Feat/imputation improvements

README.md

@@ -156,7 +156,7 @@ phenoqc \
 - `--impute-params '{"n_neighbors": 5}'` (JSON)
 - `--impute-tuning on|off`
 - `--label-column class` and `--imbalance-threshold 0.10`
-- `--quality-metrics imputation_bias redundancy` (or `all`)
+- `--quality-metrics imputation_bias redundancy` (or `all`) (alias: `--metrics`)
 - Imputation-bias thresholds: `--bias-smd-threshold`, `--bias-var-low`, `--bias-var-high`, `--bias-ks-alpha`
 - Categorical bias thresholds: `--bias-psi-threshold`, `--bias-cramer-threshold`
 - Imputation stability diagnostics: `--impute-diagnostics on|off`, `--diag-repeats`, `--diag-mask-fraction`, `--diag-scoring`
@@ -384,6 +384,22 @@ cache_expiry_days: 30
 # optional: offline (forces cache/local ontologies only for the run)
 # offline: true
 
+quality_metrics:
+  redundancy: { enable: true }
+  imputation_bias: { enable: true }
+  imputation_stability: { enable: true, repeats: 5, mask_fraction: 0.10, scoring: MAE }
+class_distribution:
+  label_column: class
+  warn_threshold: 0.10
+
+imputation_bias:
+  smd_threshold: 0.10
+  var_ratio_low: 0.5
+  var_ratio_high: 2.0
+  ks_alpha: 0.05
+  psi_threshold: 0.10
+  cramer_threshold: 0.20
+
 imputation:
   strategy: knn
   params:

docs/source/usage.rst

@@ -50,7 +50,7 @@ Parameters
 - ``--impute``: Strategy for missing data (mean, median, mode, knn, mice, svd, none)
 - ``--impute-params``: JSON object of parameters for the imputation strategy (e.g. ``{"n_neighbors": 5}``)
 - ``--impute-tuning {on,off}``: Enable quick tuning (mask-and-score) for imputation
-- ``--quality-metrics``: Choose metrics (e.g., ``imputation_bias``); ``all`` enables all
+- ``--quality-metrics`` (alias: ``--metrics``): Choose metrics (e.g., ``imputation_bias``); ``all`` enables all
  - ``--bias-smd-threshold``, ``--bias-var-low``, ``--bias-var-high``, ``--bias-ks-alpha``: thresholds for numeric bias diagnostics
  - ``--bias-psi-threshold``, ``--bias-cramer-threshold``: thresholds for categorical bias diagnostics (PSI, Cramér’s V)
 - ``--impute-diagnostics {on,off}``, ``--diag-repeats``, ``--diag-mask-fraction``, ``--diag-scoring``: stability diagnostics
@@ -108,6 +108,22 @@ PhenoQC uses a YAML configuration file to define settings. Example ``config.yaml
     cache_expiry_days: 30
     # offline: true  # optional: force cached/local ontologies only for the run
 
+    quality_metrics:
+      redundancy: { enable: true }
+      imputation_bias: { enable: true }
+      imputation_stability: { enable: true, repeats: 5, mask_fraction: 0.10, scoring: MAE }
+    class_distribution:
+      label_column: class
+      warn_threshold: 0.10
+
+    imputation_bias:
+      smd_threshold: 0.10
+      var_ratio_low: 0.5
+      var_ratio_high: 2.0
+      ks_alpha: 0.05
+      psi_threshold: 0.10
+      cramer_threshold: 0.20
+
     imputation:
       strategy: knn
       params: