# Version: 0.99.15
changing LazyData to false

# Version: 0.99.14
- update
# Version: 0.99.13

# Version: 0.99.12
- Cleaned up Rcheck.


# Version: 0.99.11
- Adding TSE Examples
- Including TSE vignettes

# DspikeIn 0.99.10

- Cleaned up Rcheck.

# DspikeIn 0.99.9

- 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.

# DspikeIn 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.

# DspikeIn 0.99.7

_No major changes recorded._

# DspikeIn 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.

# DspikeIn 0.99.0

## Initial submission

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