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NEWS
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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 Bug fixes for 'plot()' on spectra with queued processing
CHANGES IN VERSION 3.7.1 [2024-5-18]
-----------------------------------
NEW FEATURES
o Update 'spectrapply()' to support 3 index arrays
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 3.6.3 [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