CHANGES IN VERSION 3.8.3 [2024-12-18]
-----------------------------------
BUG FIXES
o Fix error in 'selectROI()' for whole-experiment images
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'
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()'
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()'
CHANGES IN VERSION 3.6.6 [2024-8-23]
-----------------------------------
BUG FIXES
o Fixes for 'simulateImage()' and 'simulateSpectra()'
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
CHANGES IN VERSION 3.6.4 [2024-7-13]
-----------------------------------
BUG FIXES
o Bug fixes for 'plot()' on spectra with queued processing
CHANGES IN VERSION 3.6.3 [2024-6-26]
-----------------------------------
BUG FIXES
o Bug fixes for 'meansTest()' when random effects are specified
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()'
CHANGES IN VERSION 3.4.3 [2023-11-22]
-----------------------------------
BUG FIXES
o Fixed default calculation of reference peaks in 'peakAlign()'
CHANGES IN VERSION 3.4.2 [2023-11-16]
-----------------------------------
BUG FIXES
o Fixed error in 'readImzML()' if spectrum representation is missing
o Fixed bug in 'writeImzML()' causing overlapping offsets
CHANGES IN VERSION 3.4.1 [2023-10-25]
-----------------------------------
BUG FIXES
o Fixed bug in 'writeImzML()' causing malformed cvParam tag
CHANGES IN VERSION 3.3.5 [2023-10-19]
-----------------------------------
BUG FIXES
o Allow 'guess.max=Inf' in 'readImzML()'
CHANGES IN VERSION 3.3.4 [2023-10-19]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Bin peaks when importing centroid spectra with 'readImzML()'
o Replaced all functions from deprecated 'sp' package
CHANGES IN VERSION 3.3.3 [2023-8-8]
-----------------------------------
BUG FIXES
o Fixed I/O bugs introduced by matter v2.3.13 changes
CHANGES IN VERSION 3.3.2 [2023-8-5]
-----------------------------------
BUG FIXES
o Fixed I/O bugs introduced by matter v2.3.11 changes
o Other I/O bugs fixed by matter v2.3.13 changes
CHANGES IN VERSION 3.3.1 [2023-5-2]
-----------------------------------
BUG FIXES
o Merged 3.2.1 fixes to resolve R CMD check warnings
CHANGES IN VERSION 3.2.1 [2023-5-2]
-----------------------------------
BUG FIXES
o Cleaned up escaped LaTeX specials in documentation
o Fixed 'sprintf()' => 'snprintf()' warning in C code
CHANGES IN VERSION 3.0.1 [2022-11-14]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Overwriting existing MSI files is now a warning instead of an error
BUG FIXES
o Fixed issue in 'peakAlign()' reference m/z's being sort and unique
CHANGES IN VERSION 2.99.1 [2022-10-31]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated vignettes for Cardinal 3
o Widened default m/z 'tolerance' for sparse spectra
o Switched to linear interpolation for sparse spectra
CHANGES IN VERSION 2.99.0 [2022-10-26]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated out-of-memory backend to Matter 2.0
o Removed support for legacy classes and methods
CHANGES IN VERSION 2.11.3 [2021-9-15]
-----------------------------------
BUG FIXES
o Fix strange behavior from random number generation in R >= 4.1.1
CHANGES IN VERSION 2.11.2 [2021-8-5]
-----------------------------------
BUG FIXES
o Fix reference naming scheme for binning and alignment methods
CHANGES IN VERSION 2.11.1 [2021-7-26]
-----------------------------------
BUG FIXES
o Use as(x, 'DFrame') instead of as(x, 'DataFrame')
o Fix logical length > 1 error in 'segmentationTest()'
CHANGES IN VERSION 2.7.2 [2020-10-21]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o For 'mzAlign()', the 'ref' parameter now expects a vector
of reference m/z-values rather than a complete spectrum
CHANGES IN VERSION 2.7.1 [2020-6-30]
-----------------------------------
BUG FIXES
o Fixed issue where 'spatialDGMM()' would sometimes
fail for features with singular segmentations
o Suppressed warnings on 'Mclust()' initialization
to 'spatialDGMM()' caused by R 4.0 changes
o Fixed pixel/feature mapping in 'spatialDGMM()' metadata
CHANGES IN VERSION 2.5.12 [2020-4-24]
-----------------------------------
BUG FIXES
o Drawing a region-of-interest using 'selectROI()' should
now update the plot properly in RStudio devices
o Fixed issues with automatically guessing a reasonable
mass tolerance for certain pre-processing methods
o In 'mzBin()', the previous value of 'centroided()'
from the original dataset is now preserved after binning
CHANGES IN VERSION 2.5.11 [2020-4-23]
-----------------------------------
BUG FIXES
o Fixed bug in 'spatialShrunkenCentroids()' that produced
in NaNs when discriminant scores were very large
o Fixed bug in 'spatialFastmap()' where subsetting produced
vectors instead of matrices due to omitting 'drop=FALSE'
CHANGES IN VERSION 2.5.10 [2020-4-22]
-----------------------------------
NEW FEATURES
o Added 'topFeatures()' method for 'spatialKMeans()'
o Added coercion to 'DataFrame' from 'MSImagingExperiment'
SIGNIFICANT USER-VISIBLE CHANGES
o Deprecated legacy classes (MSImageSet, etc.):
class definitions will remain for supporting
datasets from CardinalWorkflows, but methods
operating on them will be defunct in BioC 3.12
CHANGES IN VERSION 2.5.9 [2020-4-22]
-----------------------------------
NEW FEATURES
o Added 'aggregate()' method for imaging experiments
including 'summarizePixels()' and 'summarizeFeatures()'
o Added 'subset()' method for imaging experiments
including 'subsetPixels()' and 'subsetFeatures()'
SIGNIFICANT USER-VISIBLE CHANGES
o Deprecated 'dplyr' verbs in favor of the above functions;
this is to remove the (rather large) dependency on
the tidyverse for a relatively small functionality
BUG FIXES
o Fix bug in 'spatialDGMM()' printing caused by a change in
default.stringsAsFactors() == FALSE in R 4.0
CHANGES IN VERSION 2.5.8 [2020-4-18]
-----------------------------------
NEW FEATURES
o Automatic estimation of mass resolution will now work
for 'processed' imzML with centroid spectra
o New getter/setter options for Cardinal options such as
'getCardinalBPPARAM()' and 'setCardinalBPPARAM()'
SIGNIFICANT USER-VISIBLE CHANGES
o Default BPPARAM backend is now set to 'SerialParam()';
use 'setCardinalBPPARAM()' to change the backend
o Expose '.view' argument of 'matter::chunk_apply()' in
'pixelApply()', 'featureApply()', and 'spatialApply()'
o Previously-deprecated functions 'generateSpectrum()'
and 'generateImage()' are now defunct
o Removed defunct functions 'Binmat()' and 'topLabels()'
BUG FIXES
o Fix large intensity text cutoffs in 'image()' colorkey
CHANGES IN VERSION 2.5.7 [2020-3-30]
-----------------------------------
BUG FIXES
o Fix bug when using 'rbind()' or 'cbind()' on
'MassDataFrame' and 'PositionDataFrame'
CHANGES IN VERSION 2.5.6 [2020-3-24]
-----------------------------------
BUG FIXES
o Fix bug when assigning a dense matrix via iData()<-
for an 'MSProcessedImagingExperiment' object
CHANGES IN VERSION 2.5.5 [2020-3-14]
-----------------------------------
BUG FIXES
o Fix bug in 'show' method for 'SimpleImageList'
caused by class(matrix) -> c("matrix", "array")
CHANGES IN VERSION 2.5.4 [2020-3-13]
-----------------------------------
BUG FIXES
o Fix bugs in legacy classes caused by a change in
default.stringsAsFactors() == FALSE in R 4.0
CHANGES IN VERSION 2.5.3 [2020-3-13]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o The 'resolution' argument in all methods has been
redefined to always mean **full bin widt
for both "mz" and "ppm" units
CHANGES IN VERSION 2.5.2 [2020-3-2]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o The 'pixelApply()', 'featureApply()', and 'spatialApply()'
methods now internally use 'matter::chunk_apply()'
CHANGES IN VERSION 2.5.1 [2020-1-22]
-----------------------------------
BUG FIXES
o Fixed bug in 'mzBin()' binning spectra incorrectly
o Fixed bug in contrast enhancement with missing intensities
CHANGES IN VERSION 2.3.18 [2019-10-27]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Processing in 'crossValidate()' now allows processing
unprocessed data by performing peak-picking
on the mean spectra of the training sets
BUG FIXES
o Fixed some errors in user messages during peak processing
CHANGES IN VERSION 2.3.17 [2019-10-25]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Default for 'peakBin()' argument 'type' is now "area"
o In 'peakBin()', peak boundaries should be calculated
more accurately now, and general speed improvements
o In 'peakAlign()', peak centers are now calculated as
weighted average mass rather than the highest point
CHANGES IN VERSION 2.3.16 [2019-10-14]
-----------------------------------
NEW FEATURES
o New class 'ImagingSummary' with sub-classes including
'SparseImagingSummary' and 'MSImagingSummary' with
appropriate 'plot()' and 'image()' methods
SIGNIFICANT USER-VISIBLE CHANGES
o The 'summarize()' method for 'SparseImagingExperiment'
now returns a 'SparseImagingSummary', to more closely
reflect "tidy" data principles by returning an object
of a similar class; the previous behavior can be
reproduced by specifying '.as="DataFrame"'
CHANGES IN VERSION 2.3.15 [2019-10-13]
-----------------------------------
NEW FEATURES
o For methods requiring 'resolution' or 'tolerance',
the default arguments have been updated to
automatically guess based on the data
CHANGES IN VERSION 2.3.14 [2019-5-26]
-----------------------------------
NEW FEATURES
o Add spectraData() as an alias for 'imageData()'
for 'MSImagingExperiment' sub-classes
o Formalize 'mzData()' and 'intensityData()' getters
and setters for 'MSProcessedImagingExperiment'
o Add 'peaks()' and 'peakData()' methods for extracting
peak matrices and/or peak information
o Add 'isCentroided()' method for guessing whether spectra
are centroided (without using the @centroided slot)
SIGNIFICANT USER-VISIBLE CHANGES
o Allow 'NA' for @centroided slot for 'MSImagingExperiment'
o 'mzBin()' method now sets centroided = NA
o Update 'mzFilter()' with parameter defaults so that
'thresh.max = NA' and new arg 'rm.zero = TRUE'
o Log more pre-processing information (e.g., method name)
CHANGES IN VERSION 2.3.13 [2019-5-23]
-----------------------------------
BUG FIXES
o Try using 'parent.frame(1)' instead of 'parent.frame(2)'
to fix NSE methods when used in LHS of a maggritr pipe
o Fix weird 'iData()<-' missing argument 'i' bug
CHANGES IN VERSION 2.3.12 [2019-5-22]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Changed default 'peakPick()' method to 'mad'
o In 'peakPick()' method 'mad', change the default
number of blocks to 1 (no adaptive smoothing)
o In 'peakPick()' method 'mad', update w/ new arguments
w/ new defaults 'fun=median' and 'tform=diff'
BUG FIXES
o In 'peakPick()' methods 'simple' and 'adaptive', warn
if kurtosis cannot be estimated and try to recover
o In 'normalize()' method 'reference', provide a warning
if the reference value is 0 for a pixel
CHANGES IN VERSION 2.3.11 [2019-5-19]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Improved speed in 'spatialFastmap()'
o Improved speed in 'spatialShrunkenCentroids()'
o New dissimilarity metrics for 'spatialFastmap()'
including a new default metric='average'
BUG FIXES
o Fix error in 'print()' for facet plots where lims=NULL
CHANGES IN VERSION 2.3.10 [2019-5-18]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Improved speed in 'spatialDGMM()', by moving spatial
filtering of probabilities to C code, up to 10x faster
o Linesearch in 'spatialDGMM()' now uses 'optimize()'
rather than 'optim()' -- results may differ slightly
CHANGES IN VERSION 2.3.9 [2019-5-17]
-----------------------------------
NEW FEATURES
o Added 'Cardinal.history()' and 'Cardinal.version()'
SIGNIFICANT USER-VISIBLE CHANGES
o Removed under-used setter generic function definitions
BUG FIXES
o Cleaned up generics to reflect ProtGenerics >= 1.17.2
CHANGES IN VERSION 2.3.8 [2019-5-16]
-----------------------------------
NEW FEATURES
o Added boxplot, histogram, and bar chart functionality
to the 'plot()' method for 'XDataFrame'
o Added 'plot()' plotting for 'AnnotatedImageList'
o Added 'plot()' methods for 'SpatialDGMM',
'MeansTest', and 'SegmentationTest' result classes
o Added 'image()' method for 'MeansTest' result class
SIGNIFICANT USER-VISIBLE CHANGES
o Updated 'plot()' and 'image()' methods for 'SpatialDGMM',
'MeansTest', and 'SegmentationTest' result classes
BUG FIXES
o Various bug fixes in object printing and plot auto-layout
CHANGES IN VERSION 2.3.7 [2019-5-13]
-----------------------------------
NEW FEATURES
o Added 'image()' plotting for 'AnnotatedImageList'
BUG FIXES
o Plotting with 'add=TRUE' now respects 'par('usr')' coordinates
CHANGES IN VERSION 2.3.6 [2019-5-13]
-----------------------------------
NEW FEATURES
o Add 'AnnotatedImageList' class for list of 'AnnotatedImage' objects
o Add 'AnnotatedImagingExperiment' class for containing data for
an optical imaging experiment (e.g., a microscopy experiments)
o Add 'image()' plotting for 'AnnotatedImagingExperiment'
SIGNIFICANT USER-VISIBLE CHANGES
o Redefine '@featureData' slot of a 'SparseImagingExperiment'
to be a 'DataFrame' rather than requiring an 'XDataFrame'
BUG FIXES
o Respect 'layout' and 'byrow' passed through ... args
to 'print()' method on facet plot objects
CHANGES IN VERSION 2.3.5 [2019-5-11]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Moved some S4 method definitions from 'ImagingExperiment'
to 'SparseImagingExperiment' so that the former can be
more flexible for a wider variety of imaging modalities
BUG FIXES
o Pass more ... args through to 'par()' in plotting functions
CHANGES IN VERSION 2.3.4 [2019-5-10]
-----------------------------------
NEW FEATURES
o Added 'AnnotatedImage' class for optical images
CHANGES IN VERSION 2.3.3 [2019-5-10]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Improved facet plotting when 'add=TRUE'
BUG FIXES
o Better 'cex.axis' defaults and user setting for colorkeys
CHANGES IN VERSION 2.3.2 [2019-5-9]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Improved 'writeMSIData()' for 3D and non-gridded data
CHANGES IN VERSION 2.3.1 [2019-5-8]
-----------------------------------
NEW FEATURES
o Output directly to imzML while processing with 'process()'
SIGNIFICANT USER-VISIBLE CHANGES
o Improved auto-layout for visualization with multiple runs
o Added 'parse.only' option to 'readImzML()' for parsing only
CHANGES IN VERSION 2.2.4 [2019-5-8]
-----------------------------------
BUG FIXES
o Fix large external array offsets in 'writeImzML'
CHANGES IN VERSION 2.2.3 [2019-5-8]
-----------------------------------
BUG FIXES
o Cleaned up some 'writeImzML' mapping validity issues
CHANGES IN VERSION 2.2.2 [2019-5-7]
-----------------------------------
BUG FIXES
o Removed curly braces around UUID when writing imzML
CHANGES IN VERSION 2.2.1 [2019-5-6]
-----------------------------------
BUG FIXES
o Fixed bug in plotting results where 'column' argument
would get matched before the 'col' argument
CHANGES IN VERSION 2.1.30 [2019-4-30]
-----------------------------------
BUG FIXES
o Fixed bug where 'spatialShrunkenCentroids' classification
would change the user 'options(Cardinal.progress)'
CHANGES IN VERSION 2.1.29 [2019-4-29]
-----------------------------------
BUG FIXES
o Coercing to 'SpatialShrunkenCentroids2' now drops
empty classes for segmentations (as expected)
CHANGES IN VERSION 2.1.28 [2019-4-28]
-----------------------------------
BUG FIXES
o Fixed 'topFeatures' method for 'SpatialShrunkenCentroids2'
where 'statistic' was actually printing the 'centers'
o The 'collect' method for 'MSProcessedImagingExperiment'
now preserves sparseness when pulling into memory
CHANGES IN VERSION 2.1.27 [2019-4-26]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added 'mzFilter' as an alias for 'peakFilter' with more
suitable defaults for non-peak-picked spectra
BUG FIXES
o Minor fixes to 'print' method for plots and images
o Minor fixes to margin padding for 'colorkey' in images
CHANGES IN VERSION 2.1.26 [2019-4-25]
-----------------------------------
BUG FIXES
o Fixed 'print' method for plots and images to respect
updating plotting parameters via '...' arguments
CHANGES IN VERSION 2.1.25 [2019-4-25]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Add 'run' argument to 'pixels' for 'MSImagingExperiment'
o Add 'run' argument to 'plot' for 'MSImagingExperiment'
BUG FIXES
o Fixed bug in 'ylab' with one-sided formulas in 'plot'
o Relaxed errors for out-of-range m/z values in 'features'
o Value range of 'colorkey' now obeys 'zlim' argument
o NULL values for plot limits no longer give errors
CHANGES IN VERSION 2.1.24 [2019-4-24]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Documented new 'options(Cardinal.dark=FALSE)' default
BUG FIXES
o Fixed linear subsetting of models using '['' for
'SparseImagingResult' objects
o Check length of 'classControl' in 'segmentationTest'
CHANGES IN VERSION 2.1.23 [2019-4-24]
-----------------------------------
NEW FEATURES
o Added 'slice' for slicing imaging datasets (as a data cube)
o Added 'alpha.power' argument for 'image' methods
SIGNIFICANT USER-VISIBLE CHANGES
o Added documentation for options() under '?Cardinal'
CHANGES IN VERSION 2.1.22 [2019-4-24]
-----------------------------------
NEW FEATURES
o Added new 'Cardinal 2: Statistical methods' vignette
CHANGES IN VERSION 2.1.21 [2019-4-23]
-----------------------------------
NEW FEATURES
o Added 'image3D' methods for new classes
CHANGES IN VERSION 2.1.20 [2019-4-23]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated documentation and simulation examples
BUG FIXES
o Fixed bug in 'summary' for 'SpatialShrunkenCentroids2'
CHANGES IN VERSION 2.1.19 [2019-4-23]
-----------------------------------
NEW FEATURES
o Added 'colocalized' method for colocalization
CHANGES IN VERSION 2.1.19 [2019-4-23]
-----------------------------------
NEW FEATURES
o Added 'colocalized' method for colocalization
CHANGES IN VERSION 2.1.18 [2019-4-23]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated 'Cardinal 2: User guide' vignette
BUG FIXES
o Fixed bug in 'simulateSpectrum' when n > 1
CHANGES IN VERSION 2.1.17 [2019-4-22]
-----------------------------------
NEW FEATURES
o Added 'topFeatures' method for extracting top-ranked
features from statistical analyses
o Added 'summary' methods for new results objects
o Added 'SummaryDataFrame' for printing result summaries
SIGNIFICANT USER-VISIBLE CHANGES
o Deprecated 'topLabels' method -> use 'topFeatures'
CHANGES IN VERSION 2.1.16 [2019-4-20]
-----------------------------------
NEW FEATURES
o Added dplyr verbs for 'DataFrame' and "XDataFrame'
CHANGES IN VERSION 2.1.15 [2019-4-19]
-----------------------------------
NEW FEATURES
o Added new 'PCA' method for 'SparseImagingExperiment'
o Added new 'PLS' method for 'SparseImagingExperiment'
o Added new 'OPLS' method for 'SparseImagingExperiment'
SIGNIFICANT USER-VISIBLE CHANGES
o The 'selectROI' method will now use the last plot
if no additional plotting arguments are given
o Setting 'resolution' on 'MSProcessedImagingExperiment'
will now update the m/z values binning scheme
o The 'select' and 'filter' methods now using integers
as row/col IDs without the '.id' argument
BUG FIXES
o Fixed bug in 'OPLS' methods causing cross-validation
to produce slightly optimistic results
CHANGES IN VERSION 2.1.14 [2019-4-18]
-----------------------------------
NEW FEATURES
o New 'mzAlign' processing method for spectral alignment
o New 'mzBin' processing method for spectral binning
o New 'crossValidate' method that cleans up 'cvApply' output
o New normalization methods: 'rms' and 'reference'
o New baseline reduction method: 'locmin'
o New peak picking method: 'mad'
o New 'darkmode' and 'lightmode' plotting options
o Added 'cvApply' methods for new classes
SIGNIFICANT USER-VISIBLE CHANGES
o Image plotting now uses different 'colorkey' legend
placed beside plot that no longer obscures the image
o All plotting now uses different 'strip' labels
placed above plot that no longer obscures the plot area
o All plotting now accept hidden 'dark=TRUE' argument to
switch to plotting in new "dark mode"
o Changed/updated presets for 'presetImageDef' which
provides presets for 'simulateImage' function
CHANGES IN VERSION 2.1.13 [2019-4-15]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added message when printing a 'SparseImagingExperiment'
object without un-applied pre-processing steps
BUG FIXES
o Added C routine registration with "C_" prefix for .Call
o Cleaned up '.o' objects in /src created by accident
CHANGES IN VERSION 2.1.12 [2019-4-14]
-----------------------------------
NEW FEATURES
o Added 'meansTest' method for linear model-based
hypothesis tests of mean-summarized images
o Added 'segmentationTest' method for linear model-based
hypothesis tests of spatially-segmented images
CHANGES IN VERSION 2.1.11 [2019-4-12]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added option to set the probability regularization
parameter (p0) to 'spatialDGMM' method
o Added option to initialize 'spatialDGMM' algorithm
with either k-means or Gaussian mixture model
CHANGES IN VERSION 2.1.10 [2019-4-12]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Changed default colorscale for images to 'viridis'
o Updated 'simulateImage' presets to handle multiple runs
CHANGES IN VERSION 2.1.9 [2019-4-11]
-----------------------------------
NEW FEATURES
o Added 'spatialDGMM' method for fitting feature-wise
spatially-aware Dirichlet Gaussian mixture models
o Added 'predict' method for 'SpatialShrunkenCentroids2'
BUG FIXES
o Fixed 'spatialShrunkenCentroids' classification methods
for new ('SparseImagingExperiment'-based) classes
o Cleaned up unit tests for statistical methods
CHANGES IN VERSION 2.1.8 [2019-4-1]
-----------------------------------
BUG FIXES
o Updated 'PositionDataFrame' initialization
due to change in S4Vectors [<-,DataFrame behavior
o Updated 'MassDataFrame' initialization due to change
in S4Vectors [<-,DataFrame behavior
CHANGES IN VERSION 2.1.7 [2019-2-21]
-----------------------------------
BUG FIXES
o Updated 'filter' signature due to dplyr changes
CHANGES IN VERSION 2.1.6 [2019-1-4]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added ImmunoOncology biocViews term
CHANGES IN VERSION 2.1.5 [2018-12-14]
-----------------------------------
BUG FIXES
o Updated read/write methods for 'matter' filemode changes
CHANGES IN VERSION 2.1.4 [2018-12-12]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o In 'readImzML' and 'readAnalyze', changed defaults
from 'attach.only=FALSE' to 'attach.only=TRUE'
o In 'readImzML' and 'readAnalyze', changed defaults
from 'as=MSImageSet' to 'as=MSImagingExperiment'
BUG FIXES
o Subsetting large 'SparseImagingExperiment' objects
with 'sparse_mat' imageData should no longer hang
CHANGES IN VERSION 2.1.3 [2018-12-12]
-----------------------------------
NEW FEATURES
o Added 'ImagingResult' class for results
of statistical analyses of imaging experiments
o Added 'spatialFastmap' method for 'SparseImagingExperiment'
o Updated 'summarize' to accept a '.group_by' argument
o Added 'simulateSpectrum' and 'simulateImage' functions
SIGNIFICANT USER-VISIBLE CHANGES
o Automatically detect and setup 'layout' for new classes
o Using 'layout' now assumes (row, column) order
when creating facet plots for new classes (only)
o Updated examples in documentation to use new classes
BUG FIXES
o Fixed bug in 'spatialKMeans' that caused 'spatialFastmap'
to fail for datasets with fewer features than components
o Fixed bug where 'plot' did not facet over runs
of a 'SparseImagingExperiment' when using 'plusminus'
CHANGES IN VERSION 2.1.2 [2018-11-30]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated 'spatialKMeans' to use new 'spatialFastmap'
o Updated 'spatialShrunkenCentroids' to use new
spatially-aware discriminant scores calculation
CHANGES IN VERSION 2.1.1 [2018-11-30]
-----------------------------------
NEW FEATURES
o Added 'spatialFastmap' method for performing
spatially-aware FastMap projection more easily
CHANGES IN VERSION 2.0.2 [2018-11-30]
-----------------------------------
BUG FIXES
o Fixed bug in 'reduceDimension.peaks' that caused
peak intensities to be binned incorrectly
CHANGES IN VERSION 2.0.1 [2018-11-14]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated 'peakFilter' to check for freq.min >= 1 to
accomodate old behavior (counts)
CHANGES IN VERSION 1.99.2 [2018-10-28]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated vignettes for Cardinal 2.0
BUG FIXES
o Removed a unit test broken on Windows
CHANGES IN VERSION 1.99.1 [2018-10-26]
-----------------------------------
NEW FEATURES
o Added vignettes and documentation for Cardinal 2.0
CHANGES IN VERSION 1.99.0 [2018-10-25]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Version bump for Cardinal v2 release candidate
CHANGES IN VERSION 1.13.3 [2018-10-24]
-----------------------------------
NEW FEATURES
o Added 'process' method for queueing delayed processing
functions to an imaging dataset and applying them
o Added new processing methods for Cardinal v2 including
new versions of 'normalize', 'smoothSignal', 'reduceBaseline',
'peakPick', 'peakAlign', and 'peakFilter'
o Added new 'peakBin' function for binning peaks
o Updated 'show' method for new Cardinal v2 classes
o New support for exporting 'processed' imzML files
via the 'writeImzML' function
CHANGES IN VERSION 1.13.2 [2018-7-22]
-----------------------------------
NEW FEATURES
o Added new classes for Cardinal v2 including 'XDataFrame',
'PositionDataFrame', 'MassDataFrame', 'ImagingExperiment', 'SparseImagingExperiment', and 'MSImagingExperiment'
CHANGES IN VERSION 1.13.1 [2018-7-22]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated installation instructions for "CardinalWorkflows"
CHANGES IN VERSION 1.12.1 [2018-7-22]
-----------------------------------
BUG FIXES
o Fixed bug in reading Analyze 7.5 files
CHANGES IN VERSION 1.11.2 [2017-12-2]
-----------------------------------
NEW FEATURES
o Added 'writeMSIData', 'writeImzML', and 'writeAnalyze'
methods for writing MSI data to supported file formats
o Added support for on-disk 'processed' imzML (via argument
'attach.only' in 'readImzML' method)
SIGNIFICANT USER-VISIBLE CHANGES
o Package 'matter' is used for all file I/O now
o Switched from using 'Hashmat' to using 'sparse_mat'
class from 'matter' for 'processed' imzML data
BUG FIXES
o Changed compiler settings for parsing XML so reading
large imzML files should use much less memory now
(but may take slightly longer for smaller files)
CHANGES IN VERSION 1.11.1 [2017-10-25]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Use 'drop=NULL' from now on instead of 'drop=NA' to do
endomorphic subsetting of 'SimageData' objects
BUG FIXES
o Use 'keys' and 'keys<-' generic from 'matter'
CHANGES IN VERSION 1.9.2 [2017-10-25]
-----------------------------------
BUG FIXES
o Corrected author name in all documentation
CHANGES IN VERSION 1.9.1 [2017-10-23]
-----------------------------------
BUG FIXES
o Fixed bug in package dependency 'matter' affecting the size
of datasets that can be processed with 'batchProcess'
o Fixed bug where bin sizes for units='ppm' were twice as wide
as they should be in 'readImzML' and 'reduceDimension'
CHANGES IN VERSION 1.7.2 [2017-3-22]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o In 'image' method, 'superpose = TRUE' now supports multiple LHS
arguments in the formula (e.g., formula = a + b ~ x * y)
CHANGES IN VERSION 1.7.1 [2016-11-29]
-----------------------------------
NEW FEATURES
o PCA is now supported for larger-than-memory on-disk datasets
o External 'matter' matrices replace 'Binmat' matrices for on-disk support
o Added 'image3D' aliases for all 'ResultSet' subclasses
SIGNIFICANT USER-VISIBLE CHANGES
o Added 'matter' package to Depends list
CHANGES IN VERSION 1.5.2 [2016-10-6]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated 'batchProcess' to support reduceDimension and peakAlign
o Now 'peakAlign' looks for an existing 'mean' column in featureData
o Added 'matter' support to readAnalyze (previously only readImzML)
BUG FIXES
o Fixed bug when indexing into data cube using 'imageData' method
CHANGES IN VERSION 1.5.1 [2016-9-21]
-----------------------------------
BUG FIXES
o Corrected author and maintainer contact information
CHANGES IN VERSION 1.5.0 [2016-5-25]
-----------------------------------
NEW FEATURES
o Added experimental support for 'matter' on-disk matrices, from
package 'matter', hosted at https://github.com/kuwisdelu/matter,
as a replacement for 'Binmat' matrices
BUG FIXES
o Fixed subsetting SImageData objects with variables
CHANGES IN VERSION 1.3.3 [2016-4-20]
-----------------------------------
BUG FIXES
o Subsetting the S4 part of Binmat objects by row is now an error
o Providing non-positive m/z values to 'readImzML' is now an error
o Elements of 'imageData' that fail to 'combine' or which
are missing from one or more of the objects are now
dropped from the result with warning rather than failing
o Moved unit tests in 'ints/tests' to 'tests/testthat'
CHANGES IN VERSION 1.3.2 [2016-3-29]
-----------------------------------
NEW FEATURES
o Added 'image3D' method for plotting 3D images
o Added 'batchProcess' method for batch pre-processing
CHANGES IN VERSION 1.3.1 [2016-3-14]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added 'mass.accuracy' and 'units.accuracy' arguments for
controlling the m/z accuracy when reading 'processed' imzML
o Function 'reduceDimension.bin' now takes argument 'units' with
value 'ppm' or 'mz', and new corresponding defaults
BUG FIXES
o Fixed bug in reading 'processed' imzML format that caused
mass spectra to be reconstructed in the wrong order
o Improved speed accessing columns of Hashmat sparse matrices
o In 'pixelApply' and 'featureApply', zero-length return values
are no longer returned as a list when '.simplify=FALSE'
o Function 'peakAlign.diff' should be more memory efficient now
CHANGES IN VERSION 1.3.0 [2015-12-16]
-----------------------------------
NEW FEATURES
o Added experimental Binmat class for working with on-disk matrices
o Added experimental support for 3D files from benchmark datasets
o Added experimental support for plotting 3D images
o Added experimental support for 'processed' imzML format
SIGNIFICANT USER-VISIBLE CHANGES
o Added 'attach.only' argument to readImzML and readAnalyze
BUG FIXES
o Fixed bug in plotting 3D image slices in the z dimension
o Fixed bug where large imzML files could not be read due to byte
offsets being stored as ints; they are now stored as doubles.
o Fixed bug with strip labels in 3D plotting and with mixed labels
o Fixed bug with unique m/z feature names for high mass resolutions
CHANGES IN VERSION 1.1.0 [2015-10-1]
-----------------------------------
BUG FIXES
o Fixed bug in formatting m/z labels affecting R 3.2.2
o Removed dependency on 'fields' because 'maps' is broken on Windows
CHANGES IN VERSION 0.99.6 [2015-4-5]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Bioconductor Release Candidate 7
o Added CITATION file for citing Cardinal
BUG FIXES
o In 'readAnalyze' and 'readMSIData', removed endianness check
in Analyze 7.5 headers because some ABSciex data files
specify an incorrect header size, thereby fixing a bug where
bits would be swapped wrongly and file read incorrectly.
CHANGES IN VERSION 0.99.5 [2015-3-3]
------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Bioconductor Release Candidate 6
o Added new vignette for Cardinal design and development
o Now using ProtGenerics generics for 'spectra', 'peaks', and 'mz'
CHANGES IN VERSION 0.99.4 [2015-2-15]
-------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Bioconductor Release Candidate 5
o Updated vignette with biological examples
o Added new citations to vignette
CHANGES IN Version 0.99.3 [2015-2-3]
------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Bioconductor Release Candidate 4
o In plot and image methods, 'groups' arg now coerced to factor
BUG FIXES
o Fixed bug in subset arg in select method
o Fixed bug in plot and image methods with NA in 'groups' arg
CHANGES IN Version 0.99.2 [2015-1-20]
-------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Bioconductor Release Candidate 3
o Adjusts NIPALS unit tests for Windows build
CHANGES IN Version 0.99.1 [2015-1-12]
-------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Bioconductor Release Candidate 2
o Cleaned up biocViews
BUG FIXES
o Fixed bug in SImageData coord factor levels not being
properly updated when SImageSet is subsetted
CHANGES IN Version 0.99.0 [2014-12-22]
--------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Bioconductor Release Candidate 1
CHANGES IN Version 0.9.0 [2014-12-22]
-------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added standardizeSamples method for between-sample normalization
CHANGES IN Version 0.8.9 [2014-12-5]
------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Improved plot methods for object summaries
o Fixed minor issurs in walkthrough vignette
CHANGES IN Version 0.8.8 [2014-11-27]
-------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Changed modelData for ResultSet from facors to original parameters
o Added plot method for summaries of ResultSet objects
o Added 'normalize.image' argument for image method
o Improved plot and image methods for CrossValidated
CHANGES IN VERSION 0.8.7 [2014-11-23]
-------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Completed Cardinal-walkthrough vignette
BUG FIXES
o Fixed bug in plotting vectors from ResultSet
o Fixed bug in PCA summary in reporting explained variance
CHANGES IN Version 0.8.6 [2014-11-21]
SIGNIFICANT USER-VISIBLE CHANGES
o Completed walkthrough vignettes
o Added ImagingMassSpectrometry biocView
CHANGES IN Version 0.8.5 [2014-11-20]
-------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added 'show' and 'print' methods for most objects
o Changed 'combine' method for IAnnotatedDataFame, SImageData, and SImageSet
o Completed .Rd documentation for all public methods
o Cleaned up R CMD check warnings (except C++ .hpp headers)
BUG FIXES
o Fixed bug in between-cluster SS calculation for spatialKMeans
o Fixed bug with pre-processing 1-pixel datasets
CHANGES IN Version 0.8.4 [2014-10-16]
-------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Changed 'topIons' to 'topLabels' method for summarization
o Added MSImageData class for peakData and mzData methods
o Changed naming scheme for SImageData (.iData => iData)
BUG FIXES
o Fixed bug in plotting of classes for SpatialShrunkenCentroids
o Fixed bug in fopen in readAnalyze and readImzML affecting Windows
CHANGES IN Version 0.8.3 [2014-9-18]
------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added 'coregistration' for SpatialKMeans
o Added 'summary' methods for all ResultSet subclasses
o Added 'topIons' method for summarization
o Added plotting methods for 'ResultSet' classes
o Added 'cvApply' method for cross-validation
o Added additional statistics to SpatialKmeans class results
o Changed 'auto.key' argument to 'key' in plotting methods
BUG FIXES
o Fixed bug in spatialShrunkenCentroids with prior probabilties
o Fixed bug in OPLS with proper scaling of data matrices during prediction
CHANGES IN Version 0.8.2 [2014-7-23]
------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added 'peakFilter' method
o Minor fixes to documentation
CHANGES IN Version 0.8.1 [2014-7-10]
------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Changed 'parameters' argument to 'model' for ResultSet plot and image
o Added 'auto.key' to plot and image for when 'groups' are specified
o Added strip labels to plot and image when using base graphics
o Added 'coregister' method for 'SpatialShrunkenCentroids'
o Method 'image' is now vectorized for argument 'mz'
o Method 'plot' is now vectorized for argument 'coord'
BUG FIXES
o Fixed a bug where conditions are plotted in an incorrect order
CHANGES IN Version 0.8.0 [2014-6-16]
------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o First public beta available for ASMS 2014.
CHANGES IN Version 0.7 [2014-6-2]
---------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Refactored version of the package prepared for internal testing.
o New processing methods, renamed to 'normalize', 'smoothSignal',
'reduceBaseline', 'peakPick', 'peakAlign', 'reduceDimension'.
o New function 'readMSIData' for reading supported formats.
o Native support for imzML added (no longer requires Java).
o Methods 'pixels' and 'features' replaced with updated versions.
o In 'features' method, m/z matching now done using bisection search.
o New analysis method, renamed to spatialShrunkenCentroids.
o Analysis methods now return a new class: 'ResultSet'.
o New method 'select' to replace 'selectROI' and 'selectPixels'.
CHANGES IN Version 0.6 [2013-2-19]
----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Major revision to use Bioconductor base packages.
o New dependencies on BiocGenerics and Biobase.
o New virtual class iSet for generic imaging data.
o New classes ImageSet, SImageSet, ImageData, and SImageData.
o Revised MSImageSet that uses new parent classes.
o New class MIAPE-Imaging for Minimum Information About
a Protemics Experiment - Imaging.
o New class MSImageProcess for pre-processing information.
o Revised functions for importing Analyze 7.5 and imzML
o New plotting and image methods using lattice-style formula interface.
o New pixelApply and featureApply methods.
CHANGES IN Version 0.5 [2013-11-8]
----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added image coregistration for 3D sections.
o Added 'volume' method for 3D visualization.
CHANGES IN Version 0.4 [2013-11-7]
----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added 'summaryPlot' method for segmentation visualization.
o Exposed 'calibrateSegmentation' method to calibrate colors
between multiple MSImageSegmentation objects.
o Added more thorough verbose output for 'spatialSparseCluster'
and 'spatialSparseKMeans' methods.
o Improved behavior of 'intensities' method when reconstructing
complex datacubes and with non-contiguous pixel requests.
o Changed 'trellisImage' to plot all coordinates for dimensions
omitted from 'fixCoord' by default.
o Minor changes to the 'MSImageSegmentation' class structure.
o Improved 'likPlot' method and added AIC and BIC results and
the resulting number of classes.
CHANGES IN Version 0.3 [2013-7-5]
---------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Improved speed of imaging processing (smoothing and interpolation)
methods for use with 'image' and 'trellisImage'.
o Added option for verbose output and hooks for GUI progress bars.
o For prediction on 'MSImageSegmentation' objects, 'autoDimNames'
is now automatically passed along from the original call.
o Changed 'MSImageSegmentation' to an S4 class derived from 'list'.
o Added option for plotting the probabilities of an 'MSImageSegmentation'
using overlaid transparency masks for improved visualization.
CHANGES IN Version 0.2 [2013-6-20]
----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Package renamed from internal code-name "Canary" to "Cardinal".
o Split off GUI to a new package called "CardinaliView".
o New GUI in "CardinaliView" now based on gWidgets and RGtk2.
o Added slot 'peaks' to 'MSImageSet' class.
o Changed 'MSPeakFrame' and 'MSPeakList' to S4 classes, and added
new class 'MSPeak Alignment'.
o Changed how the 'estimateNoise' method estimates noise.
o Changed options in the 'detectPeaks' method to be more useful.
o Changed the 'alignPeaks' methods to align to the mean spectrum
as a reference when aligning a list of peaks.
o Added 'interpolate' option for images.
o Added new method "selectPeaks" for manual peak selection.
o Modified the 'type' arguments in the plotting methods.
o Changed 'crossValidate' method to now return predictions for the
full dataset for every fold instead of the test set only.
BUG FIXES
o Fixed bug where plotting mass spectra for multiple pixels fails
on datasets with missing mass spectra.
o Fixed bug where the 'unload' method did not remove the object.
o Fixed bug in the 'crossValidate' method where the dots arguments
were not passed to the 'predict' method.
CHANGES IN Version 0.1 [2013-6-6]
---------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o First internal release for Stanford Canary Center for Cancer
Early Detection as primary beta testers.
o Implementation of MSImageSet S4 class; mass spectra are stored as a
flat matrix with rows as features and columns as pixels; original
data cube can be reconstructed dynamically using a position array;
spectra stored using environments to prevent redundant data copying.
o Visualization that includes plotting ion images and mass spectra,
using both base graphics and lattice graphics, allowing trellis
display of multiple ion images and multipe mass spectra.
o Pre-processing for that includes normalization, baseline correct,
peak-picking, peak-alignment, resampling, and binning.
o Multivaritate statistical analysis includes PCA, PLS, and OPLS.
o Supervised analysis includes a spatially-aware version of nearest
shrunken centroids, PLS-DA, and OPLS-DA.
o Unsupervised analysis includes spatially-aware clustering based on
nearest shrunken centroids, and an implementation based on sparse
k-means.
o GUI based on tcltk using rpanel that supports all major
processing and statistical analysis methods in the package,
except for PLS and OPLS.