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diff --git a/docs/no_toc/07-durable-code.md b/docs/no_toc/07-durable-code.md
@@ -139,7 +139,7 @@ Keeping around old code and objects is generally more of a hindrance than a time
 
 1) You might write better code on the second try (or third or n'th). 
 2) Keeping around old code makes it harder for you to write and troubleshoot new better code -- it's easier to confuse yourself. Sometimes a fresh start can be what you need. 
-3) With version control you can always return to that old code! (We'll dive more into version control later on, but you've started the process by [uploading your code to GitHub in chapter 4](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/why-git-and-github.html)!) 
+3) With version control you can always return to that old code! (We'll dive more into version control later on, but you've started the process by [uploading your code to GitHub in chapter 4](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/making-your-project-open-source-with-github.html)!) 
 
 This means you should not comment out old code. Just delete it! No code is so precious that you need to keep it commented out (particularly if you are using version control and you can retrieve it in other ways should you need it).
 
@@ -306,7 +306,7 @@ There's so many opinions and strategies on best practices for code. And although
 
 #### R specific:
 
-- [Data Carpentry's: Best Practices for Writing R Code](https://swcarpentry.github.io/r-novice-inflammation/06-best-practices-R/) by @DataCarpentry2021b.
+- [Data Carpentry's: Best Practices for Writing R Code](https://swcarpentry.github.io/r-novice-inflammation/06-best-practices-R.html) by @DataCarpentry2021b.
 - [R Programming for Research: Reproducible Research](https://geanders.github.io/RProgrammingForResearch/reproducible-research-1.html) by @Good2021.
 - [R for Epidemiology: Coding best practices](https://www.r4epi.com/coding-best-practices.html) by @Cannell2021.
 - [Best practices for R Programming](https://towardsdatascience.com/best-practices-for-r-programming-ec0754010b5a) by @Bernardo2021.

diff --git a/docs/no_toc/404.html b/docs/no_toc/404.html
@@ -312,13 +312,18 @@ <h1>Page not found</h1>
 <p>You may want to try searching to find the page's new location, or use
 the table of contents to find the page you are looking for.</p>
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+ </div>
+</center>
+
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  </div>
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diff --git a/docs/no_toc/About.md b/docs/no_toc/About.md
@@ -46,7 +46,7 @@ These credits are based on our [course contributors table guidelines](https://ww
 ## collate en_US.UTF-8 
 ## ctype en_US.UTF-8 
 ## tz Etc/UTC 
-## date 2022-10-13 
+## date 2024-03-25 
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ## package * version date lib source 

diff --git a/docs/no_toc/about-the-authors.html b/docs/no_toc/about-the-authors.html
@@ -428,7 +428,7 @@ <h1>About the Authors</h1>
 ## collate en_US.UTF-8 
 ## ctype en_US.UTF-8 
 ## tz Etc/UTC 
-## date 2022-10-13 
+## date 2024-03-25 
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ## package * version date lib source 
@@ -486,13 +486,18 @@ <h1>About the Authors</h1>
 <!-- Links -->
 
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+ </div>
+</center>
+
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diff --git a/docs/no_toc/code-review.html b/docs/no_toc/code-review.html
@@ -407,13 +407,18 @@ <h3>References</h3>
 Team, Smartbear. 2021. <span>“Best <span>Practices</span> for <span>Code</span> <span>Review</span>.”</span> <em>Smartbear.com</em>. <a href="https://smartbear.com/en/learn/code-review/best-practices-for-peer-code-review/">https://smartbear.com/en/learn/code-review/best-practices-for-peer-code-review/</a>.
 </div>
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
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+
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 </center>

diff --git a/docs/no_toc/defining-reproducibility.html b/docs/no_toc/defining-reproducibility.html
@@ -387,13 +387,18 @@ <h3>References</h3>
 Broman, Karl. 2016. <span>“Tools for <span>Reproducible</span> <span>Research</span>.”</span> <a href="https://kbroman.org/Tools4RR/">https://kbroman.org/Tools4RR/</a>.
 </div>
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+ </div>
+</center>
+
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  </div>
 </center>

diff --git a/docs/no_toc/documenting-analyses.html b/docs/no_toc/documenting-analyses.html
@@ -367,14 +367,14 @@ <h2><span class="header-section-number">8.3</span> Get the exercise project file
 <strong>Get the Python project example files</strong>
 </summary>
 <p><a href="https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/python-heatmap-chapt-8.zip">Click this link to download</a>.</p>
-<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>).</p>
+<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>.</p>
 </details>
 <details>
 <summary>
 <strong>Get the R project example files</strong>
 </summary>
 <p><a href="https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/r-heatmap-chapt-8.zip">Click this link to download</a>.</p>
-<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>).</p>
+<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>.</p>
 </details>
 </div>
 <div id="exercise-1-practice-beefing-up-your-notebook-descriptions" class="section level2" number="8.4">
@@ -418,13 +418,18 @@ <h2><span class="header-section-number">8.5</span> Exercise 2: Write a README fo
 
 </div>
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+ </div>
+</center>
+
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 <center>
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- <br>
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  </div>
 </center>

diff --git a/docs/no_toc/index.html b/docs/no_toc/index.html
@@ -308,7 +308,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Intro to Reproducibility in Cancer Informatics</h1>
-<p class="date"><em>October, 2022</em></p>
+<p class="date"><em>March, 2024</em></p>
 </div>
 <div id="about-this-course" class="section level1 unnumbered">
 <h1>About this Course</h1>
@@ -325,13 +325,18 @@ <h2><span class="header-section-number">0.1</span> Available course formats</h2>
 
 </div>
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+ </div>
+</center>
+
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 <center>
  <div class="footer">
- Please provide any feedback with <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7">This form!</a> We appreciate your thoughts.
- <br>
  All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
- <br>
  All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
  </div>
 </center>

diff --git a/docs/no_toc/index.md b/docs/no_toc/index.md
@@ -1,6 +1,6 @@
 ---
 title: "Intro to Reproducibility in Cancer Informatics"
-date: "October, 2022"
+date: "March, 2024"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib, packages.bib]

diff --git a/docs/no_toc/introduction.html b/docs/no_toc/introduction.html
@@ -358,13 +358,18 @@ <h3>References</h3>
 Beaulieu-Jones, Brett K, and Casey S Greene. 2017. <span>“Reproducibility of Computational Workflows Is Automated Using Continuous Analysis.”</span> <em>Nature Biotechnology</em> 35 (4): 342–46. <a href="https://doi.org/10.1038/nbt.3780">https://doi.org/10.1038/nbt.3780</a>.
 </div>
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+ </div>
+</center>
+
 <hr>
 <center>
  <div class="footer">
- Please provide any feedback with <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7">This form!</a> We appreciate your thoughts.
- <br>
  All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
- <br>
  All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
  </div>
 </center>

diff --git a/docs/no_toc/making-your-project-open-source-with-github.html b/docs/no_toc/making-your-project-open-source-with-github.html
@@ -352,14 +352,14 @@ <h2><span class="header-section-number">4.2</span> Get the exercise project file
 <strong>Get the Python project example files</strong>
 </summary>
 <p><a href="https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/python-heatmap-chapt-4.zip">Click this link to download</a>.</p>
-<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>).</p>
+<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>.</p>
 </details>
 <details>
 <summary>
 <strong>Get the R project example files</strong>
 </summary>
 <p><a href="https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/r-heatmap-chapt-4.zip">Click this link to download</a>.</p>
-<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>).</p>
+<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>.</p>
 </details>
 </div>
 <div id="exercise-set-up-a-project-on-github" class="section level2" number="4.3">
@@ -383,13 +383,18 @@ <h2><span class="header-section-number">4.3</span> Exercise: Set up a project on
 
 </div>
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+ </div>
+</center>
+
 <hr>
 <center>
  <div class="footer">
- Please provide any feedback with <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7">This form!</a> We appreciate your thoughts.
- <br>
  All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
- <br>
  All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
  </div>
 </center>

diff --git a/docs/no_toc/managing-package-versions.html b/docs/no_toc/managing-package-versions.html
@@ -342,14 +342,14 @@ <h2><span class="header-section-number">6.2</span> Get the exercise project file
 <strong>Get the Python project example files</strong>
 </summary>
 <p><a href="https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/python-heatmap-chapt-6.zip">Click this link to download</a>.</p>
-<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>).</p>
+<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>.</p>
 </details>
 <details>
 <summary>
 <strong>Get the R project example files</strong>
 </summary>
 <p><a href="https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/r-heatmap-chapt-6.zip">Click this link to download</a>.</p>
-<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>).</p>
+<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>.</p>
 </details>
 </div>
 <div id="exercise-1-print-out-session-info" class="section level2" number="6.3">
@@ -485,13 +485,18 @@ <h3>References</h3>
 Beaulieu-Jones, Brett K, and Casey S Greene. 2017. <span>“Reproducibility of Computational Workflows Is Automated Using Continuous Analysis.”</span> <em>Nature Biotechnology</em> 35 (4): 342–46. <a href="https://doi.org/10.1038/nbt.3780">https://doi.org/10.1038/nbt.3780</a>.
 </div>
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+ </div>
+</center>
+
 <hr>
 <center>
  <div class="footer">
- Please provide any feedback with <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7">This form!</a> We appreciate your thoughts.
- <br>
  All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
- <br>
  All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
  </div>
 </center>

diff --git a/docs/no_toc/organizing-your-project.html b/docs/no_toc/organizing-your-project.html
@@ -410,14 +410,14 @@ <h2><span class="header-section-number">3.4</span> Get the exercise project file
 <strong>Get the Python project example files</strong>
 </summary>
 <p><a href="https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/python-heatmap-chapt-3.zip">Click this link to download</a>.</p>
-<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>).</p>
+<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>.</p>
 </details>
 <details>
 <summary>
 <strong>Get the R project example files</strong>
 </summary>
 <p><a href="https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/r-heatmap-chapt-3.zip">Click this link to download</a>.</p>
-<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>).</p>
+<p>Now double click your chapter zip file to unzip. For Windows you may have to <a href="https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc">follow these instructions</a>.</p>
 </details>
 </div>
 <div id="exercise-organize-your-project" class="section level2" number="3.5">
@@ -463,13 +463,18 @@ <h3>References</h3>
 Tayo, Benjamin Obi. 2019. <span>“How to <span>Organize</span> <span>Your</span> <span>Data</span> <span>Science</span> <span>Project</span>.”</span> <em>Medium</em>. <a href="https://towardsdatascience.com/how-to-organize-your-data-science-project-dd6599cf000a">https://towardsdatascience.com/how-to-organize-your-data-science-project-dd6599cf000a</a>.
 </div>
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+ </div>
+</center>
+
 <hr>
 <center>
  <div class="footer">
- Please provide any feedback with <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7">This form!</a> We appreciate your thoughts.
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- <br>
  All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
  </div>
 </center>

diff --git a/docs/no_toc/references.html b/docs/no_toc/references.html
@@ -498,13 +498,18 @@ <h1>References</h1>
 </div>
 </div>
 </div>
+<hr>
+<center>
+<div class="container">
+ <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=intro_to_reproducibility" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+ </div>
+</center>
+
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- <br>
  All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
  </div>
 </center>

diff --git a/...s/figure-html/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE_g106226cdd08_0_0.png b/...s/figure-html/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE_g106226cdd08_0_0.png
diff --git a/...s/figure-html/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE_g102dc56db08_0_0.png b/...s/figure-html/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE_g102dc56db08_0_0.png
diff --git a/.../figure-html/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE_gf62875ddf7_0_404.png b/.../figure-html/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE_gf62875ddf7_0_404.png
diff --git a/docs/no_toc/search_index.json b/docs/no_toc/search_index.json