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docs/05-scientific-notebooks.md

@@ -132,7 +132,7 @@ From @Shapiro2021
 More reading about RStudio's interface:
 
 - [RStudio IDE Cheatsheet (pdf)](https://rstudio.github.io/cheatsheets/html/rstudio-ide.html).
-- [Navigating the RStudio Interface - R for Epidemiology](https://www.r4epi.com/navigating-the-rstudio-interface.html)
+- [Navigating the RStudio Interface - R for Epidemiology](https://www.r4epi.com/chapters/navigating_rstudio/navigating_rstudio)
 
 </details>
 

docs/07-durable-code.md

@@ -40,7 +40,7 @@ We'll talk a bit more about code review in an upcoming chapter!
 
 - [Readable Code](https://blog.pragmaticengineer.com/readable-code/) by @Orosz2019.    
 - [Write clean R code](https://appsilon.com/write-clean-r-code/) by @Dubel2021.  
-- [Python Clean Code: 6 Best Practices to Make Your Python Functions More Readable](https://towardsdatascience.com/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60) by @Tran2021.  
+- [Python Clean Code: 6 Best Practices to Make Your Python Functions More Readable](https://medium.com/data-science/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60) by @Tran2021.  
 
 #### DRY up your code
 <img src="resources/images/DRY.png" width="12%">
@@ -185,8 +185,8 @@ Try to avoid using variable names that have no meaning like `tmp` or `x`, or `i`
 
 **More reading:**  
 
-- [R for Epidemiology - Coding best Practices](https://www.r4epi.com/coding-best-practices.html#object-variable-names) by @Cannell2021.
-- [Data Scientists: Your Variable Names Are Awful. Here’s How to Fix Them](https://towardsdatascience.com/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them-89053d2855be) by @Koehrsen2019.  
+- [R for Epidemiology - Coding best Practices](https://www.r4epi.com/chapters/best_practices/best_practices#object-variable-names) by @Cannell2021.
+- [Data Scientists: Your Variable Names Are Awful. Here’s How to Fix Them](https://willkoehrsen.github.io/data%20science/software%20engineering/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them/) by @Koehrsen2019. 
 - [Writing Variable — Informative, Descriptive & Elegant](https://medium.datadriveninvestor.com/writing-variable-informative-descriptive-elegant-1dd6f3f15db3) by @Hobert2018.   
 
 #### Follow a code style
@@ -308,7 +308,7 @@ There's so many opinions and strategies on best practices for code. And although
 
 - [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.
+- [R for Epidemiology: Coding best practices](https://www.r4epi.com/chapters/best_practices/best_practices) by @Cannell2021.
 - [Best practices for R Programming](https://towardsdatascience.com/best-practices-for-r-programming-ec0754010b5a) by @Bernardo2021.
 
 ## Get the exercise project files (or continue with the files you used in the previous chapter)

docs/08-readmes.md

@@ -59,7 +59,7 @@ You can take a look at this [template README](https://raw.githubusercontent.com/
 
 - [How to write a good README file](https://www.freecodecamp.org/news/how-to-write-a-good-readme-file/)
 - [A Beginners Guide to writing a Kicka** README](https://meakaakka.medium.com/a-beginners-guide-to-writing-a-kickass-readme-7ac01da88ab3)
-- [How to write an awesome README](https://towardsdatascience.com/how-to-write-an-awesome-readme-68bf4be91f8b)
+- [Tips for Creating Great README Docs](https://www.archbee.com/blog/readme-creating-tips)
 
 ## Get the exercise project files (or continue with the files you used in the previous chapter)
 

docs/Introduction-to-Reproducibility.docx

@@ -358,7 +358,7 @@ <h4><span class="header-section-number">8.2.2.1</span> More about writing README
 <ul>
 <li><a href="https://www.freecodecamp.org/news/how-to-write-a-good-readme-file/">How to write a good README file</a></li>
 <li><a href="https://meakaakka.medium.com/a-beginners-guide-to-writing-a-kickass-readme-7ac01da88ab3">A Beginners Guide to writing a Kicka** README</a></li>
-<li><a href="https://towardsdatascience.com/how-to-write-an-awesome-readme-68bf4be91f8b">How to write an awesome README</a></li>
+<li><a href="https://www.archbee.com/blog/readme-creating-tips">Tips for Creating Great README Docs</a></li>
 </ul>
 </div>
 </div>

docs/documenting-analyses.html

@@ -335,7 +335,7 @@ <h1>References<a href="references.html#references" class="anchor-section" aria-l
 Bryan, Jenny, and Jim Hester. 2021. <span>“Happy Git and GitHub for the useR.”</span> <a href="https://happygitwithr.com/">https://happygitwithr.com/</a>.
 </div>
 <div class="csl-entry">
-Cannell, Brad. 2021. <em>9 <span>Coding</span> Best Practices <span></span> <span>R</span> for <span>Epidemiology</span></em>. <a href="https://brad-cannell.github.io/r4epi/">https://brad-cannell.github.io/r4epi/</a>.
+Cannell, Brad. 2021. <em>9 <span>Coding</span> Best Practices <span></span> <span>R</span> for <span>Epidemiology</span></em>. <a href="https://www.r4epi.com/">https://www.r4epi.com/</a>.
 </div>
 <div class="csl-entry">
 Carrie Wright, Stephanie C. Hicks and Roger D. Peng, Shannon E. Ellis. n.d. <em>Chapter 1 <span>Introduction</span> to the <span>Tidyverse</span> <span></span> <span>Tidyverse</span> <span>Skills</span> for <span>Data</span> <span>Science</span></em>. Accessed November 2, 2021. <a href="http://jhudatascience.org/tidyversecourse/intro.html">http://jhudatascience.org/tidyversecourse/intro.html</a>.
@@ -398,7 +398,7 @@ <h1>References<a href="references.html#references" class="anchor-section" aria-l
 Klinefelter, Sarah. 2016. <span>“<span>DRY</span> <span>Programming</span> <span>Practices</span> – <span>Metova</span>.”</span> <a href="https://metova.com/dry-programming-practices/">https://metova.com/dry-programming-practices/</a>.
 </div>
 <div class="csl-entry">
-Koehrsen, Will. 2019. <span>“Data <span>Scientists</span>: <span>Your</span> <span>Variable</span> <span>Names</span> <span>Are</span> <span>Awful</span>. <span>Here</span>’s <span>How</span> to <span>Fix</span> <span>Them</span>.”</span> <em>Medium</em>. <a href="https://towardsdatascience.com/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them-89053d2855be">https://towardsdatascience.com/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them-89053d2855be</a>.
+Koehrsen, Will. 2019. <span>“Data <span>Scientists</span>: <span>Your</span> <span>Variable</span> <span>Names</span> <span>Are</span> <span>Awful</span>. <span>Here</span>’s <span>How</span> to <span>Fix</span> <span>Them</span>.”</span> <em>Medium</em>. <a href="https://willkoehrsen.github.io/data%20science/software%20engineering/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them/">https://willkoehrsen.github.io/data%20science/software%20engineering/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them/</a>.
 </div>
 <div class="csl-entry">
 Kostyuk, Victor. 2020. <span>“Data <span>Science</span> <span>Python</span> <span>Best</span> <span>Practices</span>.”</span> <em>BCG GAMMA</em>. <a href="https://medium.com/bcggamma/data-science-python-best-practices-fdb16fdedf82">https://medium.com/bcggamma/data-science-python-best-practices-fdb16fdedf82</a>.
@@ -488,7 +488,7 @@ <h1>References<a href="references.html#references" class="anchor-section" aria-l
 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 class="csl-entry">
-Tran, Khuyen. 2021. <span>“Python <span>Clean</span> <span>Code</span>: 6 <span>Best</span> <span>Practices</span> to <span>Make</span> Your <span>Python</span> <span>Functions</span> More <span>Readable</span>.”</span> <em>Medium</em>. <a href="https://towardsdatascience.com/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60">https://towardsdatascience.com/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60</a>.
+Tran, Khuyen. 2021. <span>“Python <span>Clean</span> <span>Code</span>: 6 <span>Best</span> <span>Practices</span> to <span>Make</span> Your <span>Python</span> <span>Functions</span> More <span>Readable</span>.”</span> <em>Medium</em>. <a href="https://medium.com/data-science/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60">https://medium.com/data-science/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60</a>.
 </div>
 <div class="csl-entry">
 Wickham, Hadley. 2019. <span>“Style Guide · <span>Advanced</span> <span>R</span>.”</span> <a href="http://adv-r.had.co.nz/Style.html">http://adv-r.had.co.nz/Style.html</a>.

docs/references.html

@@ -446,7 +446,7 @@ <h3><span class="header-section-number">5.3.1</span> Set up your IDE<a href="usi
 <p>More reading about RStudio’s interface:</p>
 <ul>
 <li><a href="https://rstudio.github.io/cheatsheets/html/rstudio-ide.html">RStudio IDE Cheatsheet (pdf)</a>.</li>
-<li><a href="https://www.r4epi.com/navigating-the-rstudio-interface.html">Navigating the RStudio Interface - R for Epidemiology</a></li>
+<li><a href="https://www.r4epi.com/chapters/navigating_rstudio/navigating_rstudio">Navigating the RStudio Interface - R for Epidemiology</a></li>
 </ul>
 </details>
 </div>

docs/search_index.json

@@ -345,7 +345,7 @@ <h4><span class="header-section-number">7.2.0.2</span> Prioritize readability ov
 </li>
 <li><a href="https://appsilon.com/write-clean-r-code/">Write clean R code</a> by <span class="citation">Dubel (<a href="#ref-Dubel2021">2021</a>)</span>.<br />
 </li>
-<li><a href="https://towardsdatascience.com/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60">Python Clean Code: 6 Best Practices to Make Your Python Functions More Readable</a> by <span class="citation">Tran (<a href="#ref-Tran2021">2021</a>)</span>.</li>
+<li><a href="https://medium.com/data-science/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60">Python Clean Code: 6 Best Practices to Make Your Python Functions More Readable</a> by <span class="citation">Tran (<a href="#ref-Tran2021">2021</a>)</span>.</li>
 </ul>
 </div>
 <div id="dry-up-your-code" class="section level4 hasAnchor" number="7.2.0.3">
@@ -467,9 +467,8 @@ <h4><span class="header-section-number">7.2.0.6</span> Use informative variable
 <p><span class="citation">(<a href="#ref-Hobert2018">Hobert 2018</a>)</span></p>
 <p><strong>More reading:</strong></p>
 <ul>
-<li><a href="https://www.r4epi.com/coding-best-practices.html#object-variable-names">R for Epidemiology - Coding best Practices</a> by <span class="citation">Cannell (<a href="#ref-Cannell2021">2021</a>)</span>.</li>
-<li><a href="https://towardsdatascience.com/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them-89053d2855be">Data Scientists: Your Variable Names Are Awful. Here’s How to Fix Them</a> by <span class="citation">Koehrsen (<a href="#ref-Koehrsen2019">2019</a>)</span>.<br />
-</li>
+<li><a href="https://www.r4epi.com/chapters/best_practices/best_practices#object-variable-names">R for Epidemiology - Coding best Practices</a> by <span class="citation">Cannell (<a href="#ref-Cannell2021">2021</a>)</span>.</li>
+<li><a href="https://willkoehrsen.github.io/data%20science/software%20engineering/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them/">Data Scientists: Your Variable Names Are Awful. Here’s How to Fix Them</a> by <span class="citation">Koehrsen (<a href="#ref-Koehrsen2019">2019</a>)</span>.</li>
 <li><a href="https://medium.datadriveninvestor.com/writing-variable-informative-descriptive-elegant-1dd6f3f15db3">Writing Variable — Informative, Descriptive &amp; Elegant</a> by <span class="citation">Hobert (<a href="#ref-Hobert2018">2018</a>)</span>.</li>
 </ul>
 </div>
@@ -573,7 +572,7 @@ <h4><span class="header-section-number">7.3.0.2</span> R specific:<a href="writi
 <ul>
 <li><a href="https://swcarpentry.github.io/r-novice-inflammation/06-best-practices-R.html">Data Carpentry’s: Best Practices for Writing R Code</a> by <span class="citation"><span>“Best <span>Practices</span> for <span>Writing</span> <span>R</span> <span>Code</span> – <span>Programming</span> with <span>R</span>”</span> (<a href="#ref-DataCarpentry2021b">2021</a>)</span>.</li>
 <li><a href="https://geanders.github.io/RProgrammingForResearch/reproducible-research-1.html">R Programming for Research: Reproducible Research</a> by <span class="citation">Good (<a href="#ref-Good2021">2021</a>)</span>.</li>
-<li><a href="https://www.r4epi.com/coding-best-practices.html">R for Epidemiology: Coding best practices</a> by <span class="citation">Cannell (<a href="#ref-Cannell2021">2021</a>)</span>.</li>
+<li><a href="https://www.r4epi.com/chapters/best_practices/best_practices">R for Epidemiology: Coding best practices</a> by <span class="citation">Cannell (<a href="#ref-Cannell2021">2021</a>)</span>.</li>
 <li><a href="https://towardsdatascience.com/best-practices-for-r-programming-ec0754010b5a">Best practices for R Programming</a> by <span class="citation">Bernardo (<a href="#ref-Bernardo2021">2021</a>)</span>.</li>
 </ul>
 </div>
@@ -868,7 +867,7 @@ <h3>References<a href="references.html#references" class="anchor-section" aria-l
 Bryan, Jenny. 2017. <span>“Project-Oriented Workflow.”</span> <em>Tidyverse Blog</em>. <a href="https://www.tidyverse.org/blog/2017/12/workflow-vs-script/">https://www.tidyverse.org/blog/2017/12/workflow-vs-script/</a>.
 </div>
 <div id="ref-Cannell2021" class="csl-entry">
-Cannell, Brad. 2021. <em>9 <span>Coding</span> Best Practices <span></span> <span>R</span> for <span>Epidemiology</span></em>. <a href="https://brad-cannell.github.io/r4epi/">https://brad-cannell.github.io/r4epi/</a>.
+Cannell, Brad. 2021. <em>9 <span>Coding</span> Best Practices <span></span> <span>R</span> for <span>Epidemiology</span></em>. <a href="https://www.r4epi.com/">https://www.r4epi.com/</a>.
 </div>
 <div id="ref-Wright2021" class="csl-entry">
 Carrie Wright, Stephanie C. Hicks and Roger D. Peng, Shannon E. Ellis. n.d. <em>Chapter 1 <span>Introduction</span> to the <span>Tidyverse</span> <span></span> <span>Tidyverse</span> <span>Skills</span> for <span>Data</span> <span>Science</span></em>. Accessed November 2, 2021. <a href="http://jhudatascience.org/tidyversecourse/intro.html">http://jhudatascience.org/tidyversecourse/intro.html</a>.
@@ -916,7 +915,7 @@ <h3>References<a href="references.html#references" class="anchor-section" aria-l
 Klinefelter, Sarah. 2016. <span>“<span>DRY</span> <span>Programming</span> <span>Practices</span> – <span>Metova</span>.”</span> <a href="https://metova.com/dry-programming-practices/">https://metova.com/dry-programming-practices/</a>.
 </div>
 <div id="ref-Koehrsen2019" class="csl-entry">
-Koehrsen, Will. 2019. <span>“Data <span>Scientists</span>: <span>Your</span> <span>Variable</span> <span>Names</span> <span>Are</span> <span>Awful</span>. <span>Here</span>’s <span>How</span> to <span>Fix</span> <span>Them</span>.”</span> <em>Medium</em>. <a href="https://towardsdatascience.com/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them-89053d2855be">https://towardsdatascience.com/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them-89053d2855be</a>.
+Koehrsen, Will. 2019. <span>“Data <span>Scientists</span>: <span>Your</span> <span>Variable</span> <span>Names</span> <span>Are</span> <span>Awful</span>. <span>Here</span>’s <span>How</span> to <span>Fix</span> <span>Them</span>.”</span> <em>Medium</em>. <a href="https://willkoehrsen.github.io/data%20science/software%20engineering/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them/">https://willkoehrsen.github.io/data%20science/software%20engineering/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them/</a>.
 </div>
 <div id="ref-Kostyuk2020" class="csl-entry">
 Kostyuk, Victor. 2020. <span>“Data <span>Science</span> <span>Python</span> <span>Best</span> <span>Practices</span>.”</span> <em>BCG GAMMA</em>. <a href="https://medium.com/bcggamma/data-science-python-best-practices-fdb16fdedf82">https://medium.com/bcggamma/data-science-python-best-practices-fdb16fdedf82</a>.
@@ -979,7 +978,7 @@ <h3>References<a href="references.html#references" class="anchor-section" aria-l
 Team, Analytics Vidhya. 2019. <span>“What Is <span>Tidyverse</span> <span></span> <span>Tidyverse</span> <span>Package</span> in <span>R</span>.”</span> <em>Analytics Vidhya</em>. <a href="https://www.analyticsvidhya.com/blog/2019/05/beginner-guide-tidyverse-most-powerful-collection-r-packages-data-science/">https://www.analyticsvidhya.com/blog/2019/05/beginner-guide-tidyverse-most-powerful-collection-r-packages-data-science/</a>.
 </div>
 <div id="ref-Tran2021" class="csl-entry">
-Tran, Khuyen. 2021. <span>“Python <span>Clean</span> <span>Code</span>: 6 <span>Best</span> <span>Practices</span> to <span>Make</span> Your <span>Python</span> <span>Functions</span> More <span>Readable</span>.”</span> <em>Medium</em>. <a href="https://towardsdatascience.com/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60">https://towardsdatascience.com/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60</a>.
+Tran, Khuyen. 2021. <span>“Python <span>Clean</span> <span>Code</span>: 6 <span>Best</span> <span>Practices</span> to <span>Make</span> Your <span>Python</span> <span>Functions</span> More <span>Readable</span>.”</span> <em>Medium</em>. <a href="https://medium.com/data-science/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60">https://medium.com/data-science/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60</a>.
 </div>
 <div id="ref-Wickham" class="csl-entry">
 Wickham, Hadley. 2019. <span>“Style Guide · <span>Advanced</span> <span>R</span>.”</span> <a href="http://adv-r.had.co.nz/Style.html">http://adv-r.had.co.nz/Style.html</a>.