Date: 2026-04-30
scnm.fit()@seealso cross-refences in documentation\dontrun and
\donttestswithchgrass_core object, identified
microbial core, for examplesDate: 2026-04-28
parallel_helpers.R since we have moved away
from parallel implementations.Date: 2026-04-25
Date: 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
Date: 2026-02-25
multi_rarefy() reproducibility across platforms
using deterministic iteration seeds for parallel processing and adding
floating-point tolerance in rarefaction.
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