Built site for gh-pages

.nojekyll

@@ -1 +1 @@
-38a16762
+fbf83b07

chapters/cycle.html

@@ -1507,7 +1507,7 @@ <h3 data-number="3.5.7" class="anchored" data-anchor-id="sec-cycle-enhancements-
 </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","selector":".lightbox","descPosition":"bottom","loop":false,"closeEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","selector":".lightbox","descPosition":"bottom","loop":false,"openEffect":"zoom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

chapters/governance.html

@@ -1157,7 +1157,7 @@ <h2 data-number="4.8" class="anchored" data-anchor-id="sec-governance-incident">
 </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","selector":".lightbox","loop":false,"descPosition":"bottom","closeEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","closeEffect":"zoom","selector":".lightbox","loop":false,"descPosition":"bottom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

chapters/intro.html

@@ -1184,7 +1184,7 @@ <h3 data-number="1.4.2" class="anchored" data-anchor-id="sec-intro-next-institut
 </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","selector":".lightbox","loop":false,"descPosition":"bottom","openEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","selector":".lightbox","closeEffect":"zoom","loop":false,"descPosition":"bottom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

chapters/ml.html

@@ -1562,7 +1562,7 @@ <h3 data-number="12.4.3" class="anchored" data-anchor-id="using-r-in-code-workbo
 </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","selector":".lightbox","openEffect":"zoom","loop":false,"closeEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"loop":false,"selector":".lightbox","descPosition":"bottom","openEffect":"zoom","closeEffect":"zoom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

chapters/onboarding.html

@@ -1469,7 +1469,7 @@ <h3 data-number="5.8.2" class="anchored" data-anchor-id="sec-onboarding-tools-sl
 </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"loop":false,"openEffect":"zoom","descPosition":"bottom","selector":".lightbox","closeEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"loop":false,"closeEffect":"zoom","selector":".lightbox","openEffect":"zoom","descPosition":"bottom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

chapters/practices.html

@@ -693,7 +693,7 @@ <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>.
@@ -747,7 +747,7 @@ <h3 data-number="9.2.1" class="anchored" data-anchor-id="sec-practices-protocols
 <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.
@@ -919,7 +919,7 @@ <h4 data-number="9.3.3.2" class="anchored" data-anchor-id="sec-practices-design-
 <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.
@@ -1026,7 +1026,7 @@ <h4 data-number="9.3.4.2" class="anchored" data-anchor-id="sec-practices-design-
 <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>.
@@ -1067,7 +1067,7 @@ <h4 data-number="9.4.2.2" class="anchored" data-anchor-id="sec-practices-develop
 <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.
@@ -1255,7 +1255,7 @@ <h4 data-number="9.4.4.2" class="anchored" data-anchor-id="sec-practices-develop
 <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).
@@ -1287,7 +1287,7 @@ <h4 data-number="9.4.5.4" class="anchored" data-anchor-id="sec-practices-develop
 <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.
@@ -1482,7 +1482,7 @@ <h3 data-number="9.5.3" class="anchored" data-anchor-id="sec-practices-completio
 <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>.
@@ -2283,7 +2283,7 @@ <h3 data-number="9.5.3" class="anchored" data-anchor-id="sec-practices-completio
 </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"selector":".lightbox","loop":false,"closeEffect":"zoom","descPosition":"bottom","openEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","descPosition":"bottom","selector":".lightbox","loop":false,"closeEffect":"zoom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

chapters/publishing.html

@@ -1475,7 +1475,7 @@ <h2 data-number="10.4" class="anchored" data-anchor-id="sec-publishing-ks"><span
 </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","closeEffect":"zoom","loop":false,"descPosition":"bottom","selector":".lightbox"});
+<script>var lightboxQuarto = GLightbox({"selector":".lightbox","descPosition":"bottom","closeEffect":"zoom","loop":false,"openEffect":"zoom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

chapters/story.html

@@ -547,7 +547,7 @@ <h2 id="toc-title">Table of contents</h2>
 <div id="fig-story-010-intro-to-story" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Path of a typical N3C project">
 <figure class="quarto-float quarto-float-fig figure">
 <div aria-describedby="fig-story-010-intro-to-story-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<a href="images/story/fig-story-010-intro-to-story.png" class="lightbox" data-glightbox="description: .lightbox-desc-1" data-gallery="quarto-lightbox-gallery-1"><img src="images/story/fig-story-010-intro-to-story.png" class="img-fluid figure-img" alt="Path of a typical N3C project"></a>
+<a href="images/story/fig-story-010-intro-to-story.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1"><img src="images/story/fig-story-010-intro-to-story.png" class="img-fluid figure-img" alt="Path of a typical N3C project"></a>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-story-010-intro-to-story-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Figure&nbsp;2.1: Path of a typical N3C project.
@@ -613,7 +613,7 @@ <h2 data-number="2.1" class="anchored" data-anchor-id="sec-story-onboarding"><sp
 <div id="fig-story-020-dur" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Submitted Data Use Request">
 <figure class="quarto-float quarto-float-fig figure">
 <div aria-describedby="fig-story-020-dur-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<a href="images/story/fig-story-020-dur.png" class="lightbox" data-glightbox="description: .lightbox-desc-2" data-gallery="quarto-lightbox-gallery-2"><img src="images/story/fig-story-020-dur.png" class="img-fluid figure-img" alt="Submitted Data Use Request"></a>
+<a href="images/story/fig-story-020-dur.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" data-glightbox="description: .lightbox-desc-2"><img src="images/story/fig-story-020-dur.png" class="img-fluid figure-img" alt="Submitted Data Use Request"></a>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-story-020-dur-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Figure&nbsp;2.2: Submitted Data Use Request.
@@ -648,7 +648,7 @@ <h2 data-number="2.2" class="anchored" data-anchor-id="sec-story-team"><span cla
 <div id="fig-story-030-team-formation" class="quarto-figure quarto-figure-center quarto-float anchored" alt="Typical N3C Team Composition">
 <figure class="quarto-float quarto-float-fig figure">
 <div aria-describedby="fig-story-030-team-formation-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<a href="images/story/fig-story-030-team-formation.png" class="lightbox" data-glightbox="description: .lightbox-desc-3" data-gallery="quarto-lightbox-gallery-3"><img src="images/story/fig-story-030-team-formation.png" class="img-fluid figure-img" alt="Typical N3C Team Composition"></a>
+<a href="images/story/fig-story-030-team-formation.png" class="lightbox" data-gallery="quarto-lightbox-gallery-3" data-glightbox="description: .lightbox-desc-3"><img src="images/story/fig-story-030-team-formation.png" class="img-fluid figure-img" alt="Typical N3C Team Composition"></a>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-story-030-team-formation-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Figure&nbsp;2.3: Typical N3C Team Composition.
@@ -1805,7 +1805,7 @@ <h2 data-number="2.8" class="anchored" data-anchor-id="sec-story-manuscript"><sp
 </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"selector":".lightbox","openEffect":"zoom","descPosition":"bottom","loop":false,"closeEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","descPosition":"bottom","selector":".lightbox","loop":false,"closeEffect":"zoom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;