Deploying to gh-pages from @ 32ccfb6 🚀

3mmaRand · Dec 4, 2023 · 6127018 · 6127018
1 parent 8713639
commit 6127018
Show file tree

Hide file tree

Showing 37 changed files with 169 additions and 131 deletions.
diff --git a/core/core.html b/core/core.html
@@ -341,7 +341,7 @@ <h1 class="title">Core Data Analysis</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 December, 2023</p>
+      <p class="date">4 December, 2023</p>
     </div>
   </div>
 

diff --git a/core/week-1/overview.html b/core/week-1/overview.html
@@ -337,7 +337,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 December, 2023</p>
+      <p class="date">4 December, 2023</p>
     </div>
   </div>
 

diff --git a/core/week-1/study_after_workshop.html b/core/week-1/study_after_workshop.html
@@ -337,7 +337,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 December, 2023</p>
+      <p class="date">4 December, 2023</p>
     </div>
   </div>
 

diff --git a/core/week-1/study_before_workshop.html b/core/week-1/study_before_workshop.html
@@ -330,7 +330,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 December, 2023</p>
+      <p class="date">4 December, 2023</p>
     </div>
   </div>
 

diff --git a/core/week-1/workshop.html b/core/week-1/workshop.html
@@ -390,7 +390,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 December, 2023</p>
+      <p class="date">4 December, 2023</p>
     </div>
   </div>
 

diff --git a/core/week-11/overview.html b/core/week-11/overview.html
@@ -337,7 +337,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 December, 2023</p>
+      <p class="date">4 December, 2023</p>
     </div>
   </div>
 
@@ -350,31 +350,27 @@ <h1 class="title">Overview</h1>
 <p>xxxxx</p>
 <section id="learning-objectives" class="level3">
 <h3 class="anchored" data-anchor-id="learning-objectives">Learning objectives</h3>
+<p>The successful student will be able to:</p>
 <ul>
-<li>dd</li>
-<li>dd.</li>
-<li>dd</li>
-<li>d</li>
+<li>explain what a research compendium is and describe its components</li>
+<li>relate the content and concepts in Core 1 and Core 2 to the research compendium</li>
+<li>Create a quarto document and:
+<ul>
+<li>appreciate the role of the YAML header</li>
+<li>format text as bold, italics, headings etc</li>
+<li>add citations and a bibliography</li>
+<li>create automatically numbered figures and tables with cross references in text</li>
+<li>set default code chunk behaviour and those for individual chunks</li>
+<li>use inline code to report results</li>
+<li>insert special characters and mathematical expressions with LaTeX</li>
+</ul></li>
 </ul>
 </section>
 <section id="instructions" class="level3">
 <h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
 <ol type="1">
-<li><p><a href="../../core/week-11/study_before_workshop.html">Prepare</a></p>
-<ol type="i">
-<li>📖 Read</li>
-</ol></li>
-<li><p><a href="../../core/week-11/workshop.html">Workshop</a></p>
-<ol type="i">
-<li><p>💻 dd.</p></li>
-<li><p>💻 ddd</p></li>
-<li><p>💻 ddd</p></li>
-</ol></li>
-<li><p><a href="../../core/week-11/study_after_workshop.html">Consolidate</a></p>
-<ol type="i">
-<li><p>💻 dd</p></li>
-<li><p>💻 dd</p></li>
-</ol></li>
+<li><p><a href="../../core/week-11/study_before_workshop.html">Prepare</a></p></li>
+<li><p><a href="../../core/week-11/workshop.html">Workshop</a></p></li>
 </ol>
 
 

diff --git a/core/week-11/study_after_workshop.html b/core/week-11/study_after_workshop.html
@@ -341,7 +341,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 December, 2023</p>
+      <p class="date">4 December, 2023</p>
     </div>
   </div>
 

diff --git a/core/week-11/study_before_workshop.html b/core/week-11/study_before_workshop.html
@@ -384,51 +384,55 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
 </div>
 </div>
 
-  <p class="date">3 December, 2023</p>
+  <p class="date">4 December, 2023</p>
 </section>
 <section id="module-assessment" class="slide level2">
 <h2>Module assessment</h2>
 <p>This module is assessed by:</p>
-<div>
 <ul>
-<li class="fragment"><p>Oral presentation 30%</p></li>
-<li class="fragment"><p>Project Report and Research Compendium 70% of which</p>
+<li><p>Oral presentation 30%</p></li>
+<li><p>Project Report and Research Compendium 70% of which</p>
 <ul>
-<li class="fragment">70% report (<em>i.e.</em>, 49% of the total mark)</li>
-<li class="fragment">30% compendium (<em>i.e.</em>, 21% of the total mark)</li>
+<li>70% report (<em>i.e.</em>, 49% of the total mark)</li>
+<li>30% compendium (<em>i.e.</em>, 21% of the total mark)</li>
 </ul></li>
 </ul>
 <p>These slides are a guide to Research compendium.</p>
-</div>
 </section>
 <section id="what-is-a-research-compendium" class="slide level2">
 <h2>What is a Research Compendium?</h2>
 <p><strong>Overview of assessment</strong></p>
+<div style="font-size: 60%;">
 <p><em>Stage 3 Integrated Masters students are expected to submit a Research Compendium that is a documented collection of all the digital parts of the research project including data (or access to data), code and outputs. The collection is organised and documented in such a way that reproducing all the results is straightforward for another individual.</em></p>
 <p><em>Students will be assessed on the technical complexity, completeness and organisation of their compendium and the completeness, reproducibility and clarity of their documentation at the project and code/process level. Marking will focus on the reproducibility of the results and the clarity of the decision making processes rather than the interpretation of the results which is covered in the report. There is no word or size limit for any part of the compendium but its contents should be concise and minimal. Extraneous text, code or files will be penalised.</em></p>
+</div>
 </section>
 <section id="what-is-a-research-compendium-1" class="slide level2">
 <h2>What is a Research Compendium?</h2>
 <p><strong>Overview of assessment</strong></p>
+<div style="font-size: 60%;">
 <p><em>Stage 3 Integrated Masters students are expected to submit a Research Compendium that is a <strong>documented collection of all the digital parts of the research project</strong> including data (or access to data), code and outputs. The collection is <strong>organised and documented in such a way that reproducing all the results is straightforward</strong> for another individual.</em></p>
 <p><em>Students will be assessed on the <strong>technical complexity, completeness and organisation of their compendium</strong> and the <strong>completeness, reproducibility and clarity of their documentation at the project and code/process level.</strong> Marking will focus on the reproducibility of the results and the clarity of the decision making processes rather than the interpretation of the results which is covered in the report. There is no word or size limit for any part of the compendium but its contents should be concise and minimal. Extraneous text, code or files will be penalised.</em></p>
+</div>
 </section>
 <section id="what-is-a-research-compendium-2" class="slide level2">
 <h2>What is a Research Compendium?</h2>
+<div style="font-size: 80%;">
 <div>
 <ul>
-<li class="fragment"><p>Zipped folder containing all data, code, and text associated with a research project organised and documented clearly. Any unscripted processing should be described.</p></li>
-<li class="fragment"><p>Everything needed to reproduce the results, and no more. The compendium should not be a dumping ground for data files and scripts. It needs to be curated. You may generate files that are not needed to reproduce your work and these should be removed.</p></li>
+<li class="fragment"><p>Zipped folder containing all data, code and text associated with a research project organised and documented clearly. Any unscripted processing should be described.</p></li>
+<li class="fragment"><p>Everything needed to understand what the project is and reproduce the results, and no more. The compendium should not be a dumping ground for data files and scripts. It needs to be curated. You may generate files that are not needed to reproduce your work and these should be removed.</p></li>
 <li class="fragment"><p>Your compendium might be a single Quarto/RStudio Project, or it might be folder including an RStudio Project and some additional materials including the description of unscripted processing.</p></li>
 <li class="fragment"><p>Ideally uses literate programming to create submitted report</p></li>
 </ul>
 </div>
+</div>
 </section>
 <section id="use-guidelines-from-core-1-and-2" class="slide level2">
 <h2>Use guidelines from Core 1 and 2</h2>
 <ul>
-<li><p>follow the guidance in <a href="https://3mmarand.github.io/BIO00088H-data/core/week-1/overview.html">Core 1</a> on organisation, naming things, and documentation</p></li>
-<li><p>follow the guidance in <a href="https://3mmarand.github.io/BIO00088H-data/core/week-2/overview.html">Core 2</a> well-formatted code, consistency, modularisation and documentation</p></li>
+<li><p>follow the guidance in <a href="https://3mmarand.github.io/BIO00088H-data/core/week-1/overview.html">Core 1</a> on organisation, naming things and documentation</p></li>
+<li><p>follow the guidance in <a href="https://3mmarand.github.io/BIO00088H-data/core/week-2/overview.html">Core 2</a> on well-formatted code, consistency, modularisation and documentation</p></li>
 </ul>
 </section>
 <section id="project-level-documentation" class="slide level2">
@@ -437,7 +441,7 @@ <h2>Project level documentation</h2>
 <ul>
 <li class="fragment"><p>as concise as possible, bullet points are good</p></li>
 <li class="fragment"><p>primarily in the README file but some details may be in scripts</p></li>
-<li class="fragment"><p>title, concise description of the work, date, overview of compendium contents</p></li>
+<li class="fragment"><p>title, concise description of the work, author exam number, date, overview of compendium contents</p></li>
 <li class="fragment"><p>all the software information including versions</p></li>
 <li class="fragment"><p>instructions needed to reproduce the work, order of workflow, settings/parameter values for software</p></li>
 </ul>

diff --git a/core/week-11/workshop.html b/core/week-11/workshop.html
@@ -18,6 +18,40 @@
   margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
   vertical-align: middle;
 }
+/* CSS for syntax highlighting */
+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;
+  }
+pre.numberSource { margin-left: 3em;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
 /* CSS for citations */
 div.csl-bib-body { }
 div.csl-entry {
@@ -343,7 +377,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 December, 2023</p>
+      <p class="date">4 December, 2023</p>
     </div>
   </div>
 
@@ -360,15 +394,19 @@ <h1 class="title">Workshop</h1>
 </ul></section><section id="session-overview" class="level2"><h2 class="anchored" data-anchor-id="session-overview">Session overview</h2>
 <p>In this workshop we will go through an example quarto document. You will learn:</p>
 <ul>
+<li>what the YAML header is</li>
 <li>formatting (bold, italics, headings)</li>
-<li>chunk options to control whether code and output are in the rendered document</li>
-<li>adding citations</li>
-<li>figures and tables with cross referencing and autonumberiung</li>
-<li>inline coding to report results</li>
-<li>special characters and equations</li>
+<li>to control default and individual chunk options</li>
+<li>how to add citations</li>
+<li>figures and tables with cross referencing and automatic numbering</li>
+<li>how to use inline coding to report results</li>
+<li>how to insert special characters and equations</li>
 </ul></section></section><section id="exercise" class="level1"><h1>Exercise</h1>
-<p>🎬 make a start on your compendium</p>
-<p>🎬 make a start on a quarto doc</p>
+<p>🎬 The example RStudio project containing this code here: <a href="https://github.com/3mmaRand/chaffinch">chaffinch</a>. You can download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the <code>destdir</code>:</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu">use_course</span><span class="op">(</span>url <span class="op">=</span> <span class="st">"3mmaRand/chaffinch"</span>, destdir <span class="op">=</span> <span class="st">"."</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<p>You can agree to deleting the zip. You should find RStudio restarts and you have a new project called chaffinch-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded. You can now run the code in the project.</p>
+<p>🎬 Make an outline of your compendium. This could be a sketch on paper or slide or from the mindmap software you usually use. Or it could be a skeleton of folders and files on your computer.</p>
+<p>🎬 Make a start on a quarto doc.</p>
 <p>You’re finished!</p>
 </section><section id="well-done" class="level1"><h1>🥳 Well Done! 🎉</h1>
 </section><section id="independent-study-following-the-workshop" class="level1"><h1>Independent study following the workshop</h1>

diff --git a/core/week-2/overview.html b/core/week-2/overview.html
@@ -328,7 +328,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 December, 2023</p>
+      <p class="date">4 December, 2023</p>
     </div>
   </div>
 

diff --git a/core/week-2/study_after_workshop.html b/core/week-2/study_after_workshop.html
@@ -328,7 +328,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 December, 2023</p>
+      <p class="date">4 December, 2023</p>
     </div>
   </div>
 

diff --git a/core/week-2/study_before_workshop.html b/core/week-2/study_before_workshop.html
@@ -444,7 +444,7 @@
 </div>
 </div>
 
-  <p class="date">3 December, 2023</p>
+  <p class="date">4 December, 2023</p>
 </section><section id="overview" class="slide level2"><h2>Overview</h2>
 <ul>
 <li>RStudio Projects revisited