v.1.0.0

Stable and reproducible API

Some functionalities are still evolving, but this version represents a major change in workflow and API capabilities.

What's Changed

• Release/1.0.0 by @jibarozzo in #72
• Update workflow to render only README RMarkdown files by @jibarozzo in #73

Full Changelog: v0.1.0...1.0.0

Highlights

Added functions:
R/

• add_rarefaction_metrics()
• plot_abundance_occupancy()
• plot_core_distribution()
• plot_rarefaction_metrics()
• update_otu_table() (previously do_phyloseq())

vignettes/
Static vignette for package documentation. This avoids failures in GH actions (macos runners).

• BRCore-vignette.Rmd
• BRCore-vignette.Rmd.orig
• images/
• precompile.R
• references.bib

Changed:

• identify_core has improved progress messaging, and named list outputs
  Tests:
• Added suites for added functions.

Selected commits

• 22d4b66: amending previous push: new plotting functions and minor fixes
• 1b8232d: Finalized vignette for BRCore
• 58d6d30: Gains overhaul package and NAMSPACE import in functions.
• 8ef5c78 : Changed @examplesIf requireNamespace("phyloseq", quietly = TRUE) for the more explicit `@examples
• c7e949b: Gains STATIC vignette

Contributors

Special thanks to @Gian77 for improvements in visualizations functions, tests, and vignette.

v0.1.0

BRCore NEWS

v0.1.0 (2025-09-30)

Bump version: 0.0.2 → 0.1.0

Why minor bump (pre-1.0): multiple new user-facing functions and a significant refactor that may affect behavior. API is still evolving.

Highlights

• Added (exported functions):
  • identify_core()
  • multi_rarefy()
  • do_phyloseq()
  • sncm.fit()
  • plot_identified_core()
  • fit_neutral_model()
  • plot_neutral_model()
• Changed:
  • identify_core refactor with improved error handling, progress messaging, and structured outputs
• Tests:
  • Added suites for identify_core, do_phyloseq, multi_rarefy, and related utilities
• Docs/infra:
  • README usage example updates
  • CI: RSPM usage, macOS job, and dependency setup improvements
  • Packaging: DESCRIPTION and NAMESPACE updates; new/updated deps (cli, Hmisc, minpack.lm, parallelly, stats4, tidyr, etc.)

Potentially breaking/behavioral notes

• identify_core output structure and some defaults may have changed compared to earlier workflows.
• multi_rarefy now supports parallel execution and reproducible seeding; samples below depth_level are dropped and results are averaged across iterations.

Pull request

• Release PR: #57

Notable commits (selected)

• 46a334f — feat(core): add identify_core() + plot_identified_core() + datasets with docs & tests
• ee1f023 — neutral models and related fixes, plus multi_rarefy fix
• 3ac688e — rename parallel_rarefy to multi_rarefy and additional fixes
• a9b903d — add parallel rarefaction function and documentation
• 2cf4e1d — add cli messages; rework parallel_extract_core.R and vignette
• b09ec70 — fix “elbow” method and clean pipeline; pipe-friendly refactor
• 5658f46 — guardrails: ensure at least one comparison column besides rank
• 922531b — fix do_phyloseq and macOS test for fit_neutral_model; adjust test datasets
• f6e2fa9 — fix for test-fit_neutral_model.R
• f9c56c4 — fix user datasets for tests; add imports to globals.R
• 078ab3c — remove miscellaneous functions (moved to experimental branch)
• 3a98d8a — update NAMESPACE; remove stale man/ files
• 6a3f45d — remove corresponding obsolete tests
• f71afef — remove R/utils/000_setup.R (legacy)
• 8202506 — enable public RSPM for R dependency setup
• 7890dd8 — conditionally render markdown/vignettes in workflow (not rendering for the time being)
• d1fea08 — stop tracking vignettes/ directory
• fcadeca — RSPM configuration updates

Thanks

• Thanks to contributors @Gian77 and @B-Kristy for code, tests, and CI improvements.

v0.0.2

Dependencies

• Gains R minimum version dependency R >= 4.4

v0.0.1

"License and registration"

What's Changed

• Better tests: by @jibarozzo in #9
• Enhanced Ordination Visualization & Import NAMESPACE Resolution by @jibarozzo in #11
• Develop: Resolved issues with calculate_bc() and its use in for loop (Issue #12) by @jibarozzo in #14

Full Changelog: v0.0.0.9...v0.0.1

BRCore 0.0.0.9

Hello BRCore

• Forks from germs-lab/interbrc-core-analysis to BRCore

• Gains Authors, README, Dependencies, and Function Naming Consistency by @jibarozzo in #8

• Gains README examples by @jibarozzo in #10

Full Changelog: https://github.com/germs-lab/BRCore/commits/v0.0.0.9