Deploying to gh-pages from @ 21f989d 🚀

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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

core/week-11/study_after_workshop.html

@@ -330,7 +330,7 @@ <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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

core/week-11/study_before_workshop.html

@@ -384,7 +384,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
 </div>
 </div>
 
-  <p class="date">5 December, 2023</p>
+  <p class="date">15 December, 2023</p>
 </section>
 <section id="module-assessment" class="slide level2">
 <h2>Module assessment</h2>

core/week-11/workshop.html

@@ -377,7 +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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

core/week-2/study_before_workshop.html

@@ -444,7 +444,7 @@
 </div>
 </div>
 
-  <p class="date">5 December, 2023</p>
+  <p class="date">15 December, 2023</p>
 </section><section id="overview" class="slide level2"><h2>Overview</h2>
 <ul>
 <li>RStudio Projects revisited
@@ -681,7 +681,7 @@
 </ul></section><section id="ugly-code" class="slide level2"><h2>😩 Ugly code 😩</h2>
 <div class="cell">
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">data</span><span class="op">&lt;-</span><span class="fu">read_csv</span><span class="op">(</span><span class="st">'../data-raw/Y101_Y102_Y201_Y202_Y101-5.csv'</span>,skip<span class="op">=</span><span class="fl">2</span><span class="op">)</span></span>
-<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/sfirke/janitor">janitor</a></span><span class="op">)</span>;<span class="va">sol</span><span class="op">&lt;-</span><span class="fu">clean_names</span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/sfirke/janitor">janitor</a></span><span class="op">)</span>;<span class="va">sol</span><span class="op">&lt;-</span><span class="fu"><a href="https://sfirke.github.io/janitor/reference/clean_names.html">clean_names</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span>
 <span><span class="va">data</span><span class="op">=</span><span class="va">data</span><span class="op">|&gt;</span><span class="fu"><a href="https://rdrr.io/r/stats/filter.html">filter</a></span><span class="op">(</span><span class="fu">str_detect</span><span class="op">(</span><span class="va">description</span>,<span class="st">"OS=Homo sapiens"</span><span class="op">)</span><span class="op">)</span><span class="op">|&gt;</span><span class="fu"><a href="https://rdrr.io/r/stats/filter.html">filter</a></span><span class="op">(</span><span class="va">x1pep</span><span class="op">==</span><span class="st">'x'</span><span class="op">)</span></span>
 <span><span class="va">data</span><span class="op">=</span><span class="va">data</span><span class="op">|&gt;</span></span>
 <span><span class="fu">mutate</span><span class="op">(</span>g<span class="op">=</span><span class="fu">str_extract</span><span class="op">(</span><span class="va">description</span>,</span>
@@ -711,7 +711,7 @@
 <span></span>
 <span><span class="co"># import: column headers and data are from row 3</span></span>
 <span><span class="va">solu_protein</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html">read_csv</a></span><span class="op">(</span><span class="va">file</span>, skip <span class="op">=</span> <span class="fl">2</span><span class="op">)</span> <span class="op">|&gt;</span></span>
-<span>  <span class="fu">janitor</span><span class="fu">::</span><span class="fu">clean_names</span><span class="op">(</span><span class="op">)</span></span>
+<span>  <span class="fu">janitor</span><span class="fu">::</span><span class="fu"><a href="https://sfirke.github.io/janitor/reference/clean_names.html">clean_names</a></span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># Tidy data ----------------------------------------------------------------</span></span>
 <span></span>

core/week-2/workshop.html

@@ -404,7 +404,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 
@@ -476,8 +476,8 @@ <h1 class="title">Workshop</h1>
 <div class="cell-output cell-output-stdout">
 <pre><code>data
 images
+overview.html
 overview.qmd
-study_after_workshop.html
 study_after_workshop.qmd
 study_before_workshop.html
 study_before_workshop.ipynb
@@ -493,58 +493,58 @@ <h1 class="title">Workshop</h1>
 <div class="sourceCode cell-code" id="cb9"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-l</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 228
-drwxr-xr-x 2 runner docker  4096 Dec  5 12:12 data
-drwxr-xr-x 2 runner docker  4096 Dec  5 12:12 images
--rw-r--r-- 1 runner docker  1597 Dec  5 12:12 overview.qmd
--rw-r--r-- 1 runner docker 25553 Dec  5 12:16 study_after_workshop.html
--rw-r--r-- 1 runner docker   184 Dec  5 12:12 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 70839 Dec  5 12:16 study_before_workshop.html
--rw-r--r-- 1 runner docker  4807 Dec  5 12:12 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Dec  5 12:12 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 58063 Dec  5 12:12 workshop.html
--rw-r--r-- 1 runner docker  8550 Dec  5 12:12 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Dec  5 12:16 workshop.rmarkdown
-drwxr-xr-x 3 runner docker  4096 Dec  5 12:12 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker  4096 Dec 15 12:46 data
+drwxr-xr-x 2 runner docker  4096 Dec 15 12:46 images
+-rw-r--r-- 1 runner docker 27497 Dec 15 13:09 overview.html
+-rw-r--r-- 1 runner docker  1597 Dec 15 12:46 overview.qmd
+-rw-r--r-- 1 runner docker   184 Dec 15 12:46 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 70988 Dec 15 13:09 study_before_workshop.html
+-rw-r--r-- 1 runner docker  4807 Dec 15 12:46 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Dec 15 12:46 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 58063 Dec 15 12:46 workshop.html
+-rw-r--r-- 1 runner docker  8550 Dec 15 12:46 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Dec 15 13:09 workshop.rmarkdown
+drwxr-xr-x 3 runner docker  4096 Dec 15 12:46 workshop_files</code></pre>
 </div>
 </div>
 <p>You can use more than one option at once. The <code>-h</code> option stands for “human readable” and makes the file sizes easier to understand for humans:</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb11"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-hl</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 228K
-drwxr-xr-x 2 runner docker 4.0K Dec  5 12:12 data
-drwxr-xr-x 2 runner docker 4.0K Dec  5 12:12 images
--rw-r--r-- 1 runner docker 1.6K Dec  5 12:12 overview.qmd
--rw-r--r-- 1 runner docker  25K Dec  5 12:16 study_after_workshop.html
--rw-r--r-- 1 runner docker  184 Dec  5 12:12 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  70K Dec  5 12:16 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Dec  5 12:12 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Dec  5 12:12 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Dec  5 12:12 workshop.html
--rw-r--r-- 1 runner docker 8.4K Dec  5 12:12 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Dec  5 12:16 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Dec  5 12:12 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Dec 15 12:46 data
+drwxr-xr-x 2 runner docker 4.0K Dec 15 12:46 images
+-rw-r--r-- 1 runner docker  27K Dec 15 13:09 overview.html
+-rw-r--r-- 1 runner docker 1.6K Dec 15 12:46 overview.qmd
+-rw-r--r-- 1 runner docker  184 Dec 15 12:46 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  70K Dec 15 13:09 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Dec 15 12:46 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Dec 15 12:46 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  57K Dec 15 12:46 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Dec 15 12:46 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Dec 15 13:09 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Dec 15 12:46 workshop_files</code></pre>
 </div>
 </div>
 <p>The <code>-a</code> option stands for “all” and shows us all the files, including hidden files.</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb13"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-alh</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 236K
-drwxr-xr-x 5 runner docker 4.0K Dec  5 12:16 .
-drwxr-xr-x 6 runner docker 4.0K Dec  5 12:16 ..
-drwxr-xr-x 2 runner docker 4.0K Dec  5 12:12 data
-drwxr-xr-x 2 runner docker 4.0K Dec  5 12:12 images
--rw-r--r-- 1 runner docker 1.6K Dec  5 12:12 overview.qmd
--rw-r--r-- 1 runner docker  25K Dec  5 12:16 study_after_workshop.html
--rw-r--r-- 1 runner docker  184 Dec  5 12:12 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  70K Dec  5 12:16 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Dec  5 12:12 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Dec  5 12:12 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Dec  5 12:12 workshop.html
--rw-r--r-- 1 runner docker 8.4K Dec  5 12:12 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Dec  5 12:16 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Dec  5 12:12 workshop_files</code></pre>
+drwxr-xr-x 5 runner docker 4.0K Dec 15 13:09 .
+drwxr-xr-x 6 runner docker 4.0K Dec 15 13:09 ..
+drwxr-xr-x 2 runner docker 4.0K Dec 15 12:46 data
+drwxr-xr-x 2 runner docker 4.0K Dec 15 12:46 images
+-rw-r--r-- 1 runner docker  27K Dec 15 13:09 overview.html
+-rw-r--r-- 1 runner docker 1.6K Dec 15 12:46 overview.qmd
+-rw-r--r-- 1 runner docker  184 Dec 15 12:46 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  70K Dec 15 13:09 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Dec 15 12:46 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Dec 15 12:46 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  57K Dec 15 12:46 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Dec 15 12:46 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Dec 15 13:09 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Dec 15 12:46 workshop_files</code></pre>
 </div>
 </div>
 <p>You can move about with the <code>cd</code> command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:</p>

core/week-6/overview.html

@@ -336,7 +336,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

core/week-6/study_after_workshop.html

@@ -330,7 +330,7 @@ <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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

core/week-6/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">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

core/week-6/workshop.html

@@ -365,7 +365,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

images/images.html

@@ -209,7 +209,7 @@ <h1 class="title">Image Data Analysis for Group Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 
@@ -301,7 +301,7 @@ <h1 class="title">Image Data Analysis for Group Project</h1>
 <span><span class="va">tracking</span> <span class="op">&lt;-</span> <span class="va">files</span> <span class="op">|&gt;</span> </span>
 <span>  <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html">set_names</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu"><a href="https://purrr.tidyverse.org/reference/map_dfr.html">map_dfr</a></span><span class="op">(</span><span class="va">read_table</span>, .id <span class="op">=</span> <span class="st">"file"</span><span class="op">)</span> <span class="op">|&gt;</span></span>
-<span>  <span class="fu">janitor</span><span class="fu">::</span><span class="fu">clean_names</span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span>  <span class="fu">janitor</span><span class="fu">::</span><span class="fu"><a href="https://sfirke.github.io/janitor/reference/clean_names.html">clean_names</a></span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>You will get a warning <code>Duplicated column names deduplicated: 'avgX' =&gt; 'avgX_1' [15]</code> for each of the files because the csv files each have two columns called <code>avgX</code>. If you click on the <code>tracking</code> dataframe you see is contains the data from all the files.</p>
 <p>Now we can add columns for the type and the concentration by processing the values in the <code>file</code>. The values are like <code>track/343_0.txt</code> so we need to remove <code>.txt</code> and <code>track/</code> and separate the remaining words into two columns.</p>

index.html

@@ -172,7 +172,7 @@ <h1 class="title">Data Analysis for the Group Research Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">5 December, 2023</p>
+      <p class="date">15 December, 2023</p>
     </div>
   </div>
 

omics/kelly/data-raw/mol_wt.txt

@@ -0,0 +1,9 @@
+vfa mw
+Acetate	60.05
+Propanoate	74.08
+Isobutyrate	88.11
+Butyrate	88.11
+Isopentanoate	102.13
+Pentanoate	102.13
+Isohexanoate	116.1583
+Hexanoate	116.1583