2026-05-19
2026-05-18
Relaxed version requirements for phyloseq and stats4 to improve compatibility.
5ba7a7c Added biocViews field to DESCRIPTION to allow installation of Bioconductor dependencies via install.packages().
40d79e4 Fixes to quote 'BRCore' in DESCRIPTION and typo fix of sncm.fit in _pkgdown.yaml
sncm.fit(): replaced suppressWarnings() with targeted warning capture via new internal helper .internal_warn_sncm().plot_neutral_model(): refined plot axis styling and formatted y-axis as percent. Resized box annotation.data("bcse") calls from examples and README vignette.num_iter parameter from README examples.2026-04-30
scnm.fit()@seealso cross-refences in documentation\dontrun and \donttestswithchgrass_core object, identified microbial core, for examples2026-04-28
parallel_helpers.R since we have moved away from parallel implementations.2026-04-25
2026-04-24
multi_rarefy(): .as_array logical argument replaced with .as character argument (e.g. "list", "array"). Single-iteration handling improved to support all .as formats and seeds.identify_core(): output column renamed from Index to rank.find_core() removed; ground truth logic moved to debugging branch.identify_core() major rewrite: vegan::avgdist() replaced with vegan::vegdist() via new .mean_bc_over_iters() internal helper; rarefied_list is now optional and requires ≥ 2 iterations when provided. This fixes incorrect results on unrarefied datasets caused by how vegan::avgdist() handles zeros in a matrix of ones.plot_identified_core() now returns a named list with $df and $plot instead of a bare plot object.tests/testthat/test_sets/test_vignette_data.rda reference dataset.pbinom() now receives N.int, an integer size argument (round(N)) instead of a floating-point mean. This changes model output relative to prior versions. We also added comprehensive messaging to inform user of species (N or N.int) used in model fitting.multi_rarefy() internal logic: Replaced .single_rarefy() with internal vegan::rrarefy() engine.multi_rarefy() to output 3D array or list. This handling increased speed of computation and eliminated the need for parallelization. CLI messages were improved to handle these new types and present summary statistics and information to users..brcore_theme() internal helper (brcore_theme.R) to unify plot styling (borders, title sizes, viridis palettes) across all plotting functions.plot_identified_core() gains an optional dataset_name parameter for plot titles.identify_core(): fixed proportionBC normalisation to use max() instead of last().identify_core(): fixed BC ranking and pair alignment using unique time points.plot_identified_core(): fixed deprecated size → linewidth in panel.border.plot_variance_propagation() to plot results from multi_rarefy().update_otu_table() has new parameter iteration to handle results from multi_rarefy().identify_core() now has a progress bar powered by cli::cli_progress_bar() in .calculate_bc().36285d2 Tidy eval compliance enforced throughout using .data$ pronouns and quoted column names; globals.R significantly trimmed.
Vignette and README updated to reflect the required multi-iteration workflow for identify_core().
Test suite updated for identify_core, multi_rarefy, plot_identified_core, plot_variance_propagation, update_otu_table, and the full vignette workflow. Test data regenerated (test_vignette_data.rda grew ~250 KB).
Vignette updated to include multi_rarefy() and plot_variance_propagation() as part of the Data Exploration and Parameter Selection section. This new workflow allows users to determine the adequate sequence read depth for their data and input that into identify_core().
See PR #97 and #95 for more details
@jibarozzo @Gian77
2026-02-25
Fixed multi_rarefy() reproducibility across platforms using deterministic iteration seeds for parallel processing and adding floating-point tolerance in rarefaction.
Added floating point tolerance in identify_core() rarefaction validation
a687fa3Changed rarefaction engine vegan::rrarefy() to custom .single_rarefy() reducing reliance on external dependencies.
Enhanced CLI output in multi_rarefy(): improved input validation for multi_rarefy() parameters
921dc51Added comprehensive end-to-end workflow tests that replicate the vignette workflow.
See PR #84 for more details
@Gian77 @jibarozzo @Copilot