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NEWS
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CHANGES IN VERSION 2.9.1 [2024-11-4]
------------------------------------
BUG FIXES
o Change C-level 'Free()' calls to 'R_Free()'
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!
SIGNIFICANT USER-VISIBLE CHANGES
o New 'chunkopts' argument replaces 'nchunks' and includes
the new chunk options ("chunksize" and "serialize")
BUG FIXES
o Fix leaky closures in internal chunk loop functions
causing slow parallel performance on large datasets
o Fix internal bug in 'eval_exprs()' where 'recursive'
attribute was always set to 'TRUE'
CHANGES IN VERSION 2.7.3 [2024-7-26]
------------------------------------
NEW FEATURES
o Add new functions 'knnmax()' and 'knnmin()'
o Add new functions 'filtn_ma()', 'filtn_conv()', etc.
o Add support for N-dimensional signals to 'estnoise_*()' functions
o Add 'findpeaks_knn()' for KNN-based peak detection
SIGNIFICANT USER-VISIBLE CHANGES
o Add signal processing vignette
o Faster 'knnsearch()' when the data and query are the same
o Ties in 'knnsearch()' are now broken based on data order
o Updated 'estnoise_sd()', 'estnoise_mad()', and 'estnoise_quant()'
BUG FIXES
o Improvements to 'filt1_adapt()' and 'filt2_adapt()'
CHANGES IN VERSION 2.7.2 [2024-5-23]
------------------------------------
NEW FEATURES
o Support 2D signals in 'plot_signal()' (e.g., for ion mobility)
o New argument 'alphapow' in 'plot_signal()' and 'plot_image()'
SIGNIFICANT USER-VISIBLE CHANGES
o Plot method for 'vizi_bars' now sums duplicate bar counts
BUG FIXES
o Fix chunk-apply functions for BPPARAM=NULL
o Fix 'chunkMapply()' named list errors
o Fix 'is_gridded()' so infinite 'estres()' result gives FALSE
o Give more useful error messages for 'dpal()' and 'cpal()'
o Fix alpha channel in 'plot_image()'
CHANGES IN VERSION 2.7.1 [2024-5-17]
------------------------------------
NEW FEATURES
o Support subsetting of deferred operations
o Add 'chunked' classes for chunked objects
o Add 's_stat()' for grouped streaming statistics
o For 'plot_image()', set 'useRaster' to plot 3d surface/volume vs voxels
o Add 'enhance_adj()' function for adjusting extreme values
SIGNIFICANT USER-VISIBLE CHANGES
o Performance improvements for chunk-apply functions
o Support chunk-apply functions on remote cluster workers
o Reduced memory usage for chunk-apply functions on SNOW clusters
o Image smoothing 'filt2_*()' functions support multiple channels
o Contrast enhancement 'enhance_*()' functions support multiple channels
o Remove 'biglm' from imports
BUG FIXES
o Fix subplot axis scaling and aspect ratio for 'plotly' graphics
o Fix passing colors to line charts for 'plotly' graphics
CHANGES IN VERSION 2.6.3 [2024-7-15]
------------------------------------
BUG FIXES
o Fix 'filt2_gauss()' behavior with NAs
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
CHANGES IN VERSION 2.3.18 [2023-8-21]
-----------------------------------
BUG FIXES
o Fixed bug in 'kdtree()' stack size allocation
o Cleaned up a few C++ compiler warnings
CHANGES IN VERSION 2.3.17 [2023-8-11]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Parameter 'filename' in 'struct()' is now 'path'
CHANGES IN VERSION 2.3.16 [2023-8-8]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added 'checksum' method for character vectors (i.e., files)
CHANGES IN VERSION 2.3.15 [2023-8-8]
-----------------------------------
BUG FIXES
o Fixed erroneous warning in 'matter_list' or 'matter_arr'
constructors with existing files but no 'data' argument
CHANGES IN VERSION 2.3.14 [2023-8-7]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added 'append' argument to matter constructors
o Simplified 'sparse_arr' implementation by removing
shared index representation (which was not really used)
o When writing to an output file, 'chunkApply()' and friends
now write entire chunks instead of each element
o Added coercions from 'matter_list' to 'matter_arr', etc.
BUG FIXES
o No longer truncate existing files when creating a matter object
if nonexistent files are also included in the path
CHANGES IN VERSION 2.3.13 [2023-8-5]
-----------------------------------
BUG FIXES
o Fixed translation from aliased C types to R types
CHANGES IN VERSION 2.3.12 [2023-8-5]
-----------------------------------
NEW FEATURES
o Added 'image' method for formulas
CHANGES IN VERSION 2.3.11 [2023-8-3]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Changed specification of 'atoms' data types
o Use 'int16', int32', 'uint32', etc. for integer types
o Use 'float32' and 'float64' for floating point typess
o Added aliases so 'short', 'int', 'double', etc., still work
CHANGES IN VERSION 2.3.10 [2023-8-2]
-----------------------------------
NEW FEATURES
o Added 'rowMaj' S4 generic and methods
SIGNIFICANT USER-VISIBLE CHANGES
o Remove defunct S4 generics
BUG FIXES
o Fixed bug in 'approx1' for "max" and "min" interpolation
CHANGES IN VERSION 2.3.9 [2023-8-2]
-----------------------------------
NEW FEATURES
o Added 'vizi_pixels' for image plotting
o Added 'vizi_voxels' for 3D image plotting
SIGNIFICANT USER-VISIBLE CHANGES
o In estnoise_*() functions, renamed argument 'width' to 'n'
CHANGES IN VERSION 2.3.8 [2023-7-29]
------------------------------------
NEW FEATURES
o Added PLS (partial least squares)
o Added 'pls_nipals' (NIPALS)
o Added 'pls_simpls' (SIMPLS)
o Added 'pls_kernel' (kernel algorithms #1 and #2)
o Added OPLS (orthogonal PLS)
o Added 'opls_nipals' (NIPALS)
o Added FastMap projection with 'fastmap()'
o Added 'rowDists()' and 'colDists()'
o Added 'convolve_at()'
SIGNIFICANT USER-VISIBLE CHANGES
o Added regularization to NMF functions for stability
CHANGES IN VERSION 2.3.7 [2023-7-21]
------------------------------------
NEW FEATURES
o Added NMF (nonnegative matrix factorization)
o Added 'nnmf_mult()' (multiplicative updates)
o Added 'nnmf_als()' (alternating least squares)
o Exported 'prcomp_lanczos()'
SIGNIFICANT USER-VISIBLE CHANGES
o Accessing matter objects now checks for user interrupts
CHANGES IN VERSION 2.3.6 [2023-7-20]
------------------------------------
NEW FEATURES
o Added 'rowdist()' and 'coldist()'
o Added 'rowdist_at()' and 'coldist_at()'
o Added parallelization support for matrix multiplication
CHANGES IN VERSION 2.3.5 [2023-7-10]
------------------------------------
NEW FEATURES
o Added 'enhance_hist()' for histogram equalization
o Added 'enhance_adapt()' for CLAHE
BUG FIXES
o Fixed handling of missing values in smoothing filters
CHANGES IN VERSION 2.3.4 [2023-7-7]
-----------------------------------
NEW FEATURES
o Added CWT based peak detection with
'findpeaks_cwt()', 'findridges()' and 'cwt()'
o Added 'estnoise_quant()'
o Added 'filt1_conv()'
o Added 'filt2_conv()'
CHANGES IN VERSION 2.3.3 [2023-7-5]
-----------------------------------
NEW FEATURES
o Added 'trans2d()' for affine transformations
o Added 'warp2_trans()' for transformation-based
image registration using 'optim()'
CHANGES IN VERSION 2.3.2 [2023-7-4]
-----------------------------------
NEW FEATURES
o More new signal processing features!
o Added 'approx2()' for 2D signal resampling
and interpolation of scattered data
o Added 2D filtering including: 'filt2_ma()', 'filt2_gauss()',
'filt2_bi()', 'filt2_adapt()', 'filt2_guide'
o Added nonlinear diffusion 'filt1_diff()' and 'filt2_diff()'
o Added the traditional Savitzky-Golay filter 'filt1_sg()'
o Added 'kdsearch()' and 'kdtree()' for K-dimensional searches
SIGNIFICANT USER-VISIBLE CHANGES
o Updated package DESCRIPTION
CHANGES IN VERSION 2.3.1 [2023-6-27]
-----------------------------------
NEW FEATURES
o Lots of new signal processing features!
o Added 'approx1()' for signal resampling and interpolation
o Added 1D filtering including: 'filt1_ma()', 'filt1_gauss()',
'filt1_bi()', 'filt1_adapt()', 'filt1_guide()', 'filt1_pag()'
o Added 1D warping and alignment including: 'warp1_loc()',
'warp1_dtc()', 'warp1_cow()'
o Added continuum estimation including: 'estbase_loc()',
'estbase_hull()', 'estbase_snip()', 'estbase_med()'
o Added local noise estimation including: 'estnoise_sd()',
'estnoise_mad()', 'estnoise_diff()',
'estnoise_filt()'
o Added peak processing including: 'findpeaks()',
'peakwidths()', 'peakareas()', 'binpeaks()', 'mergepeaks()'
o Added 'downsample()' for signal and time series visualization
o Added 'vizi_plot' visualization methods
BUG FIXES
o Fix missing <cstdint> include for gcc 13.1.1 compatibility
CHANGES IN VERSION 2.1.1 [2023-4-13]
-----------------------------------
BUG FIXES
o Fixed NAMESPACE issue by importing 'Matrix::rowSums()' etc.
CHANGES IN VERSION 2.0.1 [2022-11-16]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated "User guide" vignette
BUG FIXES
o Fixed combining for matter vectors and lists
o Fixed slow 'matter_mat()' constructor for large # of atoms
o Fixed bug with BPPARAM not passed in 'rowStats()'/'colStats()'
CHANGES IN VERSION 1.99.2 [2022-10-31]
-----------------------------------
BUG FIXES
o Fix 'chunkApply()' behavior for when nchunks == 1
o Fix 'atoms' failure when 'source' is a compressed 'drle'
o Properly ignore missing groups in 'rowsweep()' and 'colsweep()'
CHANGES IN VERSION 1.99.1 [2022-10-30]
-----------------------------------
BUG FIXES
o Minor bug fixes to 'matter_list' and 'struct()' behavior
o Minor bug fix to endomorphic subsetting of sparse matrices
o Minor bug fix to 'binvec()' behavior at vector endpoints
CHANGES IN VERSION 1.99.0 [2022-10-23]
-----------------------------------
NEW FEATURES
o Complete re-implementation of sparse array code in C++
o Complete re-implementation of matter object C++ backends
o New 'sparse_arr' class with 'sparse_mat' and 'sparse_vec'
o New 'matter_arr' class with 'matter_mat' and 'matter_vec'
o New 'asearch()' function for approximate search with interpolation
o New 'chunkApply()' function replacing 'chunk_apply()', etc.
o New 'colsweep()' and 'rowsweep()' functions w/ group parameter
o New 'colscale()' and 'rowscale()' functions w/ group parameter
o New 'drle_fct' class for delta-run-length encoded factors
o New interpolation options for 'sparse_arr' objects
o Simplified deferred arithmetic operations interface
SIGNIFICANT USER-VISIBLE CHANGES
o New simplified constructors for most matter objects
o Updated S4 internals for most matter objects
o Updated S4 internals for sparse array objects
o Deprecated some rarely-used functions and classes
o Deprecated some S4 generic conflicts with core BioC packages
BUG FIXES
o Fix to 'stream_var' and 'stream_sd' behavior when n=0 or n=1
CHANGES IN VERSION 1.19.1 [2021-10-20]
-----------------------------------
BUG FIXES
o Fix error in 'cbind()' on two 'matter_vec' objects
CHANGES IN VERSION 1.17.1 [2020-11-27]
-----------------------------------
BUG FIXES
o Fix 'apply()' signatures for R 4.1
CHANGES IN VERSION 1.15.1 [2020-9-3]
-----------------------------------
BUG FIXES
o Remove '...' from 'which()'
CHANGES IN VERSION 1.13.10 [2020-4-20]
-----------------------------------
NEW FEATURES
o Added 's_nnzero()' stream-stat for non-zero entries
o Added 'push()' and 'pull()' generics for future use
CHANGES IN VERSION 1.13.9 [2020-4-18]
-----------------------------------
BUG FIXES
o Minor updates to 'chunk_apply()' internals
CHANGES IN VERSION 1.13.8 [2020-3-13]
-----------------------------------
BUG FIXES
o Fixed bugs due to logical condition length > 1
CHANGES IN VERSION 1.13.7 [2020-3-11]
-----------------------------------
BUG FIXES
o Fixed to internal function 'linearInd()'
CHANGES IN VERSION 1.13.6 [2020-3-3]
-----------------------------------
BUG FIXES
o Fixed bug caused by change in R 4.0 so that
class of matrix is now c("matrix", "array")
CHANGES IN VERSION 1.13.5 [2020-3-2]
-----------------------------------
NEW FEATURES
o Support for 'view="chunk"' when specifying 'pattern'
CHANGES IN VERSION 1.13.4 [2020-2-26]
-----------------------------------
NEW FEATURES
o Added 'pattern' argument to 'chunk_mapply()'
CHANGES IN VERSION 1.13.3 [2020-2-9]
-----------------------------------
NEW FEATURES
o Implemented 'outfile' argument for writing results
to a file for 'chunk_apply()' and 'chunk_mapply()'
CHANGES IN VERSION 1.13.2 [2020-2-9]
-----------------------------------
NEW FEATURES
o Added 'pattern' argument to 'chunk_apply()'
CHANGES IN VERSION 1.13.1 [2019-10-30]
-----------------------------------
NEW FEATURES
o Added 'chunk_mapply()'
CHANGES IN VERSION 1.11.7 [2019-10-25]
-----------------------------------
BUG FIXES
o Fixed errors in 'rowStats()' and 'colStats()' when
calculating group statistics over minor dimensions
CHANGES IN VERSION 1.11.6 [2019-10-23]
-----------------------------------
NEW FEATURES
o Added 'locmax()' function for finding local maxima
o Added 'binvec()' function for binning vectors
CHANGES IN VERSION 1.11.5 [2019-10-13]
-----------------------------------
NEW FEATURES
o Exposed 'chunk_apply()' for applying functions
over parallelized chunks of vectors and matrices
CHANGES IN VERSION 1.11.4 [2019-10-13]
-----------------------------------
NEW FEATURES
o Added 'rowStats()' and 'colStats()' methods for
chunk-applying grouped summary statistics over
the rows and columns of matrices
SIGNIFICANT USER-VISIBLE CHANGES
o Family of 'apply()' and 'lapply()' methods now
attempt to respect the object's 'chunksize()'
o Added getOption('matter.default.chunksize') for
setting default chunksize for matter objects
CHANGES IN VERSION 1.11.3 [2019-10-9]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Faster subsetting of matter-backed ALTREP objects
o Updated 'bsearch()' to return the closest match when tol > 0
o Added getOption('matter.dump.dir') to control where
temporary files are stored for matter objects
CHANGES IN VERSION 1.11.2 [2019-7-24]
-----------------------------------
NEW FEATURES
o Coercing to native R types now returns an ALTREP
representation for most 'matter' objects
o Use 'as.altrep()' method to coerce an existing
'matter' object to ALTREP or to coerce native R types
to 'matter'-backed out-of-memory ALTREP objects
o ALTREP coercion can be controlled by new options:
getOption('matter.coerce.altrep')
getOption('matter.coerce.altrep.list')
getOption('matter.wrap.altrep')
o See ?`matter-options` for details
SIGNIFICANT USER-VISIBLE CHANGES
o The 'show()' method for 'matter' objects now
prints a preview of the data head
o Printing of data can be controlled with new options
getOption('matter.show.head') and
getOption('matter.show.head.n')
CHANGES IN VERSION 1.11.1 [2019-5-7]
-----------------------------------
NEW FEATURES
o Added 'stream_stat' class for streaming statistics
with functions s_mean(), s_var(), s_sd(), etc.
CHANGES IN VERSION 1.9.11 [2019-4-19]
-----------------------------------
BUG FIXES
o Fixed documentation link to 'base::lapply'
CHANGES IN VERSION 1.9.10 [2018-12-22]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Vectors can be used as 'virtual_mat' rows/columns now
CHANGES IN VERSION 1.9.9 [2018-12-22]
-----------------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Constructor for 'drle' now allows forcing delta = 0
o Updated display descriptions in 'show' methods
o Check for NULL dimensions when subsetting
'virtual_mat' and 'sparse_mat' classes
CHANGES IN VERSION 1.9.8 [2018-12-18]
-----------------------------------
BUG FIXES