matter 2.8.0

CHANGES IN VERSION 2.7.10 [2024-10-16]

NEW FEATURES

o Add 'fetch' and 'flash()' for base R types

SIGNIFICANT USER-VISIBLE CHANGES

o Update 'fetch()' and 'flash()' to pass more
    arguments to underlying 'matter' constructors

CHANGES IN VERSION 2.7.9 [2024-10-7]

NEW FEATURES

o Add 'pivots' argument to 'fastmap()' to support
    more than 2 pivot candidates per iteration

SIGNIFICANT USER-VISIBLE CHANGES

o Update 'fetch()' and 'flash()' to preserve atoms types
o Update 'fetch()' and 'flash()' to fall back to serial
    execution if BPPARAM is a distributed cluster

BUG FIXES

o Add 'chunkopts' to 'nscentroids()' and 'sgmix()'
    signatures to fix downstream '...' bugs
o Fix graphical parameters not applying to vizi plots

CHANGES IN VERSION 2.7.8 [2024-9-4]

BUG FIXES

o Fix shared memory segmentation faults on Linux
o Fix voxel plotting when length(unique(z)) == 1L

CHANGES IN VERSION 2.7.7 [2024-8-26]

NEW FEATURES

o New 'fetch()' and 'flash()' generics for moving
    data between file storage and shared memory

SIGNIFICANT USER-VISIBLE CHANGES

o Support both number of items OR size in bytes when
    setting getOption("matter.default.chunksize")
o Now using '@' prefix as shared memory identifier
    for file system compatibility (e.g., Windows)
o Deprecated 'sgmixn()'; updated 'sgmix()' to support
    multichannel images directly
o Improved RNG behavior for non-L'Ecuyer seeds

BUG FIXES

o Fix potential infinite loop in 'mi_learn()'
o Add warning in chunk-apply functions if 'RNG=TRUE'
    but 'RNGkind()' is _not_ "L'Ecuyer-CMRG"

CHANGES IN VERSION 2.7.6 [2024-8-14]

SIGNIFICANT USER-VISIBLE CHANGES

o Add 'cpals()' and 'dpals()' to list available palettes
o Moving 'simple_logger' now appends 'sessionInfo()'
o Statistical methods 'fastmap()' and 'nscentroids()'
    now use 'rowDists()' and 'colDists()' directly
o Optional argument 'distfun' has new requirements
    in methods 'fastmap()' and 'nscentroids()'
o Class 'matter_str' now inherits from 'matter_list'
    for consistency between R and C++ interfaces
o Export '.rowDists()' and '.colDists()' functions

BUG FIXES

o Fix 'simple_logger' finalizer on R session exit

CHANGES IN VERSION 2.7.5 [2024-8-5]

NEW FEATURES

o Shared memory support comes to 'matter' via boost!
o Add 'as.shared()' for coercion to shared memory 'matter' objects
o Use 'path=":memory:"' to construct 'matter' object in shared memory
o Use 'mem()' to monitor shared memory usage

SIGNIFICANT USER-VISIBLE CHANGES

o Add shared memory support to 'mem()' output
o Add cluster memory support to 'memtime()' output
o Add cluster memory monitoring with 'memcl()' function
o New documentation for several previously-undocumented
    utility functions that may be useful for others
o New 'permute' argument in chunk-apply functions

BUG FIXES

o Improved behavior for the general 'matter()' constructor
o Use private RNG for 'uuid()' to avoid collisions
    from 'set.seed()' and to avoid changing '.Random.seed'
o Fix 'is_gridded()' and 'to_raster()' behavior
    for non-integer coordinates and character rasters

CHANGES IN VERSION 2.7.4 [2024-8-2]

NEW FEATURES

o Add 'SnowfastParam' class to support PSOCK clusters
    for faster startups and faster serialization
o Add getOption("matter.default.chunksize") for setting
    the approximate size of chunks in bytes
o Add getOption("matter.default.serialize") for managing
    serialization behavior in chunk-apply functions
o New 'simple_logger' class for writing log files
o New 'options(matter.temp.dir=tempdir())' replaces
    the previous 'options(matter.dump.dir=tempdir())'
o New 'options(matter.temp.gc=TRUE)' controls whether
    temporary matter files are automatically removed when
    all R objects referencing them are garbage collected
o Temporary matter files are now garbage collected!
o Version bump for Bioconductor build system

CHANGES IN VERSION 0.99.0 [2016-9-26]

BUG FIXES

o Updated PCA example in vignette (irlba now requires 'mult'
    argument to be non-missing for non-C execution)
o Added irlba unit test

CHANGES IN VERSION 0.6 [2016-9-25]

SIGNIFICANT USER-VISIBLE CHANGES

o Updated maintainer and author email address

BUG FIXES

o Fixed bug in rowVar for matter_matc

CHANGES IN VERSION 0.5 [2016-9-25]

SIGNIFICANT USER-VISIBLE CHANGES

o Updated documentation with examples and added unit tests

BUG FIXES

o Fixed matrix multiplication on mixed data types (int x double)

CHANGES IN VERSION 0.4 [2016-8-3]

SIGNIFICANT USER-VISIBLE CHANGES

o Added support for class-preserving subsetting of 'matter'
     matrices with 'drop=NA' argument for Cardinal compatibility.
o Added new 'show' method for 'matter' vectors and matrices showing
    their size in in-memory and size on disk.

CHANGES IN VERSION 0.3 [2016-8-2]

NEW FEATURES

o Added C++ class 'MatterAccessor' for iterating through.
	a buffered version of a 'matter' vector or matrix
o Added summary statistics including 'sum', 'mean', 'var',
	'sd', 'colSums', 'colMeans', 'colVar', 'colSd',
	'rowSums', 'rowMeans', 'rowVar', and 'rowSd'.
o Added support for 'apply' method for 'matter' matrices
o Added support for 'bigglm' linear regression.
o Added basic matrix multiplication for 'matter' matrices
	with an in-memory R matrix or vector.

CHANGES IN VERSION 0.2 [2016-7-28]

SIGNIFICANT USER-VISIBLE CHANGES

o Overhauled backend to use C++ classes 'Matter' and 'Atoms',
    to maximizes use of sequential reads versus random reads.

CHANGES IN VERSION 0.1 [2016-2-17]

SIGNIFICANT USER-VISIBLE CHANGES

o First rough implementation of matter including the
    classes 'atoms' and 'matter', and subclasses 'matter_vec',
    'matter_matc', 'matter_matr', with a C backend.

matter 2.6.3

CHANGES IN VERSION 2.6.3 [2024-7-15]

BUG FIXES

o Fix 'filt2_gauss()' behavior with NAs

matter 2.6.2

CHANGES IN VERSION 2.6.2 [2024-6-10]

BUG FIXES

o Fix 'sgmixn()' on 'matter_mat' and 'sparse_mat' input

CHANGES IN VERSION 2.6.1 [2024-5-7]

BUG FIXES

o Fix 'matter_list' error on zero-length elements

CHANGES IN VERSION 2.5.22 [2024-4-26]

BUG FIXES

o Fix y-flipped raster images on non-macOS platforms

CHANGES IN VERSION 2.5.21 [2024-4-26]

NEW FEATURES

o Add new vizi mark 'image' for plotting pre-rastered images
o Add arguments 'rasterImages' and 'rasterParams' to 'plot_image()'

CHANGES IN VERSION 2.5.20 [2024-4-26]

SIGNIFICANT USER-VISIBLE CHANGES

o Update 'trans2d()' and 'warp2_trans()' to support arrays

CHANGES IN VERSION 2.5.19 [2024-4-25]

NEW FEATURES

o Add new vizi mark 'rules' for reference lines

CHANGES IN VERSION 2.5.18 [2024-4-24]

NEW FEATURES

o Add support for optional 'plotly' graphics output
o Add 'vizi_engine()' for setting the plotting engine
o Add support for 3D images to 'plot_image()'

SIGNIFICANT USER-VISIBLE CHANGES

o Export 'parse_formula()' for developer use

BUG FIXES

o Fix 'plotly' error from non-gridded voxels

CHANGES IN VERSION 2.5.17 [2024-4-19]

SIGNIFICANT USER-VISIBLE CHANGES

o Allow passing subplots to 'as_facets()' via '...'

BUG FIXES

o Fix 'rowsweep()'/'colsweep()' behavior with NA groups
o Fix 'cv_do()' and 'mi_learn()' behavior with NA labels

CHANGES IN VERSION 2.5.16 [2024-4-17]

SIGNIFICANT USER-VISIBLE CHANGES

o Add PLS 1-component regressions to 'opls' output
o Add 'fitted()' method for 'opls'
o Update 'predict()' method for 'opls'
o Add multiple instance learning support to 'cv_do()'

BUG FIXES

o Fix 'opls_nipals()' usage with 'mi_learn()'
o Fix error setting bags to negative class in 'mi_learn()'

CHANGES IN VERSION 2.5.15 [2024-4-17]

BUG FIXES

o Use names "MacroRecall"/"MacroPrecision" in 'cv_do()'

CHANGES IN VERSION 2.5.14 [2024-4-13]

NEW FEATURES

o Add function 'rocscore()' for calculating ROC AUC

BUG FIXES

o Fix bug in 'mergepeaks()' merging too aggressively
o Fix NAs in probability in 'nscentroids()'
o Fix formatting for 'size_bytes()' when vmem is 0
o Fix bug in 'cv_do()' not processing test set

CHANGES IN VERSION 2.5.13 [2024-4-8]

BUG FIXES

o Fix error in 'estnoise_filt()' when all peaks are noise

CHANGES IN VERSION 2.5.12 [2024-4-5]

SIGNIFICANT USER-VISIBLE CHANGES

o Add 'free' argument to 'plot_signal()' and 'plot_image()'
o Add 'style' argument to 'set_par()'
o Return 'fitted.values' from each fold in 'cv_do()'
o Add 'pos' argument to 'mi_learn()' to specify positive class
o Export 'chunkify()' and 'chunk_writer()' utilities
o Export 'size_bytes()' constructor

BUG FIXES

o Improve error messages for invalid plotting options
o Rescale 'alpha' channel for images when 'enhance=TRUE'
o Return 'probability' component for 'sgmixn()'
o Prevent mark 'boxplot' from plotting extra axes
o Fix 'mi_learn()' failing for missing values in response
o Fix 'plot_image()' failing for constant opacity if 'scale=TRUE'

CHANGES IN VERSION 2.5.11 [2024-4-2]

NEW FEATURES

o Add RNG utility functions 'RNGStreams()',
    'getRNGStream()', and 'setRNGStream()'
o Add 'seeds' argument for parallel-safe RNG
    for 'chunk_lapply()', etc.
o Add 'type' argument to 'drle' constructor
    to allow pure-RLE or sequential encoding
o Add function 'sgmixn()' for fitting multiple
    spatial Gaussian mixture models in parallel
o Add vizi marks 'intervals' and 'boxplot'
o Add 'predscore()' for scoring predictions
o Add 'cv_do()' for performing cross-validation

SIGNIFICANT USER-VISIBLE CHANGES

o Change 'fitted()' argument 'type' to use "response"
    (instead of "probability") for 'nscentroids'
o Print methods for models (e.g., 'pls', etc.) now
    truncate output to 'getOption("matter.show.head.n")'
o Add 'jitter' transformation for vizi mark 'points', etc.
o Export 'avg()' utility function

BUG FIXES

o Fix bug in 'nscentroids()' predictions
o Fix error in 'nscentroids()' for one-class models
o Fix error in 'sgmix()' caused by singleton classes
o Pass 'weights' argument to 'distfun()'
    in 'fastmap()' and 'nscentroids()'
o Fix error in 'plot_image()' for NA-only images

CHANGES IN VERSION 2.5.10 [2024-3-24]

NEW FEATURES

o Add function 'peakheights()'
o Add nearest shrunken centroids ('nscentroids()')
o Add spatial Gaussian mixture model ('sgmix()')
o Add colocalization coefficients ('coscore()')
o Add multiple instance learning ('mi_learn()')

SIGNIFICANT USER-VISIBLE CHANGES

o Rename 'estres()' parameter 'tol.ref' to 'ref'
o Export 'array_ind()' and 'linear_ind()'
o Add 'nchunks' argument to 'prcomp()' and 'pls()'
o Vectorize 'predict.pls()' over 'k' argument
o Set corresponding attributes to NULL when center/scale
    are FALSE in 'rowscale()' and 'colscale()'

BUG FIXES

o Fix 'tolerance()' returning invalid value for 'tolerance()<-'
o Fix error in 'peakareas()' when peak boundaries are NULL
o Remove duplicate peaks in 'findpeaks_cwt()'
o Fix potential infinite loop in 'binpeaks()'
o Fix potential incorrect vector lengths in 'simspec()'

CHANGES IN VERSION 2.5.9 [2024-3-13]

BUG FIXES

o When writing to a file in chunk apply functions, preserve
    order in file even if chunks are processed out-of-order

CHANGES IN VERSION 2.5.8 [2024-3-12]

NEW FEATURES

o Added scaling functions 'rescale_rms()', 'rescale_sum()',
    'rescale_ref()', 'rescale_range()', and 'rescale_iqr()'

CHANGES IN VERSION 2.5.7 [2024-3-11]

SIGNIFICANT USER-VISIBLE CHANGES

o Moved 'keys' and 'keys<-' generics to Cardinal
o Removed 'chunksize' and 'chunksize<-' generics

BUG FIXES

o Fix error with NAs in 'add_alpha()'
o Fix flipped x/y coordinates in 'inpoly()'

CHANGES IN VERSION 2.5.6 [2024-3-7]

BUG FIXES

o Fix error in apply functions when 'BPPARAM=NULL'
o Remove zero-height peaks in 'plot_signal()'

CHANGES IN VERSION 2.5.5 [2024-3-6]

NEW FEATURES

o Added 'plot_signal()' and 'plot_image()'
o Added new mark 'vizi_text'

SIGNIFICANT USER-VISIBLE CHANGES

o Add 'vizi' style 'classic' for transparent background
o Implement 'vm_used()' for 'sparse_arr' objects
o Implement 'combine()' for 'vizi_plot' objects
o Rename 'plot_facets()' to 'as_facets()'

BUG FIXES

o Fixed RStudio plotting bugs due to 'par(bg="transparent")'
o Fixed 'matter_list' subsetting not subsetting type
o Fixed 'vizi_pixels' issues with y-axis
o Fixed plotting functions not passing along parameters
o Handle mixed int/double types in 'ltob()' and 'lttb()'
o Implement 'vm_used()' for 'sparse_arr'

CHANGES IN VERSION 2.5.4 [2024-2-18]

BUG FIXES

o Improved 'mergepeaks()' efficiency

CHANGES IN VERSION 2.5.3 [2024-2-18]

BUG FIXES

o Fixed stack overflow in 'sparse_mat' subsetting
o Fixed 'mergepeaks()' failing for missing peaks

CHANGES IN VERSION 2.5.2 [2024-2-14]

SIGNIFICANT USER-VISIBLE CHANGES

o For 'estres()', allow 'tol=NA' or 'tol=Inf'

CHANGES IN VERSION 2.5.1 [2024-1-26]

BUG FIXES

o Fixed bug in 'simspec()' not respecting 'units'
o Enabled calling 'vizi()' with no arguments