
CHANGES IN VERSION 2.0.4 [2019-2-21]
-----------------------------------

BUG FIXES

    o Fixed 'filter' signature due to change in dplyr

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.

