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.