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core/week-2/workshop.html

@@ -489,58 +489,58 @@ <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 212
-drwxr-xr-x 2 runner docker  4096 Nov 20 15:50 data
-drwxr-xr-x 2 runner docker  4096 Nov 20 15:50 images
--rw-r--r-- 1 runner docker  1597 Nov 20 15:50 overview.qmd
--rw-r--r-- 1 runner docker 25383 Nov 20 15:55 study_after_workshop.html
--rw-r--r-- 1 runner docker   184 Nov 20 15:50 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 70840 Nov 20 15:55 study_before_workshop.html
--rw-r--r-- 1 runner docker  4807 Nov 20 15:50 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Nov 20 15:50 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 44938 Nov 20 15:50 workshop.html
--rw-r--r-- 1 runner docker  8550 Nov 20 15:50 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Nov 20 15:55 workshop.rmarkdown
-drwxr-xr-x 3 runner docker  4096 Nov 20 15:50 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker  4096 Nov 20 20:09 data
+drwxr-xr-x 2 runner docker  4096 Nov 20 20:09 images
+-rw-r--r-- 1 runner docker  1597 Nov 20 20:09 overview.qmd
+-rw-r--r-- 1 runner docker 25383 Nov 20 20:14 study_after_workshop.html
+-rw-r--r-- 1 runner docker   184 Nov 20 20:09 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 70840 Nov 20 20:14 study_before_workshop.html
+-rw-r--r-- 1 runner docker  4807 Nov 20 20:09 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Nov 20 20:09 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 44938 Nov 20 20:09 workshop.html
+-rw-r--r-- 1 runner docker  8550 Nov 20 20:09 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Nov 20 20:14 workshop.rmarkdown
+drwxr-xr-x 3 runner docker  4096 Nov 20 20:09 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 212K
-drwxr-xr-x 2 runner docker 4.0K Nov 20 15:50 data
-drwxr-xr-x 2 runner docker 4.0K Nov 20 15:50 images
--rw-r--r-- 1 runner docker 1.6K Nov 20 15:50 overview.qmd
--rw-r--r-- 1 runner docker  25K Nov 20 15:55 study_after_workshop.html
--rw-r--r-- 1 runner docker  184 Nov 20 15:50 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  70K Nov 20 15:55 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Nov 20 15:50 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Nov 20 15:50 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  44K Nov 20 15:50 workshop.html
--rw-r--r-- 1 runner docker 8.4K Nov 20 15:50 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Nov 20 15:55 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Nov 20 15:50 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Nov 20 20:09 data
+drwxr-xr-x 2 runner docker 4.0K Nov 20 20:09 images
+-rw-r--r-- 1 runner docker 1.6K Nov 20 20:09 overview.qmd
+-rw-r--r-- 1 runner docker  25K Nov 20 20:14 study_after_workshop.html
+-rw-r--r-- 1 runner docker  184 Nov 20 20:09 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  70K Nov 20 20:14 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Nov 20 20:09 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Nov 20 20:09 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  44K Nov 20 20:09 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Nov 20 20:09 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Nov 20 20:14 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Nov 20 20:09 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 220K
-drwxr-xr-x 5 runner docker 4.0K Nov 20 15:55 .
-drwxr-xr-x 6 runner docker 4.0K Nov 20 15:55 ..
-drwxr-xr-x 2 runner docker 4.0K Nov 20 15:50 data
-drwxr-xr-x 2 runner docker 4.0K Nov 20 15:50 images
--rw-r--r-- 1 runner docker 1.6K Nov 20 15:50 overview.qmd
--rw-r--r-- 1 runner docker  25K Nov 20 15:55 study_after_workshop.html
--rw-r--r-- 1 runner docker  184 Nov 20 15:50 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  70K Nov 20 15:55 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Nov 20 15:50 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Nov 20 15:50 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  44K Nov 20 15:50 workshop.html
--rw-r--r-- 1 runner docker 8.4K Nov 20 15:50 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Nov 20 15:55 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Nov 20 15:50 workshop_files</code></pre>
+drwxr-xr-x 5 runner docker 4.0K Nov 20 20:14 .
+drwxr-xr-x 6 runner docker 4.0K Nov 20 20:14 ..
+drwxr-xr-x 2 runner docker 4.0K Nov 20 20:09 data
+drwxr-xr-x 2 runner docker 4.0K Nov 20 20:09 images
+-rw-r--r-- 1 runner docker 1.6K Nov 20 20:09 overview.qmd
+-rw-r--r-- 1 runner docker  25K Nov 20 20:14 study_after_workshop.html
+-rw-r--r-- 1 runner docker  184 Nov 20 20:09 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  70K Nov 20 20:14 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Nov 20 20:09 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Nov 20 20:09 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  44K Nov 20 20:09 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Nov 20 20:09 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Nov 20 20:14 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Nov 20 20:09 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>

images/images.html

@@ -217,7 +217,7 @@ <h1 class="title">Image Data Analysis for Group Project</h1>
 <section id="worm-tracking" class="level2"><h2 class="anchored" data-anchor-id="worm-tracking">Worm Tracking</h2>
 <p>The following ImageJ workflow uses the processing steps you used in workshop 3 with one change. That change is to save the results to file rather than having the results window pop up and saving from there. Or maybe two changes: it also tells you to use meaning systematic file names that will be easy to process when importing data. The RStudio workflow shows you how to import multiple files into one dataframe with columns indicating the treatment.</p>
 <section id="imagej" class="level3"><h3 class="anchored" data-anchor-id="imagej">ImageJ</h3>
-<p>Save files with systematic names: ev_control.avi 343_control.avi ev_1.avi 343_1.avi ev_2.5.avi 343_2.5.avi</p>
+<p>Save files with systematic names: ev_0.avi 343_0.avi ev_1.avi 343_1.avi ev_2.5.avi 343_2.5.avi</p>
 <p>Open ImageJ</p>
 <p>Open video file eg <code>ev_2.5.avi</code></p>
 <ul>
@@ -274,7 +274,7 @@ <h1 class="title">Image Data Analysis for Group Project</h1>
 <p>This is the code you need to import multiple csv files into a single dataframe and add a column with the treatment information from the file name. This is why systematic file names are good.</p>
 <p>It assumes</p>
 <ul>
-<li>your files are called <em>type</em>_<em>concentration</em>.txt for example: ev_control.txt 343_control.txt ev_1.txt 343_1.txt ev_2.5.txt 343_2.5.txt.</li>
+<li>your files are called <em>type</em>_<em>concentration</em>.txt for example: ev_0.txt 343_0.txt ev_1.txt 343_1.txt ev_2.5.txt 343_2.5.txt.</li>
 <li>the .txt datafile are in a folder called <code>track</code> inside your working directory</li>
 <li>you have installed the following packages: <strong><code>tidyverse</code></strong>, <strong><code>janitor</code></strong>
 </li>