winn 0.1.5
- Marked the optional ComBat example as a longer-running example
because loading its Bioconductor dependency can exceed five seconds on
CRAN. It remains runnable with
example() and is checked by
--as-cran.
- Added routine ComBat integration coverage for preserved matrix
labels, finite non-negative output, and correction of simulated batch
effects.
- Simplified the description and clarified the title as mass
spectrometry profiling data. The full method citation remains in
CITATION and the README.
winn 0.1.4
- Made the Bioconductor package
sva optional for the
ComBat correction path; the default ANOVA workflow no longer requires a
Bioconductor installation.
- Added executable examples for all exported functions and seeded
stochastic examples for reproducible CRAN checks.
- Made drift testing and smoothing honor
run_order
independently of matrix column order. Values are sorted within batch for
testing and correction and restored to the caller’s original column
order.
- Changed the Ljung-Box default to
fitdf = 0, because
WiNN does not first fit an ARMA model. The legacy fitdf = 1
behavior remains available explicitly through
ljung_box_fitdf = 1.
- Added strict validation for finite, non-negative log-scale inputs;
complete batch and run-order metadata; unique within-batch run orders;
control indices; dilution factors; and within-batch scaling.
- Documented the preprocessing policy for zero and censored
observations. Numeric zeros remain observed values and are never
silently converted to missing values.
- Added
return_details = TRUE to winn() for
machine-readable selected parameters, batch assignments, and per-stage
decisions while retaining the corrected-matrix default.
- Clarified fixed versus auto-mode settings and the selective ANOVA
versus global ComBat correction scopes.
- Removed interactive test code from package sources and added release
CI.
winn 0.1.3
- Replaced the legacy upper-priority MAD branch with independent
two-tail shrinkage. Each metabolite’s median, MAD, thresholds, and
upper/lower masks are computed once from the original finite values;
both tails are then adjusted in one non-iterative pass.
- Added regression coverage for simultaneous-tail adjustment, one-pass
threshold reuse, missing/non-finite values, and zero-MAD features.
winn 0.1.2
- Added
winn_ablation() for fixed-parameter cumulative
and gate-factorial analyses using the same correction operators as
winn().
- Added optional decision and correction diagnostics to the drift,
batch, and dilution-normalization functions. Their default
matrix-returning behavior is unchanged.
- Made selective, forced-all, and disabled drift and batch gates
explicit for controlled method evaluation.
- Documented the historical directional MAD behavior and added
regression tests that made the legacy branch explicit before its
replacement in 0.1.3.
- Added tests for ablation equivalence, disabled-stage pass-through
behavior, diagnostic structure, and standard-smoother fallback
reporting.