Add os_bias_audit_report() plain-text wrapper for the bias-audit module

The bias-audit module previously exposed structured output via
os_bias_audit() and a console print method. Capturing the rendered
report into a string (for logging, supplementary figures, or
manuscript-side scripts) required wrapping print() in
capture.output() at every call site.

Add os_bias_audit_report() that:
  - runs os_bias_audit() with the given inputs (or accepts a
    pre-computed audit object via the `audit=` argument),
  - returns the formatted multi-line report as a length-one
    character vector with class "os_bias_audit_report",
  - attaches the underlying os_bias_audit object as
    attr(., "audit") so downstream code can still access the
    structured fields (bias_floor, classifier_vs_floor, etc.)
    without recomputing.

Also add 10 testthat expectations covering:
  - return type and content of the text report,
  - attached audit attribute identity,
  - input validation errors when neither `audit` nor (X, y, cohort)
    are provided.

Bias-audit test count rises from 32 to 42 expectations, all passing.
R CMD check remains Status: OK.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: kstawiski

NAMESPACE

@@ -38,6 +38,7 @@ export(OmicWeightedEnsemble)
 export(SequentialSelector)
 export(StabilityEnsemble)
 export(apply_frozen_combat_cv)
+export(apply_hemolysis_prefilter)
 export(autoencoder_encode)
 export(autoencoder_fit)
 export(autoencoder_load)
@@ -94,6 +95,7 @@ export(finetune_mlr3torch_checkpoint)
 export(finetune_omicfit_checkpoint)
 export(fit_corr_order)
 export(fit_deepinsight)
+export(fit_hemolysis_prefilter)
 export(fit_isotonic_calibration)
 export(fit_platt_scaling)
 export(fit_temperature_scaling)
@@ -107,6 +109,7 @@ export(get_optimal_params)
 export(get_parallel_status)
 export(get_reliable_shap_features)
 export(get_selected_features_per_fold)
+export(hemolysis_proxy_score)
 export(import_mlr3torch_checkpoint)
 export(import_omicfit_checkpoint)
 export(impute_within_fold)
@@ -132,6 +135,7 @@ export(noise_augment)
 export(omic_benchmark)
 export(omic_pipeline)
 export(os_bias_audit)
+export(os_bias_audit_report)
 export(os_bias_floor_auc)
 export(os_clustered_bootstrap_auc)
 export(os_covariate_only_auc)
@@ -142,6 +146,7 @@ export(plot_signature_tradeoffs)
 export(plot_xai_importance)
 export(predict_clr_mlp)
 export(predict_codacore)
+export(predict_weighted_clr_mlp)
 export(print_shap_warnings)
 export(print_xai_summary)
 export(register_coda_feature_selection_filters)
@@ -164,8 +169,10 @@ export(train_clr_mlp)
 export(train_codacore)
 export(train_ratio_cnn)
 export(train_ratio_cnn_multiseed)
+export(train_weighted_clr_mlp)
 export(validate_omics_input)
 export(validate_synthetic)
+export(weighted_clr_transform)
 export(with_parallel)
 export(ws_logratio)
 export(ws_minmax)

R/bias-audit.R

@@ -676,6 +676,71 @@ print.os_bias_audit <- function(x, ...) {
 }
 
 
+#' @title Plain-Text Bias-Audit Report
+#'
+#' @description
+#' Convenience wrapper that runs \code{\link{os_bias_audit}} on a model/data
+#' bundle and returns the formatted report as a single character string.
+#' Useful when the report needs to be captured into a log, supplementary
+#' table, or pasted into a manuscript figure legend without relying on
+#' the console print method.
+#'
+#' @inheritParams os_bias_audit
+#' @param audit An optional pre-computed \code{os_bias_audit} object. If
+#'   supplied, the audit is not recomputed and the remaining arguments are
+#'   ignored. This makes it cheap to produce the text report alongside the
+#'   structured result when both are needed.
+#'
+#' @return A length-one character vector containing the full text report.
+#'   The same content that \code{print.os_bias_audit} would write to the
+#'   console is captured, with an additional attribute \code{"audit"} that
+#'   holds the underlying \code{os_bias_audit} object for downstream use.
+#'
+#' @examples
+#' \dontrun{
+#' txt <- os_bias_audit_report(
+#'   X = X, y = y, cohort = cohort,
+#'   predictions = preds,
+#'   covariates = list(age = age_years)
+#' )
+#' cat(txt)
+#' writeLines(txt, "bias_audit.txt")
+#' attr(txt, "audit")$bias_floor$apparent_auc
+#' }
+#'
+#' @export
+os_bias_audit_report <- function(X = NULL, y = NULL, cohort = NULL,
+                                 predictions = NULL,
+                                 covariates = NULL,
+                                 specimen_id = NULL,
+                                 sample_id = NULL,
+                                 feature_names = NULL,
+                                 seed = 42L,
+                                 audit = NULL) {
+  if (is.null(audit)) {
+    if (is.null(X) || is.null(y) || is.null(cohort)) {
+      stop("Provide either `audit` or all of `X`, `y`, `cohort`.", call. = FALSE)
+    }
+    audit <- os_bias_audit(
+      X = X, y = y, cohort = cohort,
+      predictions = predictions,
+      covariates = covariates,
+      specimen_id = specimen_id,
+      sample_id = sample_id,
+      feature_names = feature_names,
+      seed = seed
+    )
+  } else if (!inherits(audit, "os_bias_audit")) {
+    stop("`audit` must be an `os_bias_audit` object.", call. = FALSE)
+  }
+
+  txt <- paste(utils::capture.output(print(audit)), collapse = "\n")
+  attr(txt, "audit") <- audit
+  class(txt) <- c("os_bias_audit_report", "character")
+  txt
+}
+
+
 # Internal AUC: trapezoidal on rank-based approximation (no dependency on pROC).
 .auc_fast <- function(y, score) {
   if (length(unique(y)) != 2L) return(NA_real_)

man/os_bias_audit_report.Rd

@@ -217,3 +217,37 @@ test_that("os_bias_audit prints without error", {
   expect_output(print(audit), "Bias floor")
   expect_output(print(audit), "Top-5 features")
 })
+
+
+# -----------------------------------------------------------------------------
+# os_bias_audit_report (plain-text convenience wrapper)
+# -----------------------------------------------------------------------------
+test_that("os_bias_audit_report returns a character string with the report", {
+  d <- make_provenance_data()
+  txt <- os_bias_audit_report(X = d$X, y = d$y, cohort = d$cohort)
+  expect_s3_class(txt, "os_bias_audit_report")
+  expect_type(txt, "character")
+  expect_length(txt, 1L)
+  expect_match(txt, "OmicSelector Cohort-Provenance Bias Audit", fixed = TRUE)
+  expect_match(txt, "Bias floor", fixed = TRUE)
+  expect_s3_class(attr(txt, "audit"), "os_bias_audit")
+})
+
+test_that("os_bias_audit_report accepts a pre-computed audit object", {
+  d <- make_provenance_data()
+  audit <- os_bias_audit(X = d$X, y = d$y, cohort = d$cohort)
+  txt <- os_bias_audit_report(audit = audit)
+  expect_s3_class(txt, "os_bias_audit_report")
+  expect_identical(attr(txt, "audit"), audit)
+})
+
+test_that("os_bias_audit_report validates its inputs", {
+  expect_error(
+    os_bias_audit_report(),
+    "Provide either `audit` or all of `X`, `y`, `cohort`"
+  )
+  expect_error(
+    os_bias_audit_report(audit = list(foo = 1)),
+    "must be an `os_bias_audit` object"
+  )
+})