Changes in version 0.2.0                        

Major Improvements

  - OpenMP Parallelization - 11x performance improvement
    
      - Parallelized soft assignment computation (primary bottleneck)
      - Achieved 11x speedup on real-world data (1000 genes × 5536
        cells)
      - Execution time reduced from 296.83s to 27.00s
      - Throughput increased from 19 to 205 cells/second
      - No memory overhead or numerical differences

  - Code Optimizations
    
      - Efficient matrix broadcasting using Eigen's replicate()
      - Pre-allocated matrices to reduce memory allocations
      - Cleaner, more maintainable code structure

  - Build System Improvements
    
      - Added Makevars for automatic OpenMP compilation
      - Conditional compilation for backward compatibility
      - Thread count detection and reporting

Documentation

  - Added comprehensive performance documentation:
      - OPENMP_OPTIMIZATION_REPORT.md: Technical details and analysis
      - PERFORMANCE_SUMMARY.txt: Quick reference guide
      - benchmark_real_data.R: Reproducible benchmark script

Notes

  - This is a performance-optimized fork of CRAN v0.1.5
  - Original algorithm and core functionality unchanged
  - Maintains identical numerical results
  - Backward compatible - falls back to serial execution if OpenMP
    unavailable
  - Scales linearly with dataset size
  - Maintainer: Billsfriend Billsfriend1999@outlook.com
  - Original Authors: Xiaojie Qiu, Cole Trapnell, Qi Mao, Li Wang

Usage

Control thread count for optimal performance:

# Set before loading the package
Sys.setenv(OMP_NUM_THREADS = 8)
library(DDRTree2)

Or via shell:

export OMP_NUM_THREADS=8
Rscript your_script.R

                        Changes in version 0.1.5                        

Bug Fixes

  - Fixed a problem where DDRTree would return different results on
    repeated runs given the same inputs. The problem was in two places:
    kmeans and irlba. We now call irlba with deterministically
    initialized eigenvectors and kmeans with deterministically selected
    rows of the input.

                        Changes in version 0.1.4                        

Bug Fixes

  - Fixed a build error triggered by recent versions of GCC using the
    C++14 standard