Skip to content

Commit

Permalink
Browse files Browse the repository at this point in the history
  • Loading branch information
jhudsl-robot committed Mar 25, 2024
2 parents 5761df9 + 2256d1a commit 94cb4f2
Show file tree
Hide file tree
Showing 41 changed files with 250 additions and 120 deletions.
4 changes: 2 additions & 2 deletions docs/07-durable-code.md
Original file line number Diff line number Diff line change
Expand Up @@ -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).

Expand Down Expand Up @@ -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.
Expand Down
11 changes: 8 additions & 3 deletions docs/404.html
Original file line number Diff line number Diff line change
Expand Up @@ -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>

<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>
Expand Down
2 changes: 1 addition & 1 deletion docs/About.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
Binary file modified docs/Introduction-to-Reproducibility.docx
Binary file not shown.
13 changes: 9 additions & 4 deletions docs/about-the-authors.html
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -479,13 +479,18 @@ <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>

<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>
Expand Down
11 changes: 8 additions & 3 deletions docs/code-review.html
Original file line number Diff line number Diff line change
Expand Up @@ -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>
</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>
Expand Down
11 changes: 8 additions & 3 deletions docs/defining-reproducibility.html
Original file line number Diff line number Diff line change
Expand Up @@ -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>

<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>
Expand Down
15 changes: 10 additions & 5 deletions docs/documenting-analyses.html
Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand Down Expand Up @@ -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>

<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>
Expand Down
13 changes: 9 additions & 4 deletions docs/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand All @@ -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>

<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>
Expand Down
2 changes: 1 addition & 1 deletion docs/index.md
Original file line number Diff line number Diff line change
@@ -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]
Expand Down
11 changes: 8 additions & 3 deletions docs/introduction.html
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
15 changes: 10 additions & 5 deletions docs/making-your-project-open-source-with-github.html
Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand All @@ -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>
Expand Down
15 changes: 10 additions & 5 deletions docs/managing-package-versions.html
Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand Down Expand Up @@ -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>
Expand Down
4 changes: 2 additions & 2 deletions docs/no_toc/07-durable-code.md
Original file line number Diff line number Diff line change
Expand Up @@ -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).

Expand Down Expand Up @@ -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.
Expand Down
11 changes: 8 additions & 3 deletions docs/no_toc/404.html
Original file line number Diff line number Diff line change
Expand Up @@ -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>

<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>
Expand Down
2 changes: 1 addition & 1 deletion docs/no_toc/About.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
Loading

0 comments on commit 94cb4f2

Please sign in to comment.