NEWS

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IPO 1.21.2

• move examples from mzData to mzML after xcms dropped mzData support (thx to @sneumann)

IPO 1.7.5

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

IPO 1.7.4

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

IPO 1.7.3

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

IPO 1.7.2

• bugfix: try to prevent error in calcPPS possibly caused by NAs
• replaced cat() and print() calls with message()

IPO 1.7.1

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

IPO 1.7.0

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

IPO 1.6.2

• Updated the function getNormalizedResponse() to prevent NAs

IPO 1.6.1

• Added installation script and installation description in vignette

IPO 1.6

• Added support of CAMERA isotope identification (findIsotopes.CAMERA)
• 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'
• simplified return value of calcPPS() to vector with meaningful names
• changed getDefaultXcmsSetStartingParams() for min_peakdwidth = c(12, 28) and for ppm to c(17, 32)

IPO 1.5.7.1

• using predict() to identify best levels and expand.grid to generate testdata for model

IPO 1.5.7

• supporting single parameter optimization. Only basic version with redundant levels in consecutive DoEs
• removed integer-rounding in maximum focusing for all findPeaks parameters except prefilter(I) and steps
• Update documentation to match code
• Remove use of getwd() preventing absolute subdir paths

IPO 1.5.6

• updated vignette
• generally using Central-Composite design instead of Box-Behnken design
• fixed bug when defining subdir=NULL in functions optimizeXcmsSet and optimizeRetGroup
• modified unit tests to handle versions > 1.5.6
• added function writeRScript to NAMESPACE export
• updated man for optimizeXcmsSet and optimizeRetGroup

IPO 1.5.5

• increased recall of reliable peaks in calcPPS. Changed exponent for PPS calculation from 1.5 to 2

IPO 1.5.4.8

• remove file lookup in optimizeXcmsSet, and leave that to xcmsSet()

IPO 1.5.4.7

• explicitely use serial evaluation if nSlaves=1, to help debugging

IPO 1.5.4.6

• remove dependency on Rmpi

IPO 1.5.4.5

• added examples from msdata
• fix Depends, imports and library() and require() calls

IPO 1.5.4.4

USER VISIBLE CHANGES

• packaged script
• changed method name attachparams to attachList
• changed method name calculateRGTV to getRGTVValues
• changed method name getDefaultStartingXcmsParams to getDefaultXcmsSetStartingParams
• changed method name typeCastFactor to typeCastParams
• changed method name writeRSkript to writeRScript
• changed the parameter name n_slaves to nSlaves
• resultIncreased: if last optimization score was 0, no isotopes have been found hence the dataset is not optimizable with IPO.
• 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
• removed xcmsSetsettingsAsString.R
• getResponses: now able to handle NULL value for slices parameter
• calcPPS: peaks with NA values are removed before isotopes identification
• if subdir is NULL, no rsm's are saved
• 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

IPO 1.5.1

• fix error in plotting to graphic device with too small margins (#53) (thx to @sneumann)

IPO 1.4.0

• Biocondcutor release 3.6

IPO 1.3.3

User visible

• new 'plot'-parameter for 'optimizeXcmsSet' and 'optimizeRetGroup' to control plotting (#51)

IPO 1.3.2

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

IPO 1.3.1

• bug fix regarding conflict of BPPARAM and nSlaves arguments (thx to @lauzikaite)

IPO 1.2.0

• Biocondcutor release 3.5

IPO 1.1.2

• vignette updated
• plot margins omitted

IPO 1.1.1

• use package BiocParallel (via argument 'BPPARAM') instead of 'nSlaves' to controll 'xcms'-parallelization
• depends on xcms >= 1.50.0
• formatting 'writeRScript' to output more beautifully

IPO 1.1.0

• merge Bioconductor 1.0.0 release code with Github code.

IPO 1.0.0

• 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.