guard_to_recipe: Convert guard preprocessing steps to a recipes recipe

In bioLeak: Leakage-Safe Modeling and Auditing for Genomic and Clinical Data

Convert guard preprocessing steps to a recipes recipe

Description

Maps bioLeak guard preprocessing steps (impute, normalize, filter, fs) to their closest recipes equivalents. Requires the recipes package. Steps that have no direct recipe equivalent are skipped with a warning.

Usage

guard_to_recipe(steps, formula, training_data)

Arguments

steps	A named list of guard preprocessing steps, e.g., list(impute = list(method = "median"), normalize = list(method = "zscore")).
formula	A model formula (e.g., outcome ~ .).
training_data	A data.frame used to initialize the recipe.

Details

Mapping:

• impute$method = "median": step_impute_median(all_numeric_predictors())

• impute$method = "knn": step_impute_knn(all_predictors(), neighbors = k)

• impute$method = "missForest" or "mice": Warning + step_impute_median() fallback

• normalize$method = "zscore": step_normalize(all_numeric_predictors())

• normalize$method = "robust": Warning + step_normalize() fallback

• normalize$method = "none": No step added

• filter$var_thresh > 0: step_nzv(all_numeric_predictors())

• fs$method = "pca": step_pca(all_numeric_predictors(), num_comp = ncomp)

• fs$method = "ttest" or "lasso": Warning, skipped (no recipe equivalent)

Value

A recipes::recipe object with the mapped steps added.

bioLeak documentation built on March 6, 2026, 1:06 a.m.