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2 changes: 1 addition & 1 deletion .nojekyll
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collate C.UTF-8
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date 2024-06-21
date 2024-06-24
pandoc 2.9.2.1 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.1)
digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.1)
cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.1)
digest 0.6.36 2024-06-23 [1] CRAN (R 4.4.1)
evaluate 0.24.0 2024-06-10 [1] CRAN (R 4.4.1)
fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.1)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.1)
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<div id="fig-governance-010-shared" class="quarto-figure quarto-figure-center quarto-float anchored" alt="N3C shared Governance initiatives with sign-off responsibility represented">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-governance-010-shared-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images/governance/fig-governance-010-shared.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1"><img src="images/governance/fig-governance-010-shared.png" class="img-fluid figure-img" alt="N3C shared Governance initiatives with sign-off responsibility represented"></a>
<a href="images/governance/fig-governance-010-shared.png" class="lightbox" data-glightbox="description: .lightbox-desc-1" data-gallery="quarto-lightbox-gallery-1"><img src="images/governance/fig-governance-010-shared.png" class="img-fluid figure-img" alt="N3C shared Governance initiatives with sign-off responsibility represented"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-governance-010-shared-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;4.1: N3C shared Governance initiatives with sign-off responsibility represented.
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<div id="fig-governance-020-tiers" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Data Tiers">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-governance-020-tiers-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images/governance/fig-governance-020-tiers.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" data-glightbox="description: .lightbox-desc-2"><img src="images/governance/fig-governance-020-tiers.png" class="img-fluid figure-img" alt="Data Tiers"></a>
<a href="images/governance/fig-governance-020-tiers.png" class="lightbox" data-glightbox="description: .lightbox-desc-2" data-gallery="quarto-lightbox-gallery-2"><img src="images/governance/fig-governance-020-tiers.png" class="img-fluid figure-img" alt="Data Tiers"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-governance-020-tiers-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;4.2: Data Tiers. Note that Level 1 data are deprecated.
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<div id="fig-governance-030-process" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Data Access Governance Process.">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-governance-030-process-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images//governance/fig-governance-030-process.png" class="lightbox" data-gallery="quarto-lightbox-gallery-3" data-glightbox="description: .lightbox-desc-3"><img src="images//governance/fig-governance-030-process.png" class="img-fluid figure-img" alt="Data Access Governance Process."></a>
<a href="images//governance/fig-governance-030-process.png" class="lightbox" data-glightbox="description: .lightbox-desc-3" data-gallery="quarto-lightbox-gallery-3"><img src="images//governance/fig-governance-030-process.png" class="img-fluid figure-img" alt="Data Access Governance Process."></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-governance-030-process-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;4.3: Data Access Governance Process. To lower the burden on participation, user authentication and eligibility are established once during account registration. Eligible users can then submit their Data Use Request for evaluation by the Data Access Committee. A new request must be submitted for each specific project.
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<script>var lightboxQuarto = GLightbox({"selector":".lightbox","closeEffect":"zoom","loop":false,"openEffect":"zoom","descPosition":"bottom"});
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Expand Up @@ -699,7 +699,7 @@ <h2 data-number="9.2" class="anchored" data-anchor-id="sec-practices-protocols">
<div id="fig-practices-010-research-lifecycle" class="quarto-figure quarto-figure-center quarto-float anchored" alt="The standard project-management life cycle">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-practices-010-research-lifecycle-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images/practices/fig-practices-010-research-lifecycle.png" class="lightbox" data-glightbox="description: .lightbox-desc-1" data-gallery="quarto-lightbox-gallery-1"><img src="images/practices/fig-practices-010-research-lifecycle.png" class="img-fluid figure-img" style="width:70.0%" alt="The standard project-management life cycle"></a>
<a href="images/practices/fig-practices-010-research-lifecycle.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1"><img src="images/practices/fig-practices-010-research-lifecycle.png" class="img-fluid figure-img" style="width:70.0%" alt="The standard project-management life cycle"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-practices-010-research-lifecycle-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;9.1: The standard project-management life cycle, applied to research, from project start (“Development”) to closure. Image from JHU <a href="https://www.hopkinsallchildrens.org/Academics/Research/Clinical-Research-Lifecycle">All Children’s Hospital</a>.
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<div id="fig-practices-015-protocol-pad" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Home page for a researcher's protocols">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-practices-015-protocol-pad-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images/practices/fig-practices-015-protocol-pad.png" class="lightbox" data-glightbox="description: .lightbox-desc-2" data-gallery="quarto-lightbox-gallery-2"><img src="images/practices/fig-practices-015-protocol-pad.png" class="img-fluid figure-img" alt="Home page for a researcher's protocols"></a>
<a href="images/practices/fig-practices-015-protocol-pad.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" data-glightbox="description: .lightbox-desc-2"><img src="images/practices/fig-practices-015-protocol-pad.png" class="img-fluid figure-img" alt="Home page for a researcher's protocols"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-practices-015-protocol-pad-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;9.2: Home page for a researcher’s protocols (<a href="https://unite.nih.gov/workspace/module/view/latest/ri.workshop.main.module.d7099409-b81d-4d17-951c-399b1b2f7c6f">Protocol Pad:RWE</a> <i class="fa-solid fa-lock" title="Link requires an N3C Data Enclave account" aria-label="lock"></i>). The Protocol Design, Development, and Completion sections are accessible on the left.
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<div id="fig-practices-020-site-bias" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Effect of site (data partner)">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-practices-020-site-bias-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images/practices/fig-practices-020-site-bias.png" class="lightbox" data-glightbox="description: .lightbox-desc-3" data-gallery="quarto-lightbox-gallery-3"><img src="images/practices/fig-practices-020-site-bias.png" class="img-fluid figure-img" alt="Effect of site (data partner)"></a>
<a href="images/practices/fig-practices-020-site-bias.png" class="lightbox" data-gallery="quarto-lightbox-gallery-3" data-glightbox="description: .lightbox-desc-3"><img src="images/practices/fig-practices-020-site-bias.png" class="img-fluid figure-img" alt="Effect of site (data partner)"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-practices-020-site-bias-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;9.3: Effect of site (data partner). (a) Standard relationship between Cause (independent variable) and Effect (dependent variable), allowing site as a potential covariate. (b) Recognizing that Site may have an impact on the Cause (for real or on its documentation), we see that Site is a confounder (shaded magenta) and must be addressed, for instance, by stratification.
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<div id="fig-practices-021-schneweiss-graphical-study-design" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Graphical study design for study with EHR-claims linked data">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-practices-021-schneweiss-graphical-study-design-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images/practices/fig-practices-021-schneweiss-graphical-study-design.png" class="lightbox" data-glightbox="description: .lightbox-desc-4" data-gallery="quarto-lightbox-gallery-4"><img src="images/practices/fig-practices-021-schneweiss-graphical-study-design.png" class="img-fluid figure-img" alt="Graphical study design for study with EHR-claims linked data"></a>
<a href="images/practices/fig-practices-021-schneweiss-graphical-study-design.png" class="lightbox" data-gallery="quarto-lightbox-gallery-4" data-glightbox="description: .lightbox-desc-4"><img src="images/practices/fig-practices-021-schneweiss-graphical-study-design.png" class="img-fluid figure-img" alt="Graphical study design for study with EHR-claims linked data"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-practices-021-schneweiss-graphical-study-design-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;9.4: Graphical study design for study with EHR-claims linked data. From the <a href="https://docs.google.com/viewer?url=https%3A%2F%2Fwww.repeatinitiative.org%2Fuploads%2F1%2F0%2F8%2F4%2F108495483%2Fdesign_templates_2022.pptx">Repeat Initiative</a>.
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<div id="fig-practices-022-building-block" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Relating data scientist's work to that of the analyst">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-practices-022-building-block-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images/practices/fig-practices-022-building-block.png" class="lightbox" data-glightbox="description: .lightbox-desc-5" data-gallery="quarto-lightbox-gallery-5"><img src="images/practices/fig-practices-022-building-block.png" class="img-fluid figure-img" alt="Relating data scientist's work to that of the analyst"></a>
<a href="images/practices/fig-practices-022-building-block.png" class="lightbox" data-gallery="quarto-lightbox-gallery-5" data-glightbox="description: .lightbox-desc-5"><img src="images/practices/fig-practices-022-building-block.png" class="img-fluid figure-img" alt="Relating data scientist's work to that of the analyst"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-practices-022-building-block-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;9.5: Relating data scientist’s work to that of the analyst.
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<div id="fig-practices-050-missing-data" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Possible sources of missing data">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-practices-050-missing-data-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images/practices/fig-practices-050-missing-data.gif" class="lightbox" data-glightbox="description: .lightbox-desc-6" data-gallery="quarto-lightbox-gallery-6"><img src="images/practices/fig-practices-050-missing-data.gif" class="img-fluid figure-img" alt="Possible sources of missing data"></a>
<a href="images/practices/fig-practices-050-missing-data.gif" class="lightbox" data-gallery="quarto-lightbox-gallery-6" data-glightbox="description: .lightbox-desc-6"><img src="images/practices/fig-practices-050-missing-data.gif" class="img-fluid figure-img" alt="Possible sources of missing data"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-practices-050-missing-data-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;9.6: Possible sources of missing data. Legend for icons is at the top of the figure (What…Mechanism…How Documented).
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<div id="fig-practices-060-collider-bias" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Collider bias in N3C">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-practices-060-collider-bias-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images/practices/fig-practices-060-collider-bias.png" class="lightbox" data-glightbox="description: .lightbox-desc-7" data-gallery="quarto-lightbox-gallery-7"><img src="images/practices/fig-practices-060-collider-bias.png" class="img-fluid figure-img" alt="Collider bias in N3C"></a>
<a href="images/practices/fig-practices-060-collider-bias.png" class="lightbox" data-gallery="quarto-lightbox-gallery-7" data-glightbox="description: .lightbox-desc-7"><img src="images/practices/fig-practices-060-collider-bias.png" class="img-fluid figure-img" alt="Collider bias in N3C"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-practices-060-collider-bias-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;9.7: Collider bias in N3C. (a) Assumes that each node is observed; no biases are induced. (b) “Conditioning” on coming to the hospital – i.e., having data in the EHR – induces bias (magenta arrows) in the relationship between COVID and its sequela.
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<div id="fig-practices-070-ohdsi-evidence-quality" class="quarto-figure quarto-figure-center quarto-float anchored" alt="OHDSI Scheme for Evidence Quality">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-practices-070-ohdsi-evidence-quality-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
<a href="images/practices/fig-practices-070-ohdsi-evidence-quality.png" class="lightbox" data-glightbox="description: .lightbox-desc-8" data-gallery="quarto-lightbox-gallery-8"><img src="images/practices/fig-practices-070-ohdsi-evidence-quality.png" class="img-fluid figure-img" alt="OHDSI Scheme for Evidence Quality"></a>
<a href="images/practices/fig-practices-070-ohdsi-evidence-quality.png" class="lightbox" data-gallery="quarto-lightbox-gallery-8" data-glightbox="description: .lightbox-desc-8"><img src="images/practices/fig-practices-070-ohdsi-evidence-quality.png" class="img-fluid figure-img" alt="OHDSI Scheme for Evidence Quality"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-practices-070-ohdsi-evidence-quality-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;9.8: OHDSI Scheme for Evidence Quality from the <a href="https://ohdsi.github.io/TheBookOfOhdsi/EvidenceQuality.html">Book of OHDSI</a>.
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