SafetyGraphics · jwildfire · Apr 14, 2023
diff --git a/index.html b/index.html
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+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css">
+    <link rel="stylesheet" href="styles.css">
+    <title>Safety Graphics</title>
+</head>
+
+<body>
+    <header class="header-container py-2">
+        <div class="container">
+            <div class="d-flex justify-content-between align-items-center">
+                <h1 class="text-white">Interactive Safety Graphics</h1>
+                <img src="https://github.com/SafetyGraphics/safetyGraphics/blob/dev/inst/resources/safetyGraphicsHex.png?raw=true"
+                    alt="Safety Graphics Logo" class="header-logo">
+            </div>
+        </div>
+    </header>
+    <nav class="nav-container bg-light">
+        <div class="container">
+            <ul class="nav">
+                <li class="nav-item"><a class="nav-link" href="#overview">Overview</a></li>
+                <li class="nav-item"><a class="nav-link" href="#background">Background</a></li>
+                <li class="nav-item"><a class="nav-link" href="#safetygraphics-r-package">SafetyGraphics R Package</a>
+                </li>
+            </ul>
+        </div>
+    </nav>
+    <main class="container mt-4">
+<main>
+    <section id="overview">
+        <h2>Overview</h2>
+        <p>Welcome to the Interactive Safety Graphics home page. We make open source interactive graphics for monitoring
+            clinical trial safety. Check out a <a
+                href="https://safetygraphics.github.io/hep-explorer/test-page/example1">sample graphic</a> along with
+            its paired <a
+                href="https://github.com/SafetyGraphics/SafetyGraphics.github.io/raw/master/guide/HepExplorerWorkflow_v1_2_1.pdf">clinical
+                workflow</a> based on the medical literature, or explore your own data using the <a
+                href="#safetygraphics-r-package">safetyGraphics R package</a> shown below.</p>
+        <img src="https://user-images.githubusercontent.com/3680095/51296057-e3195380-19df-11e9-971a-430c3be930a4.gif"
+            alt="Safety Graphics Example">
+    </section>
+    <section id="background">
+        <h2>Background</h2>
+        <p>The Interactive Safety Graphics (ISG) subteam of the ASA Biopharm-DIA Safety Working Group is an
+            interdisciplinary effort that, amongst other things, seeks to provide a clinical safety workflow for
+            monitoring during clinical development in an open source model. For more details see:</p>
+        <ul>
+            <li><a href="about">About Page</a> - learn more about our team's motivation and see a full list of team
+                members</li>
+            <li><a href="roadmap">Road Map</a> - learn more about our active and planned projects</li>
+            <li><a href="https://github.com/SafetyGraphics/SafetyGraphics.github.io/blob/master/CONTRIBUTING.md">Contribution
+                    guidelines</a> - learn about how to contribute code to the project</li>
+        </ul>
+    </section>
+    <section id="safetygraphics-r-package">
+        <h2>SafetyGraphics R Package</h2>
+        <p>The safetyGraphics R package makes it easy for users to evaluate their own clinical trial safety data in R.
+            The package provides a simple workflow to load lab data from clinical trials (AdAM or SDTM preferred).</p>
+        <p>To learn more you can:</p>
+        <ul>
+            <li>See the package on <a href="https://cran.r-project.org/web/packages/safetyGraphics/index.html">CRAN</a>
+            </li>
+            <li>Download the <a
+                    href="https://github.com/SafetyGraphics/SafetyGraphics.github.io/raw/master/guide/HepExplorerWorkflow_v1_2_1.pdf">clinical
+                    workflow</a></li>
+            <li>Explore the <a href="https://github.com/SafetyGraphics/safetyGraphics">github repo</a> for the package,
+                or read through the package vignettes:
+                <ul>
+                    <li><a href="https://github.com/SafetyGraphics/SafetyGraphics/wiki/Intro">Intro to
+                            safetyGraphics</a> - Introductory vignette providing the overview of the package.</li>
+                    <li><a href="https://github.com/SafetyGraphics/SafetyGraphics/wiki/ChartConfiguration">Chart
+                            Configuration Vignette</a> - Details about the charting process including technical
+                        specifications and step-by-step instructions</li>
+                    <li><a href="https://github.com/SafetyGraphics/SafetyGraphics/wiki/Cookbook">Cookbook Vignette</a> -
+                        A series of examples showing how to initialize the safetyGraphics Shiny app in different
+                        scenarios
+                    </li>
+                </ul>
+            </li>
+        </ul>
+    </section>
+    </main>
+    <footer class="footer-container py-3">
+        <div class="container">
+            <div class="text-center">
+                <p>&copy; Interactive Safety Graphics - All rights reserved.</p>
+            </div>
+        </div>
+    </footer>
+</body>
+
+</html>
diff --git a/index_raw.html b/index_raw.html
@@ -0,0 +1,90 @@
+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <link rel="stylesheet" href="styles.css">
+    <title>Safety Graphics</title>
+</head>
+
+<body>
+<div class="header-container">
+    <header>
+        <h1>Interactive Safety Graphics</h1>
+    </header>
+    <img src="https://github.com/SafetyGraphics/safetyGraphics/blob/dev/inst/resources/safetyGraphicsHex.png?raw=true"
+        alt="Safety Graphics Logo" class="header-logo">
+</div>
+    <div class="nav-container">
+        <nav>
+            <ul>
+                <li><a href="#overview">Overview</a></li>
+                <li><a href="#background">Background</a></li>
+                <li><a href="#safetygraphics-r-package">SafetyGraphics R Package</a></li>
+            </ul>
+        </nav>
+    </div>
+
+
+<main>
+    <section id="overview">
+        <h2>Overview</h2>
+        <p>Welcome to the Interactive Safety Graphics home page. We make open source interactive graphics for monitoring
+            clinical trial safety. Check out a <a
+                href="https://safetygraphics.github.io/hep-explorer/test-page/example1">sample graphic</a> along with
+            its paired <a
+                href="https://github.com/SafetyGraphics/SafetyGraphics.github.io/raw/master/guide/HepExplorerWorkflow_v1_2_1.pdf">clinical
+                workflow</a> based on the medical literature, or explore your own data using the <a
+                href="#safetygraphics-r-package">safetyGraphics R package</a> shown below.</p>
+        <img src="https://user-images.githubusercontent.com/3680095/51296057-e3195380-19df-11e9-971a-430c3be930a4.gif"
+            alt="Safety Graphics Example">
+    </section>
+    <section id="background">
+        <h2>Background</h2>
+        <p>The Interactive Safety Graphics (ISG) subteam of the ASA Biopharm-DIA Safety Working Group is an
+            interdisciplinary effort that, amongst other things, seeks to provide a clinical safety workflow for
+            monitoring during clinical development in an open source model. For more details see:</p>
+        <ul>
+            <li><a href="about">About Page</a> - learn more about our team's motivation and see a full list of team
+                members</li>
+            <li><a href="roadmap">Road Map</a> - learn more about our active and planned projects</li>
+            <li><a href="https://github.com/SafetyGraphics/SafetyGraphics.github.io/blob/master/CONTRIBUTING.md">Contribution
+                    guidelines</a> - learn about how to contribute code to the project</li>
+        </ul>
+    </section>
+    <section id="safetygraphics-r-package">
+        <h2>SafetyGraphics R Package</h2>
+        <p>The safetyGraphics R package makes it easy for users to evaluate their own clinical trial safety data in R.
+            The package provides a simple workflow to load lab data from clinical trials (AdAM or SDTM preferred).</p>
+        <p>To learn more you can:</p>
+        <ul>
+            <li>See the package on <a href="https://cran.r-project.org/web/packages/safetyGraphics/index.html">CRAN</a>
+            </li>
+            <li>Download the <a
+                    href="https://github.com/SafetyGraphics/SafetyGraphics.github.io/raw/master/guide/HepExplorerWorkflow_v1_2_1.pdf">clinical
+                    workflow</a></li>
+            <li>Explore the <a href="https://github.com/SafetyGraphics/safetyGraphics">github repo</a> for the package,
+                or read through the package vignettes:
+                <ul>
+                    <li><a href="https://github.com/SafetyGraphics/SafetyGraphics/wiki/Intro">Intro to
+                            safetyGraphics</a> - Introductory vignette providing the overview of the package.</li>
+                    <li><a href="https://github.com/SafetyGraphics/SafetyGraphics/wiki/ChartConfiguration">Chart
+                            Configuration Vignette</a> - Details about the charting process including technical
+                        specifications and step-by-step instructions</li>
+                    <li><a href="https://github.com/SafetyGraphics/SafetyGraphics/wiki/Cookbook">Cookbook Vignette</a> -
+                        A series of examples showing how to initialize the safetyGraphics Shiny app in different
+                        scenarios
+                    </li>
+                </ul>
+            </li>
+        </ul>
+    </section>
+</main>
+
+
+
+    <!-- footer... -->
+</body>
+
+</html>
diff --git a/.gitignore → old/.gitignore b/.gitignore → old/.gitignore
diff --git a/CONTRIBUTING.md → old/CONTRIBUTING.md b/CONTRIBUTING.md → old/CONTRIBUTING.md
diff --git a/...xplorer User's Manual & Workflow v1.0.pdf → ...xplorer User's Manual & Workflow v1.0.pdf b/...xplorer User's Manual & Workflow v1.0.pdf → ...xplorer User's Manual & Workflow v1.0.pdf
diff --git a/LICENSE → old/LICENSE b/LICENSE → old/LICENSE
diff --git a/README.md → old/README.md b/README.md → old/README.md
diff --git a/_config.yml → old/_config.yml b/_config.yml → old/_config.yml
diff --git a/about.md → old/about.md b/about.md → old/about.md
diff --git a/guide/HepExplorerWorkflow_v1_0.pdf → old/guide/HepExplorerWorkflow_v1_0.pdf b/guide/HepExplorerWorkflow_v1_0.pdf → old/guide/HepExplorerWorkflow_v1_0.pdf
diff --git a/guide/HepExplorerWorkflow_v1_1.pdf → old/guide/HepExplorerWorkflow_v1_1.pdf b/guide/HepExplorerWorkflow_v1_1.pdf → old/guide/HepExplorerWorkflow_v1_1.pdf
diff --git a/guide/HepExplorerWorkflow_v1_2.pdf → old/guide/HepExplorerWorkflow_v1_2.pdf b/guide/HepExplorerWorkflow_v1_2.pdf → old/guide/HepExplorerWorkflow_v1_2.pdf
diff --git a/guide/HepExplorerWorkflow_v1_2_1.pdf → old/guide/HepExplorerWorkflow_v1_2_1.pdf b/guide/HepExplorerWorkflow_v1_2_1.pdf → old/guide/HepExplorerWorkflow_v1_2_1.pdf
diff --git a/pilot/SampleData_NoStandard.csv → old/pilot/SampleData_NoStandard.csv b/pilot/SampleData_NoStandard.csv → old/pilot/SampleData_NoStandard.csv
diff --git a/pilot/SampleData_PartialADaM.csv → old/pilot/SampleData_PartialADaM.csv b/pilot/SampleData_PartialADaM.csv → old/pilot/SampleData_PartialADaM.csv
diff --git a/pilot/SampleData_PartialSDTM.csv → old/pilot/SampleData_PartialSDTM.csv b/pilot/SampleData_PartialSDTM.csv → old/pilot/SampleData_PartialSDTM.csv
diff --git a/pilot/SampleData_SDTM.csv → old/pilot/SampleData_SDTM.csv b/pilot/SampleData_SDTM.csv → old/pilot/SampleData_SDTM.csv
diff --git a/pilot/introEmail.md → old/pilot/introEmail.md b/pilot/introEmail.md → old/pilot/introEmail.md
diff --git a/pilot/testerGuide.md → old/pilot/testerGuide.md b/pilot/testerGuide.md → old/pilot/testerGuide.md
diff --git a/presentations/SafetyGraphics_RPharma2020.pdf → ...sentations/SafetyGraphics_RPharma2020.pdf b/presentations/SafetyGraphics_RPharma2020.pdf → ...sentations/SafetyGraphics_RPharma2020.pdf
diff --git a/presentations/TechIntro.pdf → old/presentations/TechIntro.pdf b/presentations/TechIntro.pdf → old/presentations/TechIntro.pdf
diff --git a/roadmap.md → old/roadmap.md b/roadmap.md → old/roadmap.md
diff --git a/training/ex.csv → old/training/ex.csv b/training/ex.csv → old/training/ex.csv
diff --git a/training/index.css → old/training/index.css b/training/index.css → old/training/index.css
diff --git a/training/index.html → old/training/index.html b/training/index.html → old/training/index.html
diff --git a/training/index.js → old/training/index.js b/training/index.js → old/training/index.js
diff --git a/styles.css b/styles.css
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+.header-container {
+    background-color: #4CAF50;
+}
+
+.nav-container .nav-link {
+    color: #333;
+}
+
+.nav-container .nav-link:hover {
+    color: #4CAF50;
+    text-decoration: none;
+}
+
+.header-logo {
+    width: 100px;
+    padding: 10px;
+}
+
+.footer-container {
+    background-color: #f8f9fa;
+    border-top: 1px solid #e5e5e5;
+}
diff --git a/styles_raw.css b/styles_raw.css
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+body {
+    font-family: Arial, sans-serif;
+    line-height: 1.6;
+    margin: 0;
+    padding: 0;
+    color: #333;
+}
+
+header {
+    background: #4CAF50;
+    padding: 20px;
+}
+
+header h1 {
+    color: #fff;
+    margin: 0;
+}
+
+nav {
+    display: flex;
+    justify-content: space-around;
+    background: #333;
+    padding: 15px 0;
+}
+
+nav ul {
+    list-style: none;
+    padding: 0;
+}
+
+nav ul li {
+    display: inline;
+    margin-left: 10px;
+}
+
+nav ul li a {
+    text-decoration: none;
+    color: #fff;
+    font-weight: bold;
+}
+
+main {
+    padding: 20px;
+}
+
+main h2 {
+    border-bottom: 1px solid #ccc;
+    padding-bottom: 10px;
+}
+
+section {
+    margin-bottom: 20px;
+}
+
+footer {
+    background: #4CAF50;
+    padding: 20px;
+    text-align: center;
+    color: #fff;
+}
+
+@media (max-width: 768px) {
+    nav {
+        flex-direction: column;
+        align-items: center;
+    }
+
+    nav ul li {
+        display: block;
+        margin-bottom: 5px;
+    }
+}
+
+/* header stuff */
+.header-container {
+    background-color: #4CAF50;
+    display: flex;
+    justify-content: space-between;
+    align-items: center;
+}
+
+.header-logo {
+    width: 70px;
+    padding: 10px;
+}