Pre-fit Design-Support Diagnostics

Python-facing port of pre-fit-design-diagnostics.Rmd from the frozen R gp3bayes 0.5.0 reference. The statistical and governance framing below follows the canonical vignette; executable Python workflows use the mapped APIs listed later.

Diagnose the design before invoking Stan

Many modeling failures can be identified from the declared design itself. Version 0.2.0 adds four reporting audits that run before MCMC:

• audit_missingness_structure();
• audit_fixed_effect_design();
• audit_random_effects_support(); and
• audit_design_support().

They do not impute, exclude, drop predictors, or simplify random effects.

Missingness is described, not repaired

Fixed-effect geometry

The fixed-effects audit reports design-matrix rank, singular values, a condition-number screen, invariant columns, and leverage. These quantities are warning signals about the declared numerical design; they do not determine a scientifically preferred model.

Repetition, crossing and random slopes

One combined preflight

For binary models, a fixed-effects separation screen can also be requested when detectseparation is installed:

A review or fail flag is a prompt for methodological inspection. It is not an automatic instruction to remove data or alter the prespecified model.

Python API mapping

• gp3bayespy.audit_design_support
• gp3bayespy.audit_fixed_effect_design
• gp3bayespy.audit_missingness_structure
• gp3bayespy.audit_random_effects_support
• gp3bayespy.create_model_contract
• gp3bayespy.simulate_hierarchical_binary_data

Python usage

import gp3bayespy as gp

# All functions listed above are available from the package root.
# Use help(gp.<function>) or the API reference for the exact Python signature.

Visual companion

These figures complement the canonical ported narrative and are generated from package functions.

Design-support diagnostics. Deterministic visual companion generated from the Python package.

The figures remain descriptive evidence and do not create automatic inferential decisions.