more additional intro chapters

oxford-pharmacoepi · Jan 7, 2025 · 14e7491 · 14e7491
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diff --git a/_book/adding_features.html b/_book/adding_features.html
diff --git a/_book/cdm_reference.html b/_book/cdm_reference.html
diff --git a/_book/comparing_cohorts.html b/_book/comparing_cohorts.html
@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>13&nbsp; Comparing cohorts – Tidy R programming with the OMOP common data model</title>
+<title>14&nbsp; Comparing cohorts – Tidy R programming with the OMOP common data model</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -80,7 +80,7 @@
       <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" role="button" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
-        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./data_analysis.html">Data analysis</a></li><li class="breadcrumb-item"><a href="./comparing_cohorts.html"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Comparing cohorts</span></a></li></ol></nav>
+        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./data_analysis.html">Data analysis</a></li><li class="breadcrumb-item"><a href="./comparing_cohorts.html"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Comparing cohorts</span></a></li></ol></nav>
         <a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
       <button type="button" class="btn quarto-search-button" aria-label="Search" onclick="window.quartoOpenSearch();">
@@ -114,7 +114,7 @@
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
             <a href="./intro.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Getting started</span></a>
+ <span class="menu-text">Getting started with working databases from R</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -123,19 +123,25 @@
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./working_with_databases_from_r.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Working with databases from R</span></span></a>
+ <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">A first analysis using data in a database</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./tidyverse_verbs.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Functions for analytic pipelines</span></span></a>
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Core verbs for analytic pipelines utilising a database</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./tidyverse_expressions.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Supported expressions</span></span></a>
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Supported expressions for database queries</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./r_data_models.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Database references in R</span></span></a>
   </div>
 </li>
       </ul>
@@ -152,25 +158,25 @@
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./cdm_reference.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Creating a cdm reference</span></span></a>
+ <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Creating a cdm reference</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./omop_person_obs_period.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Person and observation period tables</span></span></a>
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Person and observation period tables</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./omop_vocabularies.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Vocabulary tables</span></span></a>
+ <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Vocabulary tables</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./omop_clinical_tables.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Clinical tables</span></span></a>
+ <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Clinical tables</span></span></a>
   </div>
 </li>
       </ul>
@@ -187,37 +193,37 @@
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./exploring_the_cdm.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Exploring the OMOP CDM</span></span></a>
+ <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Exploring the OMOP CDM</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./creating_cohorts.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Adding cohorts to the CDM</span></span></a>
+ <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Adding cohorts to the CDM</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./adding_features.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Identifying patient characteristics</span></span></a>
+ <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Identifying patient characteristics</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./working_with_cohorts.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Working with cohorts</span></span></a>
+ <span class="menu-text"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Working with cohorts</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./summarising_cohorts.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Summarising cohorts</span></span></a>
+ <span class="menu-text"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Summarising cohorts</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./comparing_cohorts.html" class="sidebar-item-text sidebar-link active">
- <span class="menu-text"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Comparing cohorts</span></span></a>
+ <span class="menu-text"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Comparing cohorts</span></span></a>
   </div>
 </li>
       </ul>
@@ -233,9 +239,9 @@
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
-<header id="title-block-header" class="quarto-title-block default"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./data_analysis.html">Data analysis</a></li><li class="breadcrumb-item"><a href="./comparing_cohorts.html"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Comparing cohorts</span></a></li></ol></nav>
+<header id="title-block-header" class="quarto-title-block default"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./data_analysis.html">Data analysis</a></li><li class="breadcrumb-item"><a href="./comparing_cohorts.html"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Comparing cohorts</span></a></li></ol></nav>
 <div class="quarto-title">
-<h1 class="title"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Comparing cohorts</span></h1>
+<h1 class="title"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Comparing cohorts</span></h1>
 </div>
 
 
@@ -676,7 +682,7 @@ <h1 class="title"><span class="chapter-number">13</span>&nbsp; <span class="chap
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
       <a href="./summarising_cohorts.html" class="pagination-link" aria-label="Summarising cohorts">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Summarising cohorts</span></span>
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Summarising cohorts</span></span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">