Add PCNtoolkit conformance and held-out validation

[bbuchsbaum]

Summary

• Pin PCNtoolkit 1.3.0 fixtures and classify exact, converted, matched-estimator, same-estimand, and non-equivalent comparisons.
• Make mgcv fit status, model selection, calibration estimands, and held-out assessment fail closed.
• Bind cross-fit, calibration, longitudinal, frozen-bundle, HBR, and site-transfer behavior to explicit provenance and uncertainty contracts; refuse RDS deserialization unless the caller explicitly acknowledges a trusted source.
• Add a five-scenario replicated PCNtoolkit matrix, HBR/site-transfer receipts, post-hoc NHANES development evidence, and a separately frozen untouched NHANES confirmation.
• Correct the public candidate install/status wording, support denominators, site-strategy count, frozen-bundle privacy and hash claims, and clipped diagnostic plots.

Local validation

• devtools::test(stop_on_failure = TRUE): 1,233 passed, 0 failed, 0 skipped. The two recorded warnings are environment-version warnings.
• Built referent_0.1.0.tar.gz with all six vignettes, then ran R CMD check --as-cran --no-manual: 0 errors, 0 warnings, 1 expected New submission note.
• Installed-package Starlight generation rendered all six articles; post-processing, the Astro static build, and the fail-closed checker verified 37 advertised routes by file, H1 identity, canonical URL, redirect state, and image alt text.
• README quickstart output was reproduced with explicit support counts and an assessment denominator tied to finite held-out scores.
• Local, tracking, and live branch SHA: b1080373fe22fec3f424d0eb025a3c8405f8a1cd.

Scientific gate outcomes

• Replicated PCN matrix: linear Gaussian, nonlinear heteroskedastic, unequal-site, and covariate-shift scenarios are equivalent within the registered margins.
• Skew-heavy: all 20 Referent and comparator fits are valid with no critical comparator warnings. Referent's held-out log-score contrast is 0.396069 (95% replicate-bootstrap interval 0.378490 to 0.412005), calibration guardrails pass, and the registered classification is superior. The seed block and result entered version control together, so this is not described as independently preregistered.
• HBR/site transport: both HBR stages have zero divergences, maximum R-hat 1.00, and minimum bulk/tail ESS above 1,700. Every site passes separately. Observed-site-only prior selection chose the Referent adaptation priors; independent site 5 has 90% coverage 0.9067, MACE 0.0267, mean Z 0.0563, and variance Z 1.051.
• NHANES 2017-2018 is explicitly labeled post-hoc model-development evidence because its earlier failure informed the demographic scale terms before the same cohort was re-evaluated. The separately frozen 2013-2014 cohort is the untouched confirmation; all marginal, tail, shape, and conditional gates pass. Neither lane is a survey-weighted national-prevalence estimate.
• HBR and site receipts bind every retained CSV by SHA-256, row count, and schema. Validation independently recomputes row identities, divergence counts, R-hat/ESS summaries, prediction summaries, prior selection, and all per-site gates rather than trusting receipt booleans.

Release decision

The scoped registered evidence now passes, and the source is prepared as a 0.1.0 release candidate. This does not establish blanket equivalence or dominance over PCNtoolkit: estimator-divergent lanes remain labeled non-equivalent, the skew-heavy claim is limited to its named release matrix, and the NHANES confirmation is limited to the declared unweighted cross-cycle transport contract. Until this PR is merged and a release is tagged, installation and documentation should remain PR-qualified.

[cursor]

Stale comment

Approved. Cursor Security Agent completed with no findings that need human review, and Cursor Bugbot was not running on this PR. No reviewers were assigned.

  

_{Sent by Cursor Approval Agent: Pull Request Router and Approver}

[chatgpt-codex-connector]

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Dismissed the prior approval because Cursor Security Agent did not finish within the wait window, so this head no longer qualifies. Cursor Bugbot was not running on this PR. Human review is needed; no reviewers were assigned because the only recent editor is the pull request author.

[cursor]

Stale comment

Approved. Cursor Security Agent completed with no findings that need human review, and Cursor Bugbot was not running on this PR. No reviewers were assigned.

  

_{Sent by Cursor Approval Agent: Pull Request Router and Approver}

Dismissed the prior approval because Cursor Security Agent: Security Reviewer was still pending after 8 minutes. Cursor Bugbot was not running on this PR. No reviewers were assigned.

[cursor]

Stale comment

Security review of this PR found one high-confidence issue in the new ref_read() interchange path. GitHub Actions and the rest of the statistical/validation surface did not introduce additional reportable issues.

  

_{Sent by Cursor Security Agent: Security Reviewer}

[cursor]

Stale comment

Approved. Cursor Security Agent completed with no findings that need human review, and Cursor Bugbot was not running on this PR. No reviewers were assigned.

  

_{Sent by Cursor Approval Agent: Pull Request Router and Approver}

Dismissed the prior approval because Cursor Security Agent: Security Reviewer was still pending after the wait window on the current head. Cursor Bugbot was not running. No reviewers were assigned.

[cursor]

Approved. Cursor Security Agent completed with no findings that need human review, and Cursor Bugbot was not running on this PR. No reviewers were assigned.

  

_{Sent by Cursor Approval Agent: Pull Request Router and Approver}