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