Changes in version 0.99.28                       

  - Bump version

                       Changes in version 0.99.27                       

  - Bump version

                       Changes in version 0.99.26                       

  - Bump version

                       Changes in version 0.99.25                       

  - Bump version

                       Changes in version 0.99.24                       

  - Bump version

                       Changes in version 0.99.23                       

  - merging

                       Changes in version 0.99.22                       

  - merging

                       Changes in version 0.99.21                       

                       Changes in version 0.99.20                       

  - function added
  - reviewer's comments implemented

                       Changes in version 0.99.11                       

  - Adding TSE Examples
  - Including TSE vignettes

                       Changes in version 0.99.10                       

No major changes recorded.

                       Changes in version 0.99.9                        

  - Cleaned up Rcheck.

  - Documented both physeq and tse in R/data.R with proper @format,
    @source, and usage examples.
  - Fixed system hostname configuration to remove “unknown” from shell
    prompt.
  - Verified that vignettes build cleanly and only required doc/ appears
    in tarball.
  - Cleaned up redundant or empty directories during build to pass
    Bioconductor checks.

                       Changes in version 0.99.8                        

Changes

  - Streamlined the package by removing non-essential helper and
    pipeline functions.
  - Retained core spike-in quantification methods only: validation,
    scaling, bias correction, and absolute abundance estimation.
  - Removed dependencies on DESeq2, edgeR, and downstream differential
    analysis tools.
  - Updated DESCRIPTION, NAMESPACE, and internal documentation to
    reflect core-only functionality.
  - Added clarifying notes in the vignette and package description about
    the full pipeline availability on the MGhotbi branch.
  - Reorganized internal structure for improved reproducibility and
    modular design.
  - Updated R version dependency to R (>= 4.5.0) to comply with
    Bioconductor guidelines.
  - Refined biocViews to match core functionality focus and removed
    unused categories.

                       Changes in version 0.99.7                        

No major changes recorded.

                       Changes in version 0.99.6                        

Changes

  - Fixed error caused by missing geom_star() in ggstar.
  - Updated example sections to conditionally load required packages.
  - Corrected object reconstruction logic in
    random_subsample_WithReductionFactor().
  - Replaced deprecated functions and improved Bioconductor compliance.
  - Added proper LICENSE formatting to eliminate NOTE.
  - Documented dataset provenance and processing steps in
    inst/scripts/data_preparation.md, including SRA BioProject
    accessions for embedded data.

                       Changes in version 0.99.0                        

Initial submission

  - Submitted package to Bioconductor.
  - Added spike-in analysis workflows.
  - Included synthetic and real microbiome datasets.