------
  o Biocondcutor release 3.5


CHANGES IN VERSION 1.1.2
--------------------------
  o vignette updated
  o plot margins omitted

CHANGES IN VERSION 1.1.1
--------------------------
  o use package BiocParallel (via argument `BPPARAM`) instead of `nSlaves` 
    to controll `xcms`-parallelization 
  o depends on xcms >= 1.50.0
  o formatting `writeRScript` to output more beautifully

CHANGES IN VERSION 1.1.0
--------------------------
  o merge Bioconductor 1.0.0 release code with Github code.


CHANGES IN VERSION 1.0.0
--------------------------
  o Biocondcutor release 3.4

==========================
BIOCONDUCTOR release
==========================

After version 1.7.5 IPO was put on Biocondcutor. After that  the 
versioning schema changes to meet the Bioconductor version numbering 
and starts with 1.0.0.


CHANGES IN VERSION 1.7.5
--------------------------
  o added usage of clustering method FORK on unix-systems (thanks to Pablo Moreno)
  o fixed bug in parallelization to prevent conflicts with package 'snow'


CHANGES IN VERSION 1.7.4
--------------------------
  o preceded parallel-functions with 'parallel::' to use right package
  o fixed bug in function writeRScript using 'loess' retention time cor.
  o decreased runtime for R CMD check IPO


CHANGES IN VERSION 1.7.3
--------------------------
  o added runnable examples
  o decreased size of pictures in vignettes/rsmDirectory
  o decreased runtime for unit-tests
  o replaces expand.grid with expand.grid.subset (in utils.R)


CHANGES IN VERSION 1.7.2
--------------------------
  o bugfix: try to prevent error in calcPPS possibly caused by NAs
  o replaced cat() and print() calls with message()

CHANGES IN VERSION 1.7.1
--------------------------
  o checking correlation of peak-shape with sinus curve (-pi/2 to pi*1.5), normal distribution or checkBorderIntensity
  o findIsotopes.IPO renamed parameter checkBorderIntensity to checkPeakShape
  o performance improvement calcPPS for checkPeakShape=FALSE
  o calculating xcmsSet-object and respective PPS for each DoE. (PPS is not estimated from rsm anymore)
  o additionally forwarding nSlaves for xcmsSet-function (also see getDefaultXcmsSetStartingParams())

CHANGES IN VERSION 1.7.0
--------------------------
  o added support for XCMS-method retcor.loess
  o updated help files
  o changed return value of getRGTVValues
  o adapted unit tests
  o parameter scanrange for XCMS-methods findPeaks can be set
    but not optimized

CHANGES IN VERSION 1.6.2
--------------------------
  o Updated the function getNormalizedResponse() to prevent NAs

CHANGES IN VERSION 1.6.1
--------------------------
  o Added installation script and installation description in vignette

CHANGES IN VERSION 1.6
--------------------------
  o Added support of CAMERA isotope identification (findIsotopes.CAMERA)
  o selectivity of findIsotopes.IPO may be increased if checkBorderIntensity 
    is set to TRUE: 'maxo' of each peak of an isotopologue must be three 
    times higher than the intensities at 'rtmin' and 'rtmax'
  o simplified return value of calcPPS() to vector with meaningful names
  o changed getDefaultXcmsSetStartingParams() for min_peakdwidth = c(12, 28) 
    and for ppm to c(17, 32)
	
CHANGES IN VERSION 1.5.7.1
--------------------------
  o using predict() to identify best levels and expand.grid to generate testdata for model

CHANGES IN VERSION 1.5.7
--------------------------
  o supporting single parameter optimization. Only basic version with
    redundant levels in consecutive DoEs
  o removed integer-rounding in maximum focusing for all findPeaks 
    parameters except prefilter(I) and steps
  o Update documentation to match code
  o Remove use of getwd() preventing absolute subdir paths
  
CHANGES IN VERSION 1.5.6
--------------------------
  o updated vignette
  o generally using Central-Composite design instead of Box-Behnken design
	o fixed bug when defining subdir=NULL in functions optimizeXcmsSet and optimizeRetGroup
	o modified unit tests to handle versions > 1.5.6
	o added function writeRScript to NAMESPACE export
  o updated man for optimizeXcmsSet and optimizeRetGroup

CHANGES IN VERSION 1.5.5
--------------------------
    o increased recall of reliable peaks in calcPPS. Changed exponent for PPS calculation from 1.5 to 2

CHANGES IN VERSION 1.5.4.8
--------------------------
    o remove file lookup in optimizeXcmsSet, and leave that to xcmsSet()

CHANGES IN VERSION 1.5.4.7
--------------------------
    o explicitely use serial evaluation if nSlaves=1, to help debugging

CHANGES IN VERSION 1.5.4.6
--------------------------
    o remove dependency on Rmpi

CHANGES IN VERSION 1.5.4.5
--------------------------
    o added examples from msdata
    o fix Depends, imports and library() and require() calls

CHANGES IN VERSION 1.5.4.4
--------------------------

USER VISIBLE CHANGES

  o packaged script
	o changed method name attachparams to attachList
	o changed method name calculateRGTV to getRGTVValues
	o changed method name getDefaultStartingXcmsParams to getDefaultXcmsSetStartingParams
	o changed method name typeCastFactor to typeCastParams
	o changed method name writeRSkript to writeRScript
	o changed the parameter name n_slaves to nSlaves
	o resultIncreased: if last optimization score was 0, no isotopes have been found hence
					   the dataset is not optimizable with IPO.
	o added man files for attachList, calcPPS, combineParams, createModel, decode, decodeAll, 
	encode, getBbdParameter, getCcdParameter, 
	getDefaultRetCorCenterSample, getDefaultRetGroupStartingParams, getDefaultXcmsSetStartingParams, 
	getNormalizedResponse, getRGTVValues, IPO-package, optimizeRetGroup, optimizeXcmsSet, 
	startSlaves, toMatrix, typeCastParams
	o removed xcmsSetsettingsAsString.R
	o getResponses: now able to handle NULL value for slices parameter
	o calcPPS: peaks with NA values are removed before isotopes identification
	o if subdir is NULL, no rsm's are saved
	o optimizeXcmsSet: lowere minimum value for min_peakwith from 5 to 3

#IPO_V1.5.4.3: * LIP calculation in calcPPS fixed 

#IPO_V1.5.4.2: * added initial parameter check
#              * renamed all factor-variables to params
#              * in optimizeXcmsSet: - also look for mzML-files
#                                    - check if files were found
#  		   * bug in optimization for matchedFilter fixed; sigma and mzdiff have to be 
#                    definded later (combineFactors()) when sigma and step as well as steps are already known

#IPO_V1.5.4.1: changes in calcPPS: 
#                   rt_window <- rt * 0.005
#                   rt_lower <- part_peaks[,"rt"] - rt_window
#	              	  rt_upper <- part_peaks[,"rt"] + rt_window

#IPO_V1.5.4: if bad_group == 0; bad_group = 1 && good_group += 1

#IPO_V1.5.3: no parameter for isotope detection. 
#            c13_peak[,"mz"] has to be within (mzmin + isotope_mass) and (mzmax + isotope_mass)
#            c13_peak[,"rt"] has to be within (rtmin + isotope_mass) and (rtmax + isotope_mass)

#IPO_V1.5.: in RCSandGSIncreased: also used good_groups ^ 2

#IPO_V1.4.: vectorized isotope identification; 
#           no intensity window, between intensity of max carbon and 1

#IPO_V1.3.: good_groups ^ 2 to increase recall 



