Black-box rule of the handbook
Regla de caja negra del manual
This handbook does not redefine the case, rediscover variables, or decide which evidence is needed. Its task is to execute the selected method architecture, calculate all required indices, run the necessary diagnostics, quantify uncertainty, and produce a standardized technical evidence object for Module IV.
Este manual no redefine el caso, no redescubre variables ni decide qué evidencia se necesita. Su tarea es ejecutar la arquitectura metodológica seleccionada, calcular todos los índices requeridos, correr los diagnósticos necesarios, cuantificar incertidumbre y producir un objeto técnico estandarizado para el Módulo IV.
1. Position in the full framework
1. Posición dentro del framework completo
MODULE I
Case and variable eligibility
↓
MODULE II
Evidence requirements
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MODULE III — Conceptual Layer
Method capability and method selection
↓
MODULE III — Method Validation Handbook
Execution + indices + diagnostics + uncertainty
↓
METHOD EVIDENCE REPORT
↓
MODULE IV
Interpretation + decision rules + acceptance logic
↓
PASS / CONDITIONAL / FAIL / RETURN
| LayerCapa | Primary questionPregunta principal | Primary outputSalida principal |
|---|---|---|
| Module I | What parts of the case are usable?¿Qué partes del caso son utilizables? | Validated case and variablesCaso y variables validadas |
| Module II | What evidence is required?¿Qué evidencia se requiere? | ESS |
| Module III Conceptual | Which method can produce the evidence?¿Qué método puede producir la evidencia? | MSS |
| Module III Validation | What did the method calculate and how stable is it?¿Qué calculó el método y qué tan estable es? | MER |
| Module IV | What do the indices mean for this case?¿Qué significan los índices para este caso? | Decision and scientific statusDecisión y estado científico |
2. Handbook objective
2. Objetivo del manual
The objective is to convert each selected method into a reproducible quantitative execution package. Every package must specify inputs, preprocessing, parameters, algorithm execution, indices, diagnostics, uncertainty, sensitivity, robustness, failure signals, and output artifacts.
El objetivo es convertir cada método seleccionado en un paquete cuantitativo reproducible de ejecución. Cada paquete debe especificar entradas, preparación, parámetros, ejecución algorítmica, índices, diagnósticos, incertidumbre, sensibilidad, robustez, señales de fallo y artefactos de salida.
3. Universal validation pipeline
3. Pipeline universal de validación
- Receive the ESS requirement and selected MSS method.
- Recibir el requisito ESS y el método seleccionado en el MSS.
- Resolve the exact algorithmic variant and parameter space.
- Resolver la variante algorítmica exacta y el espacio de parámetros.
- Prepare the data using only transformations allowed by the ESS and MSS.
- Preparar los datos usando solamente transformaciones permitidas por ESS y MSS.
- Execute the primary method and all required companion procedures.
- Ejecutar el método principal y todos los procedimientos complementarios requeridos.
- Calculate native indices, effect measures, uncertainty, and diagnostics.
- Calcular índices nativos, medidas de efecto, incertidumbre y diagnósticos.
- Run sensitivity, robustness, resampling, and failure-detection procedures.
- Ejecutar sensibilidad, robustez, remuestreo y detección de fallos.
- Generate tables, plots, residual objects, logs, and machine-readable outputs.
- Generar tablas, gráficos, residuos, logs y salidas legibles por máquina.
- Assemble the Method Evidence Report without contextual acceptance decisions.
- Ensamblar el Method Evidence Report sin decisiones contextuales de aceptación.
4. Universal method execution specification
4. Especificación universal de ejecución del método
METHOD EXECUTION SPECIFICATION Case ID: ESS Evidence ID: MSS Method ID: Evidence Type: Scientific Question: Primary Method: Exact Algorithm / Variant: Software / Library / Version: Random Seed: Execution Environment: Input Variables: Target Variable: Unit of Analysis: Grouping Structure: Time Structure: Spatial Structure: Required Preprocessing: Excluded Transformations: Missing-Value Strategy: Scaling / Encoding: Feature Construction: Leakage Controls: Hyperparameters / Parameters: Search Space: Selection Rule: Stopping Rule: Required Companion Methods: Required Baseline: Required Resampling: Required Sensitivity Tests: Expected Output Objects:
5. Universal index architecture
5. Arquitectura universal de índices
Every method package must calculate indices in distinct families. The exact indices vary by method, but the families remain constant.
Cada paquete metodológico debe calcular índices en familias distintas. Los índices exactos varían por método, pero las familias permanecen constantes.
| Index familyFamilia de índices | PurposePropósito | ExamplesEjemplos |
|---|---|---|
| Primary estimateEstimado principal | The method’s central result.Resultado central del método. | Coefficient, correlation, odds ratio, forecast, effect, divergence, attribution. |
| MagnitudeMagnitud | How large the observed effect, error, dependence, or contribution is.Qué tan grande es el efecto, error, dependencia o contribución. | Effect size, R², Cramér’s V, distance correlation, SHAP magnitude. |
| UncertaintyIncertidumbre | How uncertain the estimate is.Qué tan incierto es el estimado. | Standard error, confidence interval, credible interval, bootstrap interval. |
| FitAjuste | How well the model reproduces or represents observed data.Qué tan bien reproduce o representa los datos. | Log-likelihood, deviance, RMSEA, CFI, residual fit. |
| GeneralizationGeneralización | How well performance transfers to unseen data.Qué tan bien se transfiere a datos no vistos. | MAE, RMSE, AUC, PR-AUC, log loss, out-of-time error. |
| CalibrationCalibración | Whether predicted probabilities or intervals match reality.Si probabilidades o intervalos corresponden con la realidad. | Brier score, calibration slope, coverage. |
| Residual diagnosticsDiagnósticos residuales | Whether unexplained structure remains.Si permanece estructura sin explicar. | Ljung–Box, residual Moran’s I, heteroscedasticity tests. |
| StabilityEstabilidad | Whether results persist under resampling or repeated execution.Si los resultados persisten bajo remuestreo o repetición. | Fold variance, seed variance, bootstrap stability, rank stability. |
| RobustnessRobustez | Whether conclusions survive plausible perturbations.Si las conclusiones sobreviven perturbaciones plausibles. | Noise sensitivity, missingness sensitivity, bandwidth sensitivity. |
| Computational profilePerfil computacional | Execution feasibility and reproducibility.Factibilidad y reproducibilidad. | Runtime, memory, convergence, iterations, GPU/CPU use. |
6. Universal diagnostics layer
6. Capa universal de diagnósticos
| Diagnostic areaÁrea diagnóstica | Required questionPregunta requerida |
|---|---|
| Input integrityIntegridad de entradas | Were the correct variables, rows, units, timestamps, and locations used?¿Se usaron variables, filas, unidades, tiempos y ubicaciones correctas? |
| Assumption diagnosticsDiagnósticos de supuestos | Which method assumptions are empirically checkable, and what did those checks show?¿Qué supuestos son comprobables y qué mostraron? |
| ConvergenceConvergencia | Did optimization, sampling, or estimation converge reliably?¿La optimización, muestreo o estimación convergió de forma fiable? |
| Residual structureEstructura residual | Does unexplained temporal, spatial, nonlinear, or distributional structure remain?¿Permanece estructura temporal, espacial, no lineal o distributiva sin explicar? |
| Outlier and influenceValores extremos e influencia | Are results driven by a few observations, regions, groups, or studies?¿Los resultados están dominados por pocas observaciones, regiones, grupos o estudios? |
| MultiplicityMultiplicidad | Were repeated tests, lags, variables, locations, or subgroups controlled?¿Se controlaron pruebas, rezagos, variables, ubicaciones o subgrupos múltiples? |
| SupportSoporte | Are estimates produced inside regions with sufficient data support?¿Los estimados se producen dentro de regiones con soporte suficiente? |
| LeakageFuga | Did future, target-derived, duplicate, or post-outcome information enter execution?¿Entró información futura, derivada del objetivo, duplicada o posterior? |
7. Sensitivity analysis protocol
7. Protocolo de análisis de sensibilidad
Sensitivity analysis determines how much the calculated evidence changes when defensible analytical choices change.
El análisis de sensibilidad determina cuánto cambia la evidencia calculada cuando cambian decisiones analíticas defendibles.
8. Robustness protocol
8. Protocolo de robustez
Robustness analysis evaluates whether the method evidence remains materially similar under plausible disturbances to the data or execution environment.
El análisis de robustez evalúa si la evidencia metodológica permanece materialmente similar bajo perturbaciones plausibles de los datos o del entorno de ejecución.
| Robustness challengeDesafío de robustez | Generic procedureProcedimiento genérico |
|---|---|
| NoiseRuido | Inject small controlled perturbations and recalculate core indices.Inyectar perturbaciones controladas y recalcular índices centrales. |
| MissingnessFaltantes | Compare approved missing-data strategies and missingness levels.Comparar estrategias aprobadas y niveles de faltantes. |
| Sample sizeTamaño muestral | Use learning curves, subsampling, or repeated reduced samples.Usar curvas de aprendizaje, submuestreo o muestras reducidas repetidas. |
| Class imbalanceDesbalance de clases | Evaluate prevalence shifts, class weighting, and threshold stability.Evaluar cambios de prevalencia, pesos y estabilidad de umbrales. |
| Distribution shiftCambio distributivo | Test performance across periods, sites, subgroups, or shifted feature distributions.Probar rendimiento entre periodos, sitios, subgrupos o distribuciones cambiadas. |
| RandomnessAleatoriedad | Repeat across seeds, folds, chains, or initialization states.Repetir entre semillas, folds, cadenas o inicializaciones. |
| ImplementationImplementación | Verify reproducibility across software versions or independent implementations when critical.Verificar reproducibilidad entre versiones o implementaciones independientes cuando sea crítico. |
9. Evidence-family validation registry
9. Registro de validación por familia de evidencia
| Evidence familyFamilia de evidencia | Typical primary indicesÍndices primarios típicos | Typical diagnosticsDiagnósticos típicos |
|---|---|---|
| AssociationAsociación | r, ρ, τ, Phi, Cramér’s V, distance correlation, MIC. | Linearity, monotonicity, ties, outliers, confidence intervals, permutation.Linealidad, monotonicidad, empates, extremos, intervalos y permutación. |
| DependenceDependencia | χ², exact p-value, mutual information, HSIC, distance covariance. | Expected counts, sparsity, kernel/bandwidth, permutation null, multiplicity.Conteos esperados, escasez, kernel/ancho, nulo por permutación y multiplicidad. |
| InformationInformación | Entropy, MI, information gain, KL, JSD, transfer entropy. | Estimator bias, support, log base, binning, surrogate tests, lag sensitivity.Sesgo del estimador, soporte, base log, bins, surrogates y rezagos. |
| TimeTiempo | ACF, CCF, forecast error, likelihood, state probabilities, DTW distance. | Stationarity, residual autocorrelation, rolling validation, interval coverage, lag stability.Estacionariedad, autocorrelación residual, validación rodante, cobertura y estabilidad. |
| SpaceEspacio | Moran’s I, Geary’s C, K/L functions, Gi*, spatial parameters, kriging error. | Weights sensitivity, edge correction, spatial cross-validation, residual spatial dependence.Sensibilidad a pesos, bordes, validación espacial y dependencia residual. |
| PredictionPredicción | MAE, RMSE, R², AUC, PR-AUC, F1, log loss, Brier, calibration. | Leakage, baseline comparison, fold stability, subgroup performance, drift.Fuga, línea base, estabilidad, subgrupos y drift. |
| ExplanationExplicación | SHAP values, local fidelity, PDP/ICE/ALE profiles, importance scores, rule fidelity. | Baseline sensitivity, correlation, support, seed stability, extrapolation.Sensibilidad a referencia, correlación, soporte, semillas y extrapolación. |
| CausalityCausalidad | Causal effect, first-stage statistics, pre-trends, cutoff effect, path coefficients. | Identification checks, placebo tests, falsification, sensitivity, weak instruments, bandwidth.Identificación, placebos, falsificación, sensibilidad, instrumentos débiles y ancho. |
| IntegrationIntegración | Posterior, ensemble gain, criteria score, pooled effect, I², τ², model weights. | Compatibility, heterogeneity, duplication, prior/weight sensitivity, influence analysis.Compatibilidad, heterogeneidad, duplicación, sensibilidad de pesos e influencia. |
10. Example: prediction method package
10. Ejemplo: paquete de método predictivo
EVIDENCE TYPE: PREDICTION PRIMARY METHOD: Random Forest CALCULATE - Accuracy - Precision - Recall / Sensitivity - Specificity - F1 - ROC-AUC - PR-AUC - Log Loss - Brier Score - Calibration Slope - Calibration Intercept - OOB Error - Confusion Matrix - Permutation Importance - Importance Stability DIAGNOSTICS - Leakage Check - Class Imbalance - Group / Time Split Validity - Calibration Curve - Learning Curve - Fold Variance - Seed Variance - Subgroup Performance - Drift Sensitivity REPORT - Values - Intervals - Fold Distribution - Plots - Runtime - Memory - Failure Flags DO NOT DECIDE HERE - Whether AUC is sufficient - Whether calibration is acceptable - Whether the model should be deployed
11. Example: temporal method package
11. Ejemplo: paquete de método temporal
EVIDENCE TYPE: TEMPORAL PRECEDENCE PRIMARY METHOD: Granger CALCULATE - Lag-Specific F Statistics - p-values - AIC - BIC - Residual Variance - Reverse-Direction Test - Forecast Improvement - Confidence Intervals DIAGNOSTICS - Event-Time Validation - Stationarity Checks - Lag Selection - Residual Autocorrelation - Ljung–Box - Stability Across Windows - Out-of-Time Validation - Common-Driver Sensitivity REPORT - Results by Lag - Direction X→Y - Direction Y→X - Stable Lag Set - Residual Diagnostics - Sensitivity Tables - Interpretation Boundary DO NOT DECIDE HERE - Whether precedence is causal - Whether one significant lag is sufficient - Whether the result supports intervention
12. Example: causal method package
12. Ejemplo: paquete de método causal
EVIDENCE TYPE: POLICY EFFECT PRIMARY METHOD: Difference in Differences CALCULATE - Treatment Effect - Standard Error - Confidence Interval - Event-Study Coefficients - Pre-Treatment Coefficients - Cluster-Robust Uncertainty - Subgroup Effects DIAGNOSTICS - Parallel-Trend Evidence - No-Anticipation Check - Spillover Review - Composition Stability - Placebo Dates - Placebo Outcomes - Alternative Control Groups - Alternative Time Windows REPORT - Main Effect - Event-Study Plot - Pre-Trend Table - Placebo Results - Sensitivity Results - Population Scope - Identification Assumptions DO NOT DECIDE HERE - Whether the causal claim is accepted - Whether the effect is practically important - Whether the policy should be adopted
13. Failure detection framework
13. Framework de detección de fallos
| Failure classClase de fallo | Generic signalSeñal genérica | Module III actionAcción del Módulo III |
|---|---|---|
| Execution failureFallo de ejecución | Algorithm does not converge or crashes.El algoritmo no converge o falla. | Retry approved variant; log failure; do not fabricate indices.Reintentar variante aprobada; registrar; no fabricar índices. |
| Input failureFallo de entrada | Wrong variable type, insufficient support, invalid order, or corrupted structure.Tipo incorrecto, soporte insuficiente, orden inválido o estructura dañada. | Return to MSS/ESS with explicit reason.Regresar a MSS/ESS con razón explícita. |
| Diagnostic failureFallo diagnóstico | Critical residual or assumption check fails.Falla un supuesto o diagnóstico crítico. | Calculate fallback or robust variant if preauthorized.Calcular variante robusta o fallback si estaba autorizada. |
| Instability failureFallo de inestabilidad | Large variation across folds, seeds, windows, priors, or weights.Gran variación entre folds, semillas, ventanas, priors o pesos. | Report instability distribution and flag for Module IV.Reportar distribución de inestabilidad y marcar para Módulo IV. |
| Support failureFallo de soporte | Estimates rely on sparse, extrapolated, or non-overlapping regions.Estimados dependen de regiones escasas, extrapoladas o sin solapamiento. | Restrict supported region and report coverage.Restringir región soportada y reportar cobertura. |
| Reproducibility failureFallo de reproducibilidad | Independent rerun does not reproduce material results.Una repetición independiente no reproduce resultados materiales. | Investigate seeds, versions, data lineage, and implementation.Investigar semillas, versiones, linaje e implementación. |
14. Method Evidence Report (MER)
14. Method Evidence Report (MER)
METHOD EVIDENCE REPORT Case ID: ESS Evidence ID: MSS Method ID: Execution ID: Timestamp: Software / Version: Data Snapshot ID: SCIENTIFIC CONFIGURATION Evidence Type: Scientific Question: Inputs: Target: Unit of Analysis: Temporal / Spatial / Group Structure: METHOD EXECUTION Primary Method: Exact Variant: Parameters: Preprocessing: Baseline: Companion Methods: Resampling: Sensitivity Plan: RESULTS Primary Estimate: Magnitude Indices: Uncertainty: Fit Indices: Generalization Indices: Calibration Indices: Residual Diagnostics: Stability Indices: Robustness Results: Computational Profile: ARTIFACTS Tables: Plots: Residual Objects: Model Object: Logs: Machine-Readable Output: FAILURE FLAGS Execution: Input: Diagnostics: Stability: Support: Reproducibility: INTERPRETATION BOUNDARY Allowed Interpretation: Prohibited Interpretation: MODULE IV HANDOFF Indices Ready: Diagnostics Ready: Sensitivity Ready: Robustness Ready: Decision Status: NOT EVALUATED IN MODULE III
15. Module III validation statuses
15. Estados de validación del Módulo III
| Status | MeaningSignificado |
|---|---|
| EXECUTED | The method ran and produced the required technical outputs.El método corrió y produjo las salidas técnicas requeridas. |
| EXECUTED WITH FLAGS | The method produced outputs, but diagnostics, support, or stability issues exist.El método produjo salidas, pero existen problemas diagnósticos, de soporte o estabilidad. |
| PARTIALLY EXECUTED | Some required indices or diagnostics could not be calculated.Algunos índices o diagnósticos no pudieron calcularse. |
| NOT EXECUTABLE | The selected method cannot run under the current data or specification.El método no puede ejecutarse con los datos o especificación actuales. |
| RETURN REQUIRED | The case must return to the MSS or ESS because a fundamental specification problem was found.El caso debe regresar al MSS o ESS por un problema fundamental de especificación. |
16. Generic workshop
16. Taller genérico
17. Final handoff contract to Module IV
17. Contrato final de entrega al Módulo IV
MODULE IV RECEIVES - What method was executed - Why it was selected - Exact configuration - Exact data used - All primary indices - All uncertainty measures - All diagnostics - All sensitivity results - All robustness results - All failure flags - All plots and tables - All interpretation boundaries - No hidden thresholds - No hidden exclusions - No pre-decided acceptance
Handbook closing
Cierre del manual
The Method Validation Handbook is the quantitative engine of Module III. It transforms a conceptual method choice into a reproducible execution, a complete set of indices, and a traceable Method Evidence Report. It does not decide whether the evidence is sufficient for the case. It ensures that Module IV receives everything required to make that decision transparently and consistently.
El Method Validation Handbook es el motor cuantitativo del Módulo III. Transforma una selección conceptual en ejecución reproducible, un conjunto completo de índices y un Method Evidence Report trazable. No decide si la evidencia es suficiente para el caso. Garantiza que el Módulo IV reciba todo lo necesario para decidir de forma transparente y consistente.