# harmony v1.2.0 - Oct 12 2023 - Major performance enhancements, using indexes for the regression - update_R - Generate blocks correctly #214 - lambda optimization - Lambda as a function of E. - New alpha parameter to estimate lambda during runtime - fail-safe for < 40 cells dataset . Setting block_size=0.2. Refuse to run with < 6 cells. - added progress bar for the integration step. # harmony v1.1.0 - Oct 12 2023 - update_R bug - All cells are corrected exactly once per invocation - Improved documentation RunHarmony generc - Fix lambda failing on multiple covariates - verbose option suppresses all messages # harmony v1.0.0 - Jul 27 2023 * API changes - removed do_pca functionality - removed reference_values functionality - removed cluster_prior functionality - beta feature: automatic parameterization of lambda when it is set to NULL - ncore parameter controls the use of multiple processors when parallelized BLAS exists. - Moved several parameters to the .options. Now they are accessible through harmony_options() * Documentation - Updated seurat vignette - Removed mudan Seurat2 and Seurat3 vignettes * Name changes - Integrated HarmonyMatrix function to the RunHarmony generic - HarmonyMatrix is deprecated * Backend changes - Sparse matrix coercion to yield performance enhancements - L2-normalization using armadillo routines - Supports parallel versions of BLAS. * Fixes - RunHarmony() for Seurat considers dimension set - RunHarmony() for SingleCellExperiment works - custom ceiling function to avoid conflicts for some block_size - Coercing covariate to factor when levels are numbers * New features - Automatic parameterization of lambda - Updated convergence plot # harmony v0.1.0 * Initial release to CRAN # harmony v0.1.1 * Updates pow to harmony_pow to avoid collision with new Armadillo pow function