Built site for gh-pages

gabrielodom · Dec 1, 2023 · c8cd561 · c8cd561
1 parent c5df826
commit c8cd561
Show file tree

Hide file tree

Showing 22 changed files with 330 additions and 85 deletions.
diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-5f6342b8
+6d2bbe37
diff --git a/about.html b/about.html
@@ -15,69 +15,6 @@
 div.column{display: inline-block; vertical-align: top; width: 50%;}
 div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
 ul.task-list{list-style: none;}
-pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
-pre > code.sourceCode > span:empty { height: 1.2em; }
-.sourceCode { overflow: visible; }
-code.sourceCode > span { color: inherit; text-decoration: inherit; }
-div.sourceCode { margin: 1em 0; }
-pre.sourceCode { margin: 0; }
-@media screen {
-div.sourceCode { overflow: auto; }
-}
-@media print {
-pre > code.sourceCode { white-space: pre-wrap; }
-pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
-}
-pre.numberSource code
-  { counter-reset: source-line 0; }
-pre.numberSource code > span
-  { position: relative; left: -4em; counter-increment: source-line; }
-pre.numberSource code > span > a:first-child::before
-  { content: counter(source-line);
-    position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; display: inline-block;
-    -webkit-touch-callout: none; -webkit-user-select: none;
-    -khtml-user-select: none; -moz-user-select: none;
-    -ms-user-select: none; user-select: none;
-    padding: 0 4px; width: 4em;
-    color: #aaaaaa;
-  }
-pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
-div.sourceCode
-  {   }
-@media screen {
-pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
-}
-code span.al { color: #ff0000; font-weight: bold; } /* Alert */
-code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
-code span.at { color: #7d9029; } /* Attribute */
-code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
-code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
-code span.ch { color: #4070a0; } /* Char */
-code span.cn { color: #880000; } /* Constant */
-code span.co { color: #60a0b0; font-style: italic; } /* Comment */
-code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
-code span.do { color: #ba2121; font-style: italic; } /* Documentation */
-code span.dt { color: #902000; } /* DataType */
-code span.dv { color: #40a070; } /* DecVal */
-code span.er { color: #ff0000; font-weight: bold; } /* Error */
-code span.ex { } /* Extension */
-code span.fl { color: #40a070; } /* Float */
-code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
-code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
-code span.kw { color: #007020; font-weight: bold; } /* Keyword */
-code span.op { color: #666666; } /* Operator */
-code span.ot { color: #007020; } /* Other */
-code span.pp { color: #bc7a00; } /* Preprocessor */
-code span.sc { color: #4070a0; } /* SpecialChar */
-code span.ss { color: #bb6688; } /* SpecialString */
-code span.st { color: #4070a0; } /* String */
-code span.va { color: #19177c; } /* Variable */
-code span.vs { color: #4070a0; } /* VerbatimString */
-code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
 
@@ -88,6 +25,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
+<link href="./lessons/lesson13_eda_w_tidyverse.html" rel="prev">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -266,13 +204,9 @@ <h1 class="title d-none d-lg-block">About</h1>
 
 </header>
 
-<p>About this site</p>
-<div class="cell">
-<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="dv">1</span> <span class="sc">+</span> <span class="dv">1</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-<div class="cell-output cell-output-stdout">
-<pre><code>[1] 2</code></pre>
-</div>
-</div>
+<p>Hi folks! I’m <a href="https://gabriel.quarto.pub/">Gabriel Odom</a>, and I hope that this material was helpful to you.</p>
+<p><strong>History of this material:</strong> I started writing the very first versions of these lessons back in spring of 2018 when I was a postdoc at the Sylvester Comprehensive Cancer Center. The Biostats/Bioinformatics group had weekly “research clinics” for the other postdocs and junior faculty to learn about various computational topics that could be helpful in their work. This material started off as four lessons (I can’t remember exactly what the topics were, but I think it was intro to R, <code>ggplot</code>, organizing work into scripts, and <code>dplyr</code>). The lessons were well received. That fall, I ended up teaching 9 weeks on R as part of “Survey of Statistical Computing” for the grad students in the school of medicine, and I also joined <a href="https://carpentries.org/index.html">The Carpentries</a> group at the University of Miami. After I joined Florida International University, I spent some time building out these lessons semester after semester (and with help and feedback from some awesome graduate students), and I taught this class every year. Now, I’m finally organizing and restructuring most of the lessons and scripts that I’ve worked on and taught from these past few years into a website to help my students have easy access to the material even after they finish class.</p>
+<p><strong>Motivation:</strong> My experiences teaching with The Carpentries, to medical school students, and to public health students gave me a lot of one-on-one time with high-performing people who did not come from math / computer science backgrounds. I want to present the material in a logical way to people with hardly any computing background, but who still want to learn the basics for their research. As my friend <a href="https://github.com/RaymondBalise">Prof.&nbsp;Raymond Balise</a> points out, we should assume students “can both point and click with a mouse”, and that’s about it. In that vein, if you come across parts of these lessons where I assume you know more than you do, please <a href="https://github.com/gabrielodom/PHC6701_r4ds/issues">leave an issue ticket</a> on the GitHub repository for this book (if you don’t know how to create a new issue, here’s a guide: <a href="https://www.techrepublic.com/article/how-to-create-github-issue/" class="uri">https://www.techrepublic.com/article/how-to-create-github-issue/</a>). I hope that this material is accessible to everyone.</p>
 
 
 
@@ -374,6 +308,15 @@ <h1 class="title d-none d-lg-block">About</h1>
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="./lessons/lesson13_eda_w_tidyverse.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Lesson 13: Exploring Data with the Tidyverse</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+  </div>
+</nav>
 </div> <!-- /content -->
 
 

diff --git a/index.html b/index.html
@@ -25,6 +25,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
+<link href="./lessons/lesson01_greater_data_science.html" rel="next">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -212,7 +213,7 @@ <h1 class="title d-none d-lg-block">PHC 6701: R for Data Science // Advanced R</
 
 <section id="about" class="level1">
 <h1>About</h1>
-<p>These are the written lecture materials for the class PHC 6701 (commonly known as “Advanced R”) at Florida International University’s Stempel College of Public Health.</p>
+<p>These are the written lecture materials for the class PHC 6701 (commonly known as “Advanced R”) at Florida International University’s Stempel College of Public Health. The source code and data sets for this book are available here: <a href="https://github.com/gabrielodom/PHC6701_r4ds" class="uri">https://github.com/gabrielodom/PHC6701_r4ds</a>.</p>
 </section>
 <section id="getting-started" class="level1">
 <h1>Getting Started</h1>
@@ -229,6 +230,7 @@ <h1>Getting Started</h1>
 </ul></li>
 <li>Setting up R/RStudio: <a href="https://derailment.netlify.app/2019-12-22-configuring-rstudio/" class="uri">https://derailment.netlify.app/2019-12-22-configuring-rstudio/</a></li>
 <li>If you want help, there is a great community of R programmers on Slack: <a href="https://rfordatasci.com/" class="uri">https://rfordatasci.com/</a>.</li>
+<li>Sign up for GitHub <strong>using your student email address</strong>: <a href="https://docs.github.com/en/get-started/quickstart/creating-an-account-on-github" class="uri">https://docs.github.com/en/get-started/quickstart/creating-an-account-on-github</a></li>
 </ul>
 
 
@@ -332,6 +334,15 @@ <h1>Getting Started</h1>
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="./lessons/lesson01_greater_data_science.html" class="pagination-link">
+        <span class="nav-page-text">Lesson 1: Overview of Data Science</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->
 
 

diff --git a/lessons/lesson01_greater_data_science.html b/lessons/lesson01_greater_data_science.html
@@ -90,6 +90,8 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
+<link href="../lessons/lesson02_introduction_to_R.html" rel="next">
+<link href="../index.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -598,6 +600,18 @@ <h3 class="anchored" data-anchor-id="our-very-first-r-code">Our Very First R Cod
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../index.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Home</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../lessons/lesson02_introduction_to_R.html" class="pagination-link">
+        <span class="nav-page-text">Lesson 2: Introduction to R</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->
 
 

diff --git a/lessons/lesson02_introduction_to_R.html b/lessons/lesson02_introduction_to_R.html
@@ -90,6 +90,8 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
+<link href="../lessons/lesson02s_scripts.html" rel="next">
+<link href="../lessons/lesson01_greater_data_science.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -844,6 +846,18 @@ <h1>Getting Help</h1>
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../lessons/lesson01_greater_data_science.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Lesson 1: Overview of Data Science</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../lessons/lesson02s_scripts.html" class="pagination-link">
+        <span class="nav-page-text">Lesson 2 Supplement: R Scripts</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->
 
 

diff --git a/lessons/lesson02s_scripts.html b/lessons/lesson02s_scripts.html
@@ -27,6 +27,8 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
+<link href="../lessons/lesson03_introduction_to_Quarto.html" rel="next">
+<link href="../lessons/lesson02_introduction_to_R.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -358,6 +360,18 @@ <h2 class="anchored" data-anchor-id="my-first-r-script">My First R Script</h2>
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../lessons/lesson02_introduction_to_R.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Lesson 2: Introduction to R</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../lessons/lesson03_introduction_to_Quarto.html" class="pagination-link">
+        <span class="nav-page-text">Lesson 3: Quarto for Reproducible Reports</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->
 
 

diff --git a/lessons/lesson03_introduction_to_Quarto.html b/lessons/lesson03_introduction_to_Quarto.html
@@ -27,6 +27,8 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
+<link href="../lessons/lesson04_ggplot.html" rel="next">
+<link href="../lessons/lesson02s_scripts.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -636,6 +638,18 @@ <h2 class="anchored" data-anchor-id="annotating-your-work">Annotating your Work<
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../lessons/lesson02s_scripts.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Lesson 2 Supplement: R Scripts</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../lessons/lesson04_ggplot.html" class="pagination-link">
+        <span class="nav-page-text">Lesson 4: ggplot and the Layered Grammar of Graphics</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->
 
 

diff --git a/lessons/lesson04_ggplot.html b/lessons/lesson04_ggplot.html
@@ -90,6 +90,8 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
+<link href="../lessons/lesson04s_examples.html" rel="next">
+<link href="../lessons/lesson03_introduction_to_Quarto.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -1051,6 +1053,18 @@ <h1>Online examples:</h1>
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../lessons/lesson03_introduction_to_Quarto.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Lesson 3: Quarto for Reproducible Reports</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../lessons/lesson04s_examples.html" class="pagination-link">
+        <span class="nav-page-text">Lesson 4 Supplement: ggplot Examples</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->
 
 

diff --git a/lessons/lesson04s_examples.html b/lessons/lesson04s_examples.html
@@ -90,6 +90,8 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
+<link href="../lessons/lesson05_RStudio_projects.html" rel="next">
+<link href="../lessons/lesson04_ggplot.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -1125,6 +1127,18 @@ <h2 class="anchored" data-anchor-id="editing-your-own-theme">Editing your own th
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../lessons/lesson04_ggplot.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Lesson 4: ggplot and the Layered Grammar of Graphics</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../lessons/lesson05_RStudio_projects.html" class="pagination-link">
+        <span class="nav-page-text">Lesson 5: RStudio Projects</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->
 
 

diff --git a/lessons/lesson05_RStudio_projects.html b/lessons/lesson05_RStudio_projects.html
@@ -90,6 +90,8 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
+<link href="../lessons/lesson06_atomic_vectors.html" rel="next">
+<link href="../lessons/lesson04s_examples.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -852,6 +854,18 @@ <h2 class="anchored" data-anchor-id="do-create-a-project">DO: Create a Project</
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../lessons/lesson04s_examples.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Lesson 4 Supplement: ggplot Examples</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../lessons/lesson06_atomic_vectors.html" class="pagination-link">
+        <span class="nav-page-text">Lesson 6: Atomic Vectors</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->
 
 

diff --git a/lessons/lesson06_atomic_vectors.html b/lessons/lesson06_atomic_vectors.html
@@ -90,6 +90,8 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
+<link href="../lessons/lesson07_lists_and_tibbles.html" rel="next">
+<link href="../lessons/lesson05_RStudio_projects.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -1277,6 +1279,18 @@ <h2 class="anchored" data-anchor-id="missing-values-in-non-atomic-vector-types">
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../lessons/lesson05_RStudio_projects.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Lesson 5: RStudio Projects</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../lessons/lesson07_lists_and_tibbles.html" class="pagination-link">
+        <span class="nav-page-text">Lesson 7: Lists and Tibbles</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->