
CHANGES IN VERSION 1.1.3 [2017-3-15]
---------------------------------

NEW FEATURES

    o Added class 'drle' for delta-run-length encoding vectors
    o Added '+', '-', '*', '/', '^', 'exp', 'log', 'log2', and 'log10'
        as possible delayed operations to on-disk atoms

SIGNIFICANT USER-VISIBLE CHANGES

    o Slots of 'atoms' class now use delta-run-length encoding
    o Reduced metadata size by changing 'atoms' class to use
        groups rather then relying on a 'list' of 'atoms'
    o The 'scale' method for 'matter_mat' now matches 'scale.default'
        more correctly when 'center = FALSE' and 'scale = TRUE'

CHANGES IN VERSION 1.1.2 [2017-3-12]
---------------------------------

NEW FEATURES

    o Added support for char, uchar, ushort, uint, and ulong datamodes
    o Added support for raw (Rbyte) matter objects

SIGNIFICANT USER-VISIBLE CHANGES

    o S4 methods for matrix-specific summary statistics are
        now only defined on matter_mat and its subclasses

BUG FIXES

    o Dramatically improved speed of matrix multiplication 

CHANGES IN VERSION 1.1.1 [2016-11-29]
---------------------------------

NEW FEATURES

    o Added 'crossprod' (t(x) %*% y) and 'tcrossprod' (x %*% t(y)) methods
    o Added 'atomdata' accessor method, for which 'adata' is now an alias

BUG FIXES

    o Added S3 versions of some S4 methods to fix scoping issues
    o Removed Cardinal package from Suggests to avoid circular dependency
    o Reduced memory consumption in bigglm-matter method

CHANGES IN VERSION 0.99.11 [2016-10-11]
---------------------------------

BUG FIXES

    o Updated documentation details.

CHANGES IN VERSION 0.99.10 [2016-10-11]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Updated vignettes with installation instructions, faster build time
    o Added 'adata' method for accessing 'matter' class @data slot

CHANGES IN VERSION 0.99.9 [2016-10-5]
---------------------------------

NEW FEATURES

    o Added delayed scaling and centering via 'scale' method
    o Added 'prcomp' method for principal components analysis

SIGNIFICANT USER-VISIBLE CHANGES

    o Renamed 'colSd' -> 'colSds', 'colVar' -> 'colVars', etc.
    o Renamed 'filepaths' -> 'paths' and 'file_id' -> 'source_id'
    o Moved 'irlba' from Suggests to Imports to support new 'prcomp' method
    o Updated vignette to use new 'prcomp' method in the PCA example

BUG FIXES

    o Fixed bug when combining 'matter' objects with multiple data sources

CHANGES IN VERSION 0.99.8 [2016-10-3]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o In S4 class 'atoms', slot 'file_id' is now type 'integer' to save space
    o In S4 class 'atoms', slot 'datamode' is now type 'integer' to save space
    o More comprehensive error messages in constructors for S4 classes

CHANGES IN VERSION 0.99.7 [2016-10-1]
---------------------------------

BUG FIXES

    o Try to fix namespace std::isnan scoping issues on Windows

CHANGES IN VERSION 0.99.6 [2016-10-1]
---------------------------------

BUG FIXES

    o Fixed handling of NA, NaN, Inf, and -Inf during C type coercion
    o Improved handling of NA, NaN, Inf, and -Inf in summary stats
    o Fixed handling of NAs in matrix multiplication for integers

CHANGES IN VERSION 0.99.5 [2016-9-27]
---------------------------------

BUG FIXES

    o Fixed .Call native routine registration for C++ methods
    o Added "C_" prefix for C++ methods called through .Call

CHANGES IN VERSION 0.99.4 [2016-9-27]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added .Call native routine registration for C++ methods

CHANGES IN VERSION 0.99.3 [2016-9-27]
---------------------------------

BUG FIXES

    o Import generics from S4Vectors for 'colMeans', 'colSums',
        'rowMeans', and 'rowSums'
    o Cleaned up method signatures and class unions

CHANGES IN VERSION 0.99.2 [2016-9-26]
---------------------------------

BUG FIXES

    o Cleaned up double assignments in C++ code

CHANGES IN VERSION 0.99.1 [2016-9-26]
---------------------------------

BUG FIXES

    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.
