Releases: kuwisdelu/Cardinal
Releases · kuwisdelu/Cardinal
Cardinal 3.8.3
Cardinal 3.8.2
CHANGES IN VERSION 3.8.2 [2024-12-11]
SIGNIFICANT USER-VISIBLE CHANGES
o Update 'peakAlign()' with 'binfun' parameter
o Previous (3.6) behavior corresponds to 'binfun="median"'
BUG FIXES
o Fix error in 'peakAlign()' for high resolution peaks
o Set minimum relative alignment resolution of 0.5 ppm
o Set minimum absolute alignment resolution of 0.0001 mz
o Fix 'peakProcess()' not processing centroided 'MSImagingArrays'
Cardinal 3.8.1
CHANGES IN VERSION 3.8.1 [2024-12-10]
BUG FIXES
o Fix error in 'simulateSpectra()' when 'mz' is unsorted
o Add 'resolution' and 'fmax' to 'simulateImage()'
Cardinal 3.8.0
CHANGES IN VERSION 3.7.8 [2024-10-26]
SIGNIFICANT USER-VISIBLE CHANGES
o Deprecate 'slice()' in factor of 'sliceImage()'
to avoid conflicts with users attaching dplyr
CHANGES IN VERSION 3.7.7 [2024-10-24]
SIGNIFICANT USER-VISIBLE CHANGES
o Update 'peakAlign()' with 'binratio' parameter
CHANGES IN VERSION 3.7.6 [2024-10-16]
NEW FEATURES
o Reading/writing imzML now preserves 'metadata' slot
o Reading/writing imzML now supports parallel processing
SIGNIFICANT USER-VISIBLE CHANGES
o Update 'estimateDomain()' to select resolution
based on 'median', 'min', 'max', or 'mean'
o Update 'peakAlign()' to build domain bins based on
the minimum of peak gaps (instead of the median)
o Write log file when writing imzML/Analyze files
BUG FIXES
o Fix bug in 'process()' resulting in output matrix
with 'list' elements under certain conditions
CHANGES IN VERSION 3.7.5 [2024-9-3]
NEW FEATURES
o Add 'setCardinalParallel()' for setting a parallelization
backend with reasonably-selected defaults
SIGNIFICANT USER-VISIBLE CHANGES
o Add 'SAR=FALSE' option to 'simulateImage()' for faster
simulation if spatial autoregressive model is not needed
o Change default array order for 'MSImagingArrays' so that
'intensity' is first array and 'mz' is second array
o Improved logging with pre-processing functions
BUG FIXES
o Fix leaky 'meansTest()' closures
CHANGES IN VERSION 3.7.4 [2024-8-28]
NEW FEATURES
o Add 'saveCardinalLog()' for saving log file
o Add 'getCardinalLogger()' + 'setCardinalLogger()'
o Add 'fetch()' and 'flash()' methods for moving
spectra between shared memory and temporary files
SIGNIFICANT USER-VISIBLE CHANGES
o Update compatibility with matter 2.7.6
o Changes to 'simulateSpectra()' and 'simulateImage()'
in parallelization and spectral noise generation
o RNG in 'simulateSpectra()' and 'simulateImage()'
now warn if 'RNGkind()' is not "L'Ecuyer-CMRG"
BUG FIXES
o Fix calculation of "adaptive" spatial weights
in 'spatialWeights()' for accuracy and stability
CHANGES IN VERSION 3.7.3 [2024-7-29]
SIGNIFICANT USER-VISIBLE CHANGES
o Add 'setCardinalChunksize()' + 'getCardinalChunksize()'
o Update vignettes due to spectral processing updates
BUG FIXES
o Fix plot() and image() not always respecting dimnames
o Fix plot() and image() not plotting multiple columns
o Fix plot() and image() failing for non-syntactic names
CHANGES IN VERSION 3.7.2 [2024-7-13]
BUG FIXES
o Merge bug fix from 3.6.4.
CHANGES IN VERSION 3.7.1 [2024-5-18]
NEW FEATURES
o Update 'spectrapply()' so index array is optional
o Update 'plot()' to support 2 domains (e.g., for ion mobility)
o Add plotting methods for 'XDataFrame' and 'PositionDataFrame'
BUG FIXES
o Fix default 'tolerance' in 'pixels()'
Cardinal v3.6.5
CHANGES IN VERSION 3.6.5 [2024-8-9]
BUG FIXES
o Fix 'spatialShrunkenCentroids()' failing when 'r=0'
or when a pixel has no neighboring pixels
Cardinal 3.6.4
CHANGES IN VERSION 3.6.4 [2024-7-13]
BUG FIXES
o Bug fixes for 'plot()' on spectra with queued processing
Cardinal 3.6.3
CHANGES IN VERSION 3.6.3 [2024-6-26]
BUG FIXES
o Bug fixes for 'meansTest()' when random effects are specified
Cardinal 3.6.2
CHANGES IN VERSION 3.6.2 [2024-6-10]
BUG FIXES
o Version bump for 'matter' 2.6.2 bugfixes
CHANGES IN VERSION 3.6.1 [2024-5-17]
SIGNIFICANT USER-VISIBLE CHANGES
o Add 'mass.range' and tolerance' arguments to 'bin()'
BUG FIXES
o Fix 'readImzML' error if imzML fails conversion to 'ImzMeta'
CHANGES IN VERSION 3.5.6 [2024-4-26]
SIGNIFICANT USER-VISIBLE CHANGES
o Add optional 'run' argument to 'slice()'
o Add optional 'plotly' support for all plotting methods
CHANGES IN VERSION 3.5.5 [2024-4-25]
BUG FIXES
o Fix bug in 'selectROI()' region plot updates
CHANGES IN VERSION 3.5.4 [2024-4-24]
NEW FEATURES
o Re-add support for 3D coordinates and 'image3D()'
SIGNIFICANT USER-VISIBLE CHANGES
o Export 'vizi_style()' and 'vizi_engine()' functions
o Add 'check' argument to 'readMSIData()' for uuid+checksum
BUG FIXES
o Fix bug in plotting PLS/OPLS coefficients
o Fix removing position columns with 'coord()<-'
CHANGES IN VERSION 3.5.3 [2024-4-13]
NEW FEATURES
o Add support for multiple instance learning for 'PLS()'
and 'spatialShrunkenCentroids()' with 'bags' argument
o Add 'estimateReferenceMz()' for more easily estimating
profile m/z-values from 'MSImagingArrays'
BUG FIXES
o Make sure 'bin()' still respects 'resolution' when 'ref' is
specified (in which case the range is taken from 'ref')
o Fix 'crossValidate()' for multiple instance learning
CHANGES IN VERSION 3.5.2 [2024-4-13]
BUG FIXES
o Fix passing 'tolerance' in 'peakProcess()' when not needed
o Fix bugs in 'selectROI()' not updating the plot
o Fix bugs in 'selectROI()' selecting wrong pixels
o Make sure 'peakAlign()' produces similar results when
re-aligning peaks with the same tolerance
CHANGES IN VERSION 3.5.1 [2024-4-7]
NEW FEATURES
o Ground-up rewrite to take advantage of matter v2.5 features
o New class 'SpectraArrays' for arrays of spectra
o New class 'SpectralImagingData' for spectral imaging data
o New class 'SpectralImagingArrays' for raw spectra
o New class 'SpectralImagingExperiment' for centroided spectra
o New class 'MSImagingArrays' for raw mass spectra
o Updated class 'MSImagingExperiment'
o Updated class 'XDataFrame'
o Updated classes 'PositionDataFrame' and 'MassDataFrame'
o New apply method 'spectrapply()'
o New processing method 'recalibrate()'
o New processing method 'bin()'
o New processing method 'peakProcess()'
o New classes 'SpatialResults' and 'ResultsList'
o Updated spatial methods 'findNeighbors()' and 'spatialWeights()'
o Updated spatial methods 'colocalized()'
o Updated projection methods 'PCA()' and 'spatialFastmap()'
o New projection method 'NMF()'
o Updated stats methods 'PLS()' and 'OPLS()'
o Updated stats method 'spatialKMeans()'
o Updated stats method 'spatialShrunkenCentroids()'
o Updated stats method 'spatialDGMM()'
o Improved visualization methods 'plot()' and 'image()'
SIGNIFICANT USER-VISIBLE CHANGES
o Deprecated 'smoothSignal()' -- use 'smooth()'
o Deprecated 'mzBin()' -- use 'bin()'
o Deprecated 'mzAlign()' -- use 'recalibrate()'
o Deprecated 'mzFilter()' -- use 'subsetFeatures()'
o Deprecated 'peakFilter()' -- use 'subsetFeatures()'
o Deprecated 'aggregate()' -- use 'summarizeFeatures()'
o Deprecated 'featureApply()' -- use 'summarizeFeatures()'
o Deprecated 'pixelApply()' -- use 'summarizePixels()'