From b3bcc3a56aa78bff4b6022c1b1e50ffacb152f2c Mon Sep 17 00:00:00 2001
From: 3mmaRand <7593411+3mmaRand@users.noreply.github.com>
Date: Thu, 31 Aug 2023 13:57:12 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=203mmaRand?=
 =?UTF-8?q?/BIO00088H-data@624bf409c32870f83ac916b9342ea6eef1186ac2=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 core/core.html                         |  68 ++-
 core/week-1/overview.html              |  20 +-
 core/week-1/study_after_workshop.html  |  16 +-
 core/week-1/study_before_workshop.html |  16 +-
 core/week-1/workshop.html              |  47 +-
 core/week-2/overview.html              | 572 ++++++++++++++++++++++
 core/week-2/study_after_workshop.html  | 587 +++++++++++++++++++++++
 core/week-2/study_before_workshop.html | 545 +++++++++++++++++++++
 core/week-2/workshop.html              | 636 +++++++++++++++++++++++++
 core/week-6/overview.html              | 572 ++++++++++++++++++++++
 core/week-6/study_after_workshop.html  | 587 +++++++++++++++++++++++
 core/week-6/study_before_workshop.html | 545 +++++++++++++++++++++
 core/week-6/workshop.html              | 636 +++++++++++++++++++++++++
 search.json                            | 103 +++-
 14 files changed, 4844 insertions(+), 106 deletions(-)
 create mode 100644 core/week-2/overview.html
 create mode 100644 core/week-2/study_after_workshop.html
 create mode 100644 core/week-2/study_before_workshop.html
 create mode 100644 core/week-2/workshop.html
 create mode 100644 core/week-6/overview.html
 create mode 100644 core/week-6/study_after_workshop.html
 create mode 100644 core/week-6/study_before_workshop.html
 create mode 100644 core/week-6/workshop.html

diff --git a/core/core.html b/core/core.html
index efb4bd6..b1327b0 100644
--- a/core/core.html
+++ b/core/core.html
@@ -173,25 +173,25 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-2/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-2/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-2/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-2/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
@@ -209,25 +209,25 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-6/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-6/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-6/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-6/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
@@ -245,9 +245,9 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#content" id="toc-content" class="nav-link active" data-scroll-target="#content">Content</a>
   <ul class="collapse">
-  <li><a href="#core-1" id="toc-core-1" class="nav-link" data-scroll-target="#core-1">Core 1</a></li>
-  <li><a href="#core-2" id="toc-core-2" class="nav-link" data-scroll-target="#core-2">Core 2</a></li>
-  <li><a href="#core-3-quarto" id="toc-core-3-quarto" class="nav-link" data-scroll-target="#core-3-quarto">Core 3: Quarto</a></li>
+  <li><a href="#week-1-core-1-organising-reproducible-data-analyses" id="toc-week-1-core-1-organising-reproducible-data-analyses" class="nav-link" data-scroll-target="#week-1-core-1-organising-reproducible-data-analyses">Week 1 Core 1 Organising Reproducible Data Analyses</a></li>
+  <li><a href="#week-2-core-2-needs-a-title" id="toc-week-2-core-2-needs-a-title" class="nav-link" data-scroll-target="#week-2-core-2-needs-a-title">Week 2 Core 2 NEEDS A TITLE</a></li>
+  <li><a href="#week-6-core-3-reproducible-reporting" id="toc-week-6-core-3-reproducible-reporting" class="nav-link" data-scroll-target="#week-6-core-3-reproducible-reporting">Week 6 Core 3 Reproducible Reporting</a></li>
   </ul></li>
   </ul>
 </nav>
@@ -274,32 +274,50 @@ <h1 class="title">Core Data Analysis for Group Project</h1>
 
 <section id="content" class="level1">
 <h1>Content</h1>
-<section id="core-1" class="level2">
-<h2 class="anchored" data-anchor-id="core-1">Core 1</h2>
-<p>Note no R coding (too early for 70M)</p>
+<p>Overview You are either an integrated masters student doing 88H Group Project or a MSc Bioinformatics student doing 70M</p>
+<section id="week-1-core-1-organising-reproducible-data-analyses" class="level2">
+<h2 class="anchored" data-anchor-id="week-1-core-1-organising-reproducible-data-analyses">Week 1 Core 1 Organising Reproducible Data Analyses</h2>
+<p>Note no R coding (too early for MSc BIN 70M who share the core and omics teaching)</p>
+<p>Before - Optional revision: What they forgot to teach you about computers: operating systems, file systems, file types, working directories and paths</p>
+<ul>
+<li>Why reproducibility (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown)</li>
+</ul>
+<p>Workshop</p>
 <ul>
 <li>Project organisation: folders, files</li>
 <li>Project oriented workflow</li>
-<li>Readme</li>
 <li>Naming things</li>
-<li>Keeping notes</li>
-<li>Data management, google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6</li>
-<li>file formats</li>
-<li>Introduction to data in general. Similarities and differences
+<li>File formats</li>
+<li>Data management
+<ul>
+<li>google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6</li>
+<li>documenting</li>
+<li>organisation within files</li>
+</ul></li>
+<li>Data files. Similarities and differences
 <ul>
 <li>Sequences data</li>
 <li>Image data</li>
 <li>Structure data.</li>
 </ul></li>
+<li>Keeping notes</li>
+<li>Readme</li>
+<li>Reference managers: Zotero</li>
 </ul>
+<p>After</p>
 </section>
-<section id="core-2" class="level2">
-<h2 class="anchored" data-anchor-id="core-2">Core 2</h2>
-<p>rgetgretger</p>
+<section id="week-2-core-2-needs-a-title" class="level2">
+<h2 class="anchored" data-anchor-id="week-2-core-2-needs-a-title">Week 2 Core 2 NEEDS A TITLE</h2>
+<p>Before Possibly: Code formatting and style, 😎 Cool code Tips, Code ‘algorithmically.’, Writing functions (R and python??) (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown)</p>
+<p>Workshop</p>
+<p>After</p>
 </section>
-<section id="core-3-quarto" class="level2">
-<h2 class="anchored" data-anchor-id="core-3-quarto">Core 3: Quarto</h2>
-<p>fgzzdfghdfhg</p>
+<section id="week-6-core-3-reproducible-reporting" class="level2">
+<h2 class="anchored" data-anchor-id="week-6-core-3-reproducible-reporting">Week 6 Core 3 Reproducible Reporting</h2>
+<p>Before (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown and BIO00058M-Data-science-2020/slides/04_advanced_rmarkdown.html) Literate programming What is quarto markdown basics: text, code chunks, headings yaml automatic numbering of figures and tables cross references special characters citations</p>
+<p>Workshop</p>
+<p>practice doing the above with your project and data</p>
+<p>After</p>
 
 
 </section>
diff --git a/core/week-1/overview.html b/core/week-1/overview.html
index 0c5fad4..0afd139 100644
--- a/core/week-1/overview.html
+++ b/core/week-1/overview.html
@@ -173,25 +173,25 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
@@ -209,25 +209,25 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
@@ -245,7 +245,7 @@
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
 <h1 class="title">Overview</h1>
-<p class="subtitle lead">Core 1</p>
+<p class="subtitle lead">Core 1: Organising Data Analyses</p>
 </div>
 
 
@@ -275,7 +275,7 @@ <h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
 <ol type="1">
 <li><p><a href="../../core/week-1/study_before_workshop.html">Prepare</a></p>
 <ol type="i">
-<li>📖 Read ddd</li>
+<li>📖 Read <a href="https://3mmarand.github.io/comp4biosci/what_they_forgot.html">What they forgot to teach you about computers</a></li>
 </ol></li>
 <li><p><a href="../../core/week-1/workshop.html">Workshop</a></p>
 <ol type="i">
diff --git a/core/week-1/study_after_workshop.html b/core/week-1/study_after_workshop.html
index e538f7a..0f461a9 100644
--- a/core/week-1/study_after_workshop.html
+++ b/core/week-1/study_after_workshop.html
@@ -207,25 +207,25 @@
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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
@@ -243,25 +243,25 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
diff --git a/core/week-1/study_before_workshop.html b/core/week-1/study_before_workshop.html
index b913a5b..88377d4 100644
--- a/core/week-1/study_before_workshop.html
+++ b/core/week-1/study_before_workshop.html
@@ -173,25 +173,25 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
@@ -209,25 +209,25 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
diff --git a/core/week-1/workshop.html b/core/week-1/workshop.html
index 2837838..c304172 100644
--- a/core/week-1/workshop.html
+++ b/core/week-1/workshop.html
@@ -192,25 +192,25 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
@@ -228,25 +228,25 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
@@ -265,7 +265,6 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#introduction" id="toc-introduction" class="nav-link active" data-scroll-target="#introduction">Introduction</a>
   <ul class="collapse">
   <li><a href="#session-overview" id="toc-session-overview" class="nav-link" data-scroll-target="#session-overview">Session overview</a></li>
-  <li><a href="#philosophy" id="toc-philosophy" class="nav-link" data-scroll-target="#philosophy">Philosophy</a></li>
   </ul></li>
   <li><a href="#getting-started" id="toc-getting-started" class="nav-link" data-scroll-target="#getting-started">Getting started</a></li>
   <li><a href="#exercises" id="toc-exercises" class="nav-link" data-scroll-target="#exercises">Exercises</a></li>
@@ -282,7 +281,7 @@ <h2 id="toc-title">On this page</h2>
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
 <h1 class="title">Workshop</h1>
-<p class="subtitle lead">xxx</p>
+<p class="subtitle lead">Organising Reproducible Data Analyses</p>
 </div>
 
 
@@ -301,19 +300,7 @@ <h1 class="title">Workshop</h1>
 <h1>Introduction</h1>
 <section id="session-overview" class="level2">
 <h2 class="anchored" data-anchor-id="session-overview">Session overview</h2>
-<p>In this workshop you will learn to summarise and plot datasets with more than one variable and how to write figures to files. You will also get more practice with working directories, importing data, formatting figures and the pipe.</p>
-</section>
-<section id="philosophy" class="level2">
-<h2 class="anchored" data-anchor-id="philosophy">Philosophy</h2>
-<p>Workshops are not a test. It is expected that you often don’t know how to start, make a lot of mistakes and need help. It is expected that you are familiar with independent study content before the workshop. However, you need not remember or understand every detail as the workshop should build and consolidate your understanding. Tips</p>
-<ul>
-<li>don’t worry about making mistakes</li>
-<li>don’t let what you can not do interfere with what you can do</li>
-<li>discussing code with your neighbours will help</li>
-<li>look things up in the independent study material</li>
-<li>look things up in your own code from earlier workshops</li>
-<li>there are no stupid questions</li>
-</ul>
+<p>In this workshop you will</p>
 <div class="callout callout-style-default callout-note callout-titled">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">
@@ -324,24 +311,17 @@ <h2 class="anchored" data-anchor-id="philosophy">Philosophy</h2>
 </div>
 </div>
 <div class="callout-body-container callout-body">
-<p>These four symbols are used at the beginning of each instruction so you know where to carry out the instruction.</p>
-<p><img src="images/do_on_your_computer.png" class="img-fluid"> Something you need to do on your computer. It may be opening programs or documents or locating a file.</p>
-<p><img src="images/do_in_R.png" class="img-fluid"> Something you should do in RStudio. It will often be typing a command or using the menus but might also be creating folders, locating or moving files.</p>
-<p><img src="images/do_on_internet.png" class="img-fluid"> Something you should do in your browser on the internet. It may be searching for information, going to the VLE or downloading a file.</p>
-<p><img src="images/answer.png" class="img-fluid"> A question for you to think about and answer. Record your answers in your script for future reference.</p>
+
 </div>
 </div>
 </section>
 </section>
 <section id="getting-started" class="level1">
 <h1>Getting started</h1>
-<p>Start RStudio make an RStudio project for this workshop.</p>
-<p>Make a new folder called <code>data-raw</code>.</p>
-<p>Make a new script then save it to carry out the rest of the work.</p>
-<p>Add code to load the <strong><code>tidyverse</code></strong> package <span class="citation" data-cites="tidyverse">(<a href="#ref-tidyverse" role="doc-biblioref">Wickham et al. 2019</a>)</span></p>
 </section>
 <section id="exercises" class="level1">
 <h1>Exercises</h1>
+<p>🎬 - Project organisation: folders, files - Project oriented workflow - Naming things - File formats - Data management - google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6 - documenting - organisation within files - Data files. Similarities and differences - Sequences data - Image data - Structure data. - Keeping notes - Readme - Reference managers: Zotero</p>
 <p>You’re finished!</p>
 </section>
 <section id="well-done" class="level1">
@@ -371,9 +351,6 @@ <h1>The Code file</h1>
 <div id="ref-R-core" class="csl-entry" role="listitem">
 R Core Team. 2023. <em>R: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org/">https://www.R-project.org/</a>.
 </div>
-<div id="ref-tidyverse" class="csl-entry" role="listitem">
-Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. <span>“Welcome to the <span></span>Tidyverse<span></span>”</span> 4: 1686. <a href="https://doi.org/10.21105/joss.01686">https://doi.org/10.21105/joss.01686</a>.
-</div>
 <div id="ref-knitr" class="csl-entry" role="listitem">
 Xie, Yihui. 2022. <span>“Knitr: A General-Purpose Package for Dynamic Report Generation in r.”</span> <a href="https://yihui.org/knitr/">https://yihui.org/knitr/</a>.
 </div>
diff --git a/core/week-2/overview.html b/core/week-2/overview.html
new file mode 100644
index 0000000..2bc0bc2
--- /dev/null
+++ b/core/week-2/overview.html
@@ -0,0 +1,572 @@
+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
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+
+
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+
+    
+  
+    
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+<h3 class="anchored" data-anchor-id="learning-objectives">Learning objectives</h3>
+<ul>
+<li>dd</li>
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+<li><p><a href="../../core/week-2/study_after_workshop.html">Consolidate</a></p>
+<ol type="i">
+<li><p>💻 dd</p></li>
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new file mode 100644
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+ <span class="menu-text">Prepare!</span></a>
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+ <span class="menu-text">Workshop</span></a>
+  </div>
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+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link active">
+ <span class="menu-text">Consolidate!</span></a>
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+ <span class="menu-text">Week 6: Quarto</span></a>
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+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
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+ <span class="menu-text">About</span></a>
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+<header id="title-block-header" class="quarto-title-block default">
+<div class="quarto-title">
+<h1 class="title">Independent Study to consolidate this week</h1>
+<p class="subtitle lead">Core 2</p>
+</div>
+
+
+
+<div class="quarto-title-meta">
+
+    
+  
+    
+  </div>
+  
+
+</header>
+
+<section id="set-up" class="level1">
+<h1>Set up</h1>
+<p>If you have just opened RStudio you will want to load the packages and import the data.</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="fu">library</span>(tidyverse)</span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(readxl)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+</div>
+<ol type="1">
+<li>💻 xx.</li>
+</ol>
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+    <div class="nav-footer-left"><code>r cffr::cff_to_bibtex("CITATION.cff")</code></div>   
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+</body></html>
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diff --git a/core/week-2/study_before_workshop.html b/core/week-2/study_before_workshop.html
new file mode 100644
index 0000000..5c40f9f
--- /dev/null
+++ b/core/week-2/study_before_workshop.html
@@ -0,0 +1,545 @@
+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
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+
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+<div id="quarto-search-results"></div>
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+    <nav class="navbar navbar-expand-lg navbar-dark ">
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+      <div class="navbar-brand-container">
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+            <div id="quarto-search" class="" title="Search"></div>
+          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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+          <div class="collapse navbar-collapse" id="navbarCollapse">
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+            <div class="quarto-navbar-tools ms-auto">
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+          </div> <!-- /navcollapse -->
+      </div> <!-- /container-fluid -->
+    </nav>
+  <nav class="quarto-secondary-nav">
+    <div class="container-fluid d-flex">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../core/week-2/overview.html">Week 2: xxx</a></li><li class="breadcrumb-item"><a href="../../core/week-2/study_before_workshop.html">Prepare!</a></li></ol></nav>
+      <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
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+  <div class="sidebar-item-container"> 
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+ <span class="menu-text">Core Data Analysis for Group Project</span></a>
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+        <li class="px-0"><hr class="sidebar-divider hi "></li>
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+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true">
+ <span class="menu-text">Week 1: xxx</span></a>
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+      <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
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+  <div class="sidebar-item-container"> 
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+          <li class="sidebar-item">
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+ <span class="menu-text">Prepare!</span></a>
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+  <div class="sidebar-item-container"> 
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+ <span class="menu-text">Week 2: xxx</span></a>
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+          </a> 
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+      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
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+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
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+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Week 6: Quarto</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
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+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
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+          <li class="sidebar-item">
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+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
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+  <div class="sidebar-item-container"> 
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+ <span class="menu-text">Consolidate!</span></a>
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+<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
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+<h1 class="title">Independent Study to prepare for workshop</h1>
+<p class="subtitle lead">Core 2</p>
+</div>
+
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+      const unselectCodeLines = () => {
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+  var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
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+    const citeInfo = findCites(ref);
+    if (citeInfo) {
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+          citeDiv.classList.add('csl-entry');
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+            citeDiv.innerHTML = biblioDiv.innerHTML;
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+          popup.appendChild(citeDiv);
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+        return popup.innerHTML;
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+  }
+    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+      var filterRegex = new RegExp("^(?:http:|https:)\/\/3mmarand\.github\.io\/BIO00088H-data");
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+    for (var i=0; i<links.length; i++) {
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+          // target, if specified
+          link.setAttribute("target", "_blank");
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+    }
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+</script>
+</div> <!-- /content -->
+<footer class="footer">
+  <div class="nav-footer">
+    <div class="nav-footer-left"><code>r cffr::cff_to_bibtex("CITATION.cff")</code></div>   
+    <div class="nav-footer-center">
+      &nbsp;
+    </div>
+    <div class="nav-footer-right">
+      <ul class="footer-items list-unstyled">
+    <li class="nav-item compact">
+    <a class="nav-link" href="https://twitter.com/er_13">
+      <i class="bi bi-twitter" role="img" aria-label="Twitter">
+</i> 
+    </a>
+  </li>  
+    <li class="nav-item compact">
+    <a class="nav-link" href="https://github.com/3mmaRand/BIO00088H-data">
+      <i class="bi bi-github" role="img" aria-label="BIO00088H-data GitHub">
+</i> 
+    </a>
+  </li>  
+</ul>
+    </div>
+  </div>
+</footer>
+
+
+
+</body></html>
\ No newline at end of file
diff --git a/core/week-2/workshop.html b/core/week-2/workshop.html
new file mode 100644
index 0000000..3eb4c59
--- /dev/null
+++ b/core/week-2/workshop.html
@@ -0,0 +1,636 @@
+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
+
+<meta charset="utf-8">
+<meta name="generator" content="quarto-1.3.450">
+
+<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
+
+<meta name="author" content="Emma Rand">
+
+<title>Data Analysis for Group Project - Workshop</title>
+<style>
+code{white-space: pre-wrap;}
+span.smallcaps{font-variant: small-caps;}
+div.columns{display: flex; gap: min(4vw, 1.5em);}
+div.column{flex: auto; overflow-x: auto;}
+div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+ul.task-list{list-style: none;}
+ul.task-list li input[type="checkbox"] {
+  width: 0.8em;
+  margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
+  vertical-align: middle;
+}
+/* CSS for citations */
+div.csl-bib-body { }
+div.csl-entry {
+  clear: both;
+}
+.hanging-indent div.csl-entry {
+  margin-left:2em;
+  text-indent:-2em;
+}
+div.csl-left-margin {
+  min-width:2em;
+  float:left;
+}
+div.csl-right-inline {
+  margin-left:2em;
+  padding-left:1em;
+}
+div.csl-indent {
+  margin-left: 2em;
+}</style>
+
+
+<script src="../../site_libs/quarto-nav/quarto-nav.js"></script>
+<script src="../../site_libs/quarto-nav/headroom.min.js"></script>
+<script src="../../site_libs/clipboard/clipboard.min.js"></script>
+<script src="../../site_libs/quarto-search/autocomplete.umd.js"></script>
+<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="../../">
+<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>
+<script src="../../site_libs/quarto-html/anchor.min.js"></script>
+<link href="../../site_libs/quarto-html/tippy.css" rel="stylesheet">
+<link href="../../site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
+<script src="../../site_libs/bootstrap/bootstrap.min.js"></script>
+<link href="../../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
+<link href="../../site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
+<script id="quarto-search-options" type="application/json">{
+  "location": "navbar",
+  "copy-button": false,
+  "collapse-after": 3,
+  "panel-placement": "end",
+  "type": "overlay",
+  "limit": 20,
+  "language": {
+    "search-no-results-text": "No results",
+    "search-matching-documents-text": "matching documents",
+    "search-copy-link-title": "Copy link to search",
+    "search-hide-matches-text": "Hide additional matches",
+    "search-more-match-text": "more match in this document",
+    "search-more-matches-text": "more matches in this document",
+    "search-clear-button-title": "Clear",
+    "search-detached-cancel-button-title": "Cancel",
+    "search-submit-button-title": "Submit",
+    "search-label": "Search"
+  }
+}</script>
+
+
+</head>
+
+<body class="nav-sidebar floating nav-fixed">
+
+<div id="quarto-search-results"></div>
+  <header id="quarto-header" class="headroom fixed-top">
+    <nav class="navbar navbar-expand-lg navbar-dark ">
+      <div class="navbar-container container-fluid">
+      <div class="navbar-brand-container">
+    <a class="navbar-brand" href="../../index.html">
+    <span class="navbar-title">Data Analysis for Group Project</span>
+    </a>
+  </div>
+            <div id="quarto-search" class="" title="Search"></div>
+          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+  <span class="navbar-toggler-icon"></span>
+</button>
+          <div class="collapse navbar-collapse" id="navbarCollapse">
+            <ul class="navbar-nav navbar-nav-scroll me-auto">
+  <li class="nav-item">
+    <a class="nav-link" href="../../index.html" rel="" target="">
+ <span class="menu-text">Welcome!</span></a>
+  </li>  
+  <li class="nav-item">
+    <a class="nav-link active" href="../../core/core.html" rel="" target="" aria-current="page">
+ <span class="menu-text">Core</span></a>
+  </li>  
+  <li class="nav-item">
+    <a class="nav-link" href="../../omics/omics.html" rel="" target="">
+ <span class="menu-text">Omics</span></a>
+  </li>  
+</ul>
+            <div class="quarto-navbar-tools ms-auto">
+    <a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
+    <a href="https://github.com/3mmaRand/BIO00088H-data" rel="" title="BIO00088H-data GitHub" class="quarto-navigation-tool px-1" aria-label="BIO00088H-data GitHub"><i class="bi bi-github"></i></a>
+</div>
+          </div> <!-- /navcollapse -->
+      </div> <!-- /container-fluid -->
+    </nav>
+  <nav class="quarto-secondary-nav">
+    <div class="container-fluid d-flex">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" 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="../../core/week-2/overview.html">Week 2: xxx</a></li><li class="breadcrumb-item"><a href="../../core/week-2/workshop.html">Workshop</a></li></ol></nav>
+      <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+      </a>
+    </div>
+  </nav>
+</header>
+<!-- content -->
+<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
+<!-- sidebar -->
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+    <div class="sidebar-menu-container"> 
+    <ul class="list-unstyled mt-1">
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/core.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Core Data Analysis for Group Project</span></a>
+  </div>
+</li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true">
+ <span class="menu-text">Week 1: xxx</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
+ <span class="menu-text">Week 2: xxx</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link active">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Week 6: Quarto</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+    </ul>
+    </div>
+</nav>
+<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<!-- margin-sidebar -->
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+        <nav id="TOC" role="doc-toc" class="toc-active">
+    <h2 id="toc-title">On this page</h2>
+   
+  <ul>
+  <li><a href="#introduction" id="toc-introduction" class="nav-link active" data-scroll-target="#introduction">Introduction</a>
+  <ul class="collapse">
+  <li><a href="#session-overview" id="toc-session-overview" class="nav-link" data-scroll-target="#session-overview">Session overview</a></li>
+  </ul></li>
+  <li><a href="#getting-started" id="toc-getting-started" class="nav-link" data-scroll-target="#getting-started">Getting started</a></li>
+  <li><a href="#exercises" id="toc-exercises" class="nav-link" data-scroll-target="#exercises">Exercises</a></li>
+  <li><a href="#well-done" id="toc-well-done" class="nav-link" data-scroll-target="#well-done">🥳 Well Done! 🎉</a></li>
+  <li><a href="#independent-study-following-the-workshop" id="toc-independent-study-following-the-workshop" class="nav-link" data-scroll-target="#independent-study-following-the-workshop">Independent study following the workshop</a></li>
+  <li><a href="#the-code-file" id="toc-the-code-file" class="nav-link" data-scroll-target="#the-code-file">The Code file</a></li>
+  <li><a href="#references" id="toc-references" class="nav-link" data-scroll-target="#references">References</a></li>
+  </ul>
+</nav>
+    </div>
+<!-- main -->
+<main class="content" id="quarto-document-content">
+
+<header id="title-block-header" class="quarto-title-block default">
+<div class="quarto-title">
+<h1 class="title">Workshop</h1>
+<p class="subtitle lead">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</p>
+</div>
+
+
+
+<div class="quarto-title-meta">
+
+    
+  
+    
+  </div>
+  
+
+</header>
+
+<section id="introduction" class="level1">
+<h1>Introduction</h1>
+<section id="session-overview" class="level2">
+<h2 class="anchored" data-anchor-id="session-overview">Session overview</h2>
+<p>In this workshop you will</p>
+<div class="callout callout-style-default callout-note callout-titled">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+Key
+</div>
+</div>
+<div class="callout-body-container callout-body">
+
+</div>
+</div>
+</section>
+</section>
+<section id="getting-started" class="level1">
+<h1>Getting started</h1>
+</section>
+<section id="exercises" class="level1">
+<h1>Exercises</h1>
+<p>🎬</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>
+<p><a href="../../core/week-2/study_after_workshop.html">Consolidate</a></p>
+</section>
+<section id="the-code-file" class="level1">
+<h1>The Code file</h1>
+<p>These contain all the code needed in the workshop even where it is not visible on the webpage.</p>
+<p>The <a href="../../core/week-2/workshop.html">workshop.qmd</a> file is the file I use to compile the practical. Qmd stands for Quarto markdown. It allows code and ordinary text to be interleaved to produce well-formatted reports including webpages. Right-click on the link and choose Save-As to download. You will be able to open the Qmd file in RStudio. Alternatively, <a href="https://github.com/3mmaRand/">View in Browser</a>. Coding and thinking answers are marked with <code>#---CODING ANSWER---</code> and <code>#---THINKING ANSWER---</code></p>
+<p>Pages made with R <span class="citation" data-cites="R-core">(<a href="#ref-R-core" role="doc-biblioref">R Core Team 2023</a>)</span>, Quarto <span class="citation" data-cites="allaire2022">(<a href="#ref-allaire2022" role="doc-biblioref">Allaire et al. 2022</a>)</span>, <code>knitr</code> <span class="citation" data-cites="knitr">(<a href="#ref-knitr" role="doc-biblioref">Xie 2022</a>)</span>, <code>kableExtra</code> <span class="citation" data-cites="kableExtra">(<a href="#ref-kableExtra" role="doc-biblioref">Zhu 2021</a>)</span></p>
+</section>
+<section id="references" class="level1">
+
+
+
+
+</section>
+
+<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" role="doc-bibliography"><h2 class="anchored quarto-appendix-heading">References</h2><div id="refs" class="references csl-bib-body hanging-indent" role="list">
+<div id="ref-allaire2022" class="csl-entry" role="listitem">
+Allaire, J. J., Charles Teague, Carlos Scheidegger, Yihui Xie, and Christophe Dervieux. 2022. <em>Quarto</em>. <a href="https://doi.org/10.5281/zenodo.5960048">https://doi.org/10.5281/zenodo.5960048</a>.
+</div>
+<div id="ref-R-core" class="csl-entry" role="listitem">
+R Core Team. 2023. <em>R: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org/">https://www.R-project.org/</a>.
+</div>
+<div id="ref-knitr" class="csl-entry" role="listitem">
+Xie, Yihui. 2022. <span>“Knitr: A General-Purpose Package for Dynamic Report Generation in r.”</span> <a href="https://yihui.org/knitr/">https://yihui.org/knitr/</a>.
+</div>
+<div id="ref-kableExtra" class="csl-entry" role="listitem">
+Zhu, Hao. 2021. <span>“kableExtra: Construct Complex Table with ’Kable’ and Pipe Syntax.”</span> <a href="https://CRAN.R-project.org/package=kableExtra">https://CRAN.R-project.org/package=kableExtra</a>.
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diff --git a/core/week-6/overview.html b/core/week-6/overview.html
new file mode 100644
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+
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+<style>
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+ <span class="menu-text">Core Data Analysis for Group Project</span></a>
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+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true">
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+  <div class="sidebar-item-container"> 
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+ <span class="menu-text">Prepare!</span></a>
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+</li>
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+ <span class="menu-text">Week 6: Quarto</span></a>
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+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
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+</li>
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+
+
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+
+    
+  
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+  
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+<section id="learning-objectives" class="level3">
+<h3 class="anchored" data-anchor-id="learning-objectives">Learning objectives</h3>
+<ul>
+<li>dd</li>
+<li>dd.</li>
+<li>dd</li>
+<li>d</li>
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+</section>
+<section id="instructions" class="level3">
+<h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
+<ol type="1">
+<li><p><a href="../../core/week-6/study_before_workshop.html">Prepare</a></p>
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+<li><p>💻 ddd</p></li>
+<li><p>💻 ddd</p></li>
+</ol></li>
+<li><p><a href="../../core/week-6/study_after_workshop.html">Consolidate</a></p>
+<ol type="i">
+<li><p>💻 dd</p></li>
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diff --git a/core/week-6/study_after_workshop.html b/core/week-6/study_after_workshop.html
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+<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
+<!-- sidebar -->
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+    <div class="sidebar-menu-container"> 
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+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/core.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Core Data Analysis for Group Project</span></a>
+  </div>
+</li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true">
+ <span class="menu-text">Week 1: xxx</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
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+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
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+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
+ <span class="menu-text">Week 2: xxx</span></a>
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+  <a href="../../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
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+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Week 6: Quarto</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link active">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+    </ul>
+    </div>
+</nav>
+<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<!-- margin-sidebar -->
+    
+<!-- main -->
+<main class="content" id="quarto-document-content">
+
+<header id="title-block-header" class="quarto-title-block default">
+<div class="quarto-title">
+<h1 class="title">Independent Study to consolidate this week</h1>
+<p class="subtitle lead">Core 3 Reproducible Reporting</p>
+</div>
+
+
+
+<div class="quarto-title-meta">
+
+    
+  
+    
+  </div>
+  
+
+</header>
+
+<section id="set-up" class="level1">
+<h1>Set up</h1>
+<p>If you have just opened RStudio you will want to load the packages and import the data.</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="fu">library</span>(tidyverse)</span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(readxl)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+</div>
+<ol type="1">
+<li>💻 xx.</li>
+</ol>
+
+
+</section>
+
+</main> <!-- /main -->
+<script id="quarto-html-after-body" type="application/javascript">
+window.document.addEventListener("DOMContentLoaded", function (event) {
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+  var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
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+    const ref = bibliorefs[i];
+    const citeInfo = findCites(ref);
+    if (citeInfo) {
+      tippyHover(citeInfo.el, function() {
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+          citeDiv.classList.add('hanging-indent');
+          citeDiv.classList.add('csl-entry');
+          var biblioDiv = window.document.getElementById('ref-' + cite);
+          if (biblioDiv) {
+            citeDiv.innerHTML = biblioDiv.innerHTML;
+          }
+          popup.appendChild(citeDiv);
+        });
+        return popup.innerHTML;
+      });
+    }
+  }
+    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+      var filterRegex = new RegExp("^(?:http:|https:)\/\/3mmarand\.github\.io\/BIO00088H-data");
+    var isInternal = (href) => {
+        return filterRegex.test(href) || localhostRegex.test(href);
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diff --git a/core/week-6/study_before_workshop.html b/core/week-6/study_before_workshop.html
new file mode 100644
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+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../core/week-6/overview.html">Week 6: Quarto</a></li><li class="breadcrumb-item"><a href="../../core/week-6/study_before_workshop.html">Prepare!</a></li></ol></nav>
+      <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
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+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true">
+ <span class="menu-text">Week 1: xxx</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
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+      <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
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+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
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+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-1/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
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+        <li class="sidebar-item sidebar-item-section">
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+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
+ <span class="menu-text">Week 2: xxx</span></a>
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+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Week 6: Quarto</span></a>
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+          </a> 
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+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link active">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+    </ul>
+    </div>
+</nav>
+<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
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+<!-- main -->
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+
+<header id="title-block-header" class="quarto-title-block default">
+<div class="quarto-title">
+<h1 class="title">Independent Study to prepare for workshop</h1>
+<p class="subtitle lead">Core 3 Reproducible Reporting</p>
+</div>
+
+
+
+<div class="quarto-title-meta">
+
+    
+  
+    
+  </div>
+  
+
+</header>
+
+<ol type="1">
+<li>📖 Read xxxx</li>
+</ol>
+
+
+
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+          citeDiv.classList.add('csl-entry');
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diff --git a/core/week-6/workshop.html b/core/week-6/workshop.html
new file mode 100644
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+}
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+  margin-left:2em;
+  padding-left:1em;
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+div.csl-indent {
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+  <div class="sidebar-item-container"> 
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+ <span class="menu-text">Core Data Analysis for Group Project</span></a>
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+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
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+  </div>
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+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
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+ <span class="menu-text">Consolidate!</span></a>
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+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Week 6: Quarto</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
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+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link active">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+    </ul>
+    </div>
+</nav>
+<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<!-- margin-sidebar -->
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+        <nav id="TOC" role="doc-toc" class="toc-active">
+    <h2 id="toc-title">On this page</h2>
+   
+  <ul>
+  <li><a href="#introduction" id="toc-introduction" class="nav-link active" data-scroll-target="#introduction">Introduction</a>
+  <ul class="collapse">
+  <li><a href="#session-overview" id="toc-session-overview" class="nav-link" data-scroll-target="#session-overview">Session overview</a></li>
+  </ul></li>
+  <li><a href="#getting-started" id="toc-getting-started" class="nav-link" data-scroll-target="#getting-started">Getting started</a></li>
+  <li><a href="#exercises" id="toc-exercises" class="nav-link" data-scroll-target="#exercises">Exercises</a></li>
+  <li><a href="#well-done" id="toc-well-done" class="nav-link" data-scroll-target="#well-done">🥳 Well Done! 🎉</a></li>
+  <li><a href="#independent-study-following-the-workshop" id="toc-independent-study-following-the-workshop" class="nav-link" data-scroll-target="#independent-study-following-the-workshop">Independent study following the workshop</a></li>
+  <li><a href="#the-code-file" id="toc-the-code-file" class="nav-link" data-scroll-target="#the-code-file">The Code file</a></li>
+  <li><a href="#references" id="toc-references" class="nav-link" data-scroll-target="#references">References</a></li>
+  </ul>
+</nav>
+    </div>
+<!-- main -->
+<main class="content" id="quarto-document-content">
+
+<header id="title-block-header" class="quarto-title-block default">
+<div class="quarto-title">
+<h1 class="title">Workshop</h1>
+<p class="subtitle lead">Reproducible Reporting</p>
+</div>
+
+
+
+<div class="quarto-title-meta">
+
+    
+  
+    
+  </div>
+  
+
+</header>
+
+<section id="introduction" class="level1">
+<h1>Introduction</h1>
+<section id="session-overview" class="level2">
+<h2 class="anchored" data-anchor-id="session-overview">Session overview</h2>
+<p>In this workshop you will</p>
+<div class="callout callout-style-default callout-note callout-titled">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+Key
+</div>
+</div>
+<div class="callout-body-container callout-body">
+
+</div>
+</div>
+</section>
+</section>
+<section id="getting-started" class="level1">
+<h1>Getting started</h1>
+</section>
+<section id="exercises" class="level1">
+<h1>Exercises</h1>
+<p>🎬</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>
+<p><a href="../../core/week-6/study_after_workshop.html">Consolidate</a></p>
+</section>
+<section id="the-code-file" class="level1">
+<h1>The Code file</h1>
+<p>These contain all the code needed in the workshop even where it is not visible on the webpage.</p>
+<p>The <a href="../../core/week-6/workshop.html">workshop.qmd</a> file is the file I use to compile the practical. Qmd stands for Quarto markdown. It allows code and ordinary text to be interleaved to produce well-formatted reports including webpages. Right-click on the link and choose Save-As to download. You will be able to open the Qmd file in RStudio. Alternatively, <a href="https://github.com/3mmaRand/">View in Browser</a>. Coding and thinking answers are marked with <code>#---CODING ANSWER---</code> and <code>#---THINKING ANSWER---</code></p>
+<p>Pages made with R <span class="citation" data-cites="R-core">(<a href="#ref-R-core" role="doc-biblioref">R Core Team 2023</a>)</span>, Quarto <span class="citation" data-cites="allaire2022">(<a href="#ref-allaire2022" role="doc-biblioref">Allaire et al. 2022</a>)</span>, <code>knitr</code> <span class="citation" data-cites="knitr">(<a href="#ref-knitr" role="doc-biblioref">Xie 2022</a>)</span>, <code>kableExtra</code> <span class="citation" data-cites="kableExtra">(<a href="#ref-kableExtra" role="doc-biblioref">Zhu 2021</a>)</span></p>
+</section>
+<section id="references" class="level1">
+
+
+
+
+</section>
+
+<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" role="doc-bibliography"><h2 class="anchored quarto-appendix-heading">References</h2><div id="refs" class="references csl-bib-body hanging-indent" role="list">
+<div id="ref-allaire2022" class="csl-entry" role="listitem">
+Allaire, J. J., Charles Teague, Carlos Scheidegger, Yihui Xie, and Christophe Dervieux. 2022. <em>Quarto</em>. <a href="https://doi.org/10.5281/zenodo.5960048">https://doi.org/10.5281/zenodo.5960048</a>.
+</div>
+<div id="ref-R-core" class="csl-entry" role="listitem">
+R Core Team. 2023. <em>R: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org/">https://www.R-project.org/</a>.
+</div>
+<div id="ref-knitr" class="csl-entry" role="listitem">
+Xie, Yihui. 2022. <span>“Knitr: A General-Purpose Package for Dynamic Report Generation in r.”</span> <a href="https://yihui.org/knitr/">https://yihui.org/knitr/</a>.
+</div>
+<div id="ref-kableExtra" class="csl-entry" role="listitem">
+Zhu, Hao. 2021. <span>“kableExtra: Construct Complex Table with ’Kable’ and Pipe Syntax.”</span> <a href="https://CRAN.R-project.org/package=kableExtra">https://CRAN.R-project.org/package=kableExtra</a>.
+</div>
+</div></section></div></main> <!-- /main -->
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+</body></html>
\ No newline at end of file
diff --git a/search.json b/search.json
index ce2164a..f89eada 100644
--- a/search.json
+++ b/search.json
@@ -32,7 +32,7 @@
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+    "text": "Set up\nIf you have just opened RStudio you will want to load the packages and import the data.\n\nlibrary(tidyverse)\nlibrary(readxl)\n\n\n💻 xx."
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+    "text": "xxxxx\n\nLearning objectives\n\ndd\ndd.\ndd\nd\n\n\n\nInstructions\n\nPrepare\n\n📖 Read\n\nWorkshop\n\n💻 dd.\n💻 ddd\n💻 ddd\n\nConsolidate\n\n💻 dd\n💻 dd"
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+  {
+    "objectID": "core/week-6/study_after_workshop.html",
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+    "text": "Set up\nIf you have just opened RStudio you will want to load the packages and import the data.\n\nlibrary(tidyverse)\nlibrary(readxl)\n\n\n💻 xx."
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+    "href": "core/core.html#week-1-core-1-organising-reproducible-data-analyses",
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-    "text": "Note no R coding (too early for 70M)\n\nProject organisation: folders, files\nProject oriented workflow\nReadme\nNaming things\nKeeping notes\nData management, google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6\nfile formats\nIntroduction to data in general. Similarities and differences\n\nSequences data\nImage data\nStructure data."
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     "section": "",
-    "text": "rgetgretger"
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     "section": "",
-    "text": "fgzzdfghdfhg"
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