Merge branch 'main' into update-subsetting-lab

fhdsl · Sep 27, 2024 · 82ee5e5 · 82ee5e5
2 parents 577b780 + e3d1494
commit 82ee5e5
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diff --git a/config.yml b/config.yml
@@ -11,7 +11,7 @@ default:
   #final_due_date: "January 24th at 11:59pm ET"
   #grades_due: "January 26"
   holiday: "In recognition of [Martin Luther King Jr. Day](https://en.wikipedia.org/wiki/Martin_Luther_King_Jr._Day), there will be **no class on Monday January 15th, 2024**."
-  google_survey: "https://forms.gle/hQ7jdHZSZoDpHAdE6"
+  google_survey: "https://forms.gle/JAsLbyRDtCtxwgFG9"
   slack_workspace: "https://daseh.slack.com/"
   # ta: "Padmashri Saravanan (psarava1 at jhu.edu), Alex Newman (anewma28 at jhu.edu)"
   ds: "Candace Savonen (csavonen at fredhutch.org)"

diff --git a/config_automation.yml b/config_automation.yml
@@ -2,7 +2,7 @@
 # Check quiz formatting
 check-quizzes: no
 # Check that urls in the content are not broken
-url-checker: yes
+url-checker: no
 # Render preview of content with changes (Rmd's and md's are checked)
 render-preview: yes
 # Spell check Rmds and quizzes

diff --git a/docs/_schedule_table.Rmd b/docs/_schedule_table.Rmd
diff --git a/docs/module_details/day0.html b/docs/module_details/day0.html
@@ -180,9 +180,8 @@ <h2>Material</h2>
 <tr class="header">
 <th align="center"><strong>Day</strong></th>
 <th align="center"><strong>Module</strong></th>
-<th align="center"><strong>Slides</strong></th>
-<th align="center"><strong>Code</strong></th>
-<th align="center"><strong>Resource</strong></th>
+<th align="center"><strong>Lecture</strong></th>
+<th align="center"><strong>Activity</strong></th>
 <th align="center"><strong>Cheatsheets/Guides</strong></th>
 </tr>
 </thead>
@@ -193,7 +192,6 @@ <h2>Material</h2>
 <td align="center"></td>
 <td align="center"><a href="../../modules/HW/homework1.html">HTML</a></td>
 <td align="center"></td>
-<td align="center"></td>
 </tr>
 </tbody>
 </table>

diff --git a/docs/module_details/day1.html b/docs/module_details/day1.html
@@ -186,35 +186,31 @@ <h2>Material</h2>
 <tr class="header">
 <th align="center"><strong>Day</strong></th>
 <th align="center"><strong>Module</strong></th>
-<th align="center"><strong>Slides</strong></th>
-<th align="center"><strong>Code</strong></th>
-<th align="center"><strong>Resource</strong></th>
+<th align="center"><strong>Lecture</strong></th>
+<th align="center"><strong>Activity</strong></th>
 <th align="center"><strong>Cheatsheets/Guides</strong></th>
 </tr>
 </thead>
 <tbody>
 <tr class="odd">
 <td align="center"><a href="../../docs/module_details/day1.html">Day 1</a></td>
 <td align="center">Intro</td>
-<td align="center"><a href="../../modules/Intro/Intro.html">HTML</a>, <a href="../../modules/Intro/Intro.pdf">PDF</a></td>
-<td align="center"><a href="../../modules/Intro/Intro.Rmd">Rmd</a></td>
+<td align="center"><a href="../../modules/Intro/Intro.html">HTML</a>, <a href="../../modules/Intro/Intro.pdf">PDF</a>, <a href="../../modules/Intro/Intro.Rmd">Rmd</a></td>
 <td align="center"></td>
 <td align="center"><a href="../../modules/cheatsheets/Day-1.pdf">Day 1 Cheatsheet</a></td>
 </tr>
 <tr class="even">
 <td align="center"></td>
-<td align="center">RStudio</td>
-<td align="center"><a href="../../modules/RStudio/RStudio.html">HTML</a>, <a href="../../modules/RStudio/RStudio.pdf">PDF</a></td>
-<td align="center"><a href="../../modules/RStudio/RStudio.Rmd">Rmd</a></td>
-<td align="center"><a href="../../modules/RStudio/lab/RStudio_Lab.Rmd">Lab</a>, <a href="../../modules/RStudio/lab/RStudio_Lab_Key.Rmd">Key</a>, <a href="../../modules/RStudio/lab/RStudio_Lab_Key.html">Key HTML</a></td>
+<td align="center">Basic R</td>
+<td align="center"><a href="../../modules/Basic_R/Basic_R.html">HTML</a>, <a href="../../modules/Basic_R/Basic_R.pdf">PDF</a>, <a href="../../modules/Basic_R/Basic_R.Rmd">Rmd</a></td>
+<td align="center"><a href="../../modules/Basic_R/lab/Basic_R_Lab.Rmd">Lab Rmd</a>, <a href="../../modules/Basic_R/lab/Basic_R_Lab_Key.Rmd">Key</a>, <a href="../../modules/Basic_R/lab/Basic_R_Lab_Key.html">Key HTML</a></td>
 <td align="center"></td>
 </tr>
 <tr class="odd">
 <td align="center"></td>
-<td align="center">Basic R</td>
-<td align="center"><a href="../../modules/Basic_R/Basic_R.html">HTML</a>, <a href="../../modules/Basic_R/Basic_R.pdf">PDF</a></td>
-<td align="center"><a href="../../modules/Basic_R/Basic_R.Rmd">Rmd</a></td>
-<td align="center"><a href="../../modules/Basic_R/lab/Basic_R_Lab.Rmd">Lab</a>, <a href="../../modules/Basic_R/lab/Basic_R_Lab_Key.Rmd">Key</a>, <a href="../../modules/Basic_R/lab/Basic_R_Lab_Key.html">Key HTML</a></td>
+<td align="center">RStudio</td>
+<td align="center"><a href="../../modules/RStudio/RStudio.html">HTML</a>, <a href="../../modules/RStudio/RStudio.pdf">PDF</a>, <a href="../../modules/RStudio/RStudio.Rmd">Rmd</a></td>
+<td align="center"><a href="../../modules/RStudio/lab/RStudio_Lab.Rmd">Lab Rmd</a>, <a href="../../modules/RStudio/lab/RStudio_Lab_Key.Rmd">Key</a>, <a href="../../modules/RStudio/lab/RStudio_Lab_Key.html">Key HTML</a></td>
 <td align="center"></td>
 </tr>
 </tbody>

diff --git a/docs/module_details/day2.html b/docs/module_details/day2.html
@@ -185,45 +185,33 @@ <h2>Material</h2>
 <colgroup>
 <col width="8%" />
 <col width="3%" />
-<col width="22%" />
-<col width="10%" />
-<col width="39%" />
-<col width="15%" />
+<col width="31%" />
+<col width="38%" />
+<col width="19%" />
 </colgroup>
 <thead>
 <tr class="header">
 <th align="center"><strong>Day</strong></th>
 <th align="center"><strong>Module</strong></th>
-<th align="center"><strong>Slides</strong></th>
-<th align="center"><strong>Code</strong></th>
-<th align="center"><strong>Resource</strong></th>
+<th align="center"><strong>Lecture</strong></th>
+<th align="center"><strong>Activity</strong></th>
 <th align="center"><strong>Cheatsheets/Guides</strong></th>
 </tr>
 </thead>
 <tbody>
 <tr class="odd">
 <td align="center"><a href="../../docs/module_details/day2.html">Day 2</a></td>
-<td align="center">Basic R (cont.)</td>
-<td align="center"><a href="../../modules/Basic_R/Basic_R.html">HTML</a>, <a href="../../modules/Basic_R/Basic_R.pdf">PDF</a></td>
-<td align="center"><a href="../../modules/Basic_R/Basic_R.Rmd">Rmd</a></td>
-<td align="center"><a href="../../modules/Basic_R/lab/Basic_R_Lab.Rmd">Lab</a>, <a href="../../modules/Basic_R/lab/Basic_R_Lab_Key.Rmd">Key</a>, <a href="../../modules/Basic_R/lab/Basic_R_Lab_Key.html">Key HTML</a></td>
-<td align="center"><a href="../../modules/cheatsheets/Day-2.pdf">Day 2 Cheatsheet</a></td>
-</tr>
-<tr class="even">
-<td align="center"></td>
 <td align="center">Reproducibility</td>
-<td align="center"><a href="../../modules/Reproducibility/Reproducibility.html">HTML</a>, <a href="../../modules/Reproducibility/Reproducibility.pdf">PDF</a></td>
-<td align="center"><a href="../../modules/Reproducibility/Reproducibility.Rmd">Rmd</a></td>
-<td align="center"><a href="../../modules/Reproducibility/lab/Reproducibility_Lab.Rmd">Lab</a>, <a href="../../modules/Reproducibility/lab/Reproducibility_Lab_Key.Rmd">Key</a>, <a href="../../modules/Reproducibility/lab/Reproducibility_Lab_Key.html">Key HTML</a></td>
+<td align="center"><a href="../../modules/Reproducibility/Reproducibility.html">HTML</a>, <a href="../../modules/Reproducibility/Reproducibility.pdf">PDF</a>, <a href="../../modules/Reproducibility/Reproducibility.Rmd">Rmd</a></td>
+<td align="center"><a href="../../modules/Reproducibility/lab/Reproducibility_Lab.Rmd">Lab Rmd</a>, <a href="../../modules/Reproducibility/lab/Reproducibility_Lab_Key.Rmd">Key</a>, <a href="../../modules/Reproducibility/lab/Reproducibility_Lab_Key.html">Key HTML</a></td>
 <td align="center"><a href="resources/good-scientific-coding-practices.pdf">Good scientific coding practices</a></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center"></td>
 <td align="center">Data Input</td>
-<td align="center"><a href="../../modules/Data_Input/Data_Input.html">HTML</a>, <a href="../../modules/Data_Input/Data_Input.pdf">PDF</a></td>
-<td align="center"><a href="../../modules/Data_Input/Data_Input.Rmd">Rmd</a></td>
-<td align="center"><a href="../../modules/Data_Input/lab/Data_Input_Lab.Rmd">Lab</a>, <a href="../../modules/Data_Input/lab/Data_Input_Lab_Key.Rmd">Key</a>, <a href="../../modules/Data_Input/lab/Data_Input_Lab_Key.html">Key HTML</a></td>
-<td align="center"><a href="resources/debugging_guide.pdf">Debugging tips guide</a></td>
+<td align="center"><a href="../../modules/Data_Input/Data_Input.html">HTML</a>, <a href="../../modules/Data_Input/Data_Input.pdf">PDF</a>, <a href="../../modules/Data_Input/Data_Input.Rmd">Rmd</a></td>
+<td align="center"><a href="../../modules/Data_Input/lab/Data_Input_Lab.Rmd">Lab Rmd</a>, <a href="../../modules/Data_Input/lab/Data_Input_Lab_Key.Rmd">Key</a>, <a href="../../modules/Data_Input/lab/Data_Input_Lab_Key.html">Key HTML</a></td>
+<td align="center"><a href="resources/debugging_guide.pdf">Debugging tips guide</a> <a href="../../modules/cheatsheets/Day-2.pdf">Day 2 Cheatsheet</a></td>
 </tr>
 </tbody>
 </table>

diff --git a/docs/module_details/day3.html b/docs/module_details/day3.html
@@ -181,31 +181,35 @@ <h2>Lectures</h2>
 <div id="material" class="section level2">
 <h2>Material</h2>
 <table>
+<colgroup>
+<col width="7%" />
+<col width="3%" />
+<col width="35%" />
+<col width="42%" />
+<col width="9%" />
+</colgroup>
 <thead>
 <tr class="header">
 <th align="center"><strong>Day</strong></th>
 <th align="center"><strong>Module</strong></th>
-<th align="center"><strong>Slides</strong></th>
-<th align="center"><strong>Code</strong></th>
-<th align="center"><strong>Resource</strong></th>
+<th align="center"><strong>Lecture</strong></th>
+<th align="center"><strong>Activity</strong></th>
 <th align="center"><strong>Cheatsheets/Guides</strong></th>
 </tr>
 </thead>
 <tbody>
 <tr class="odd">
 <td align="center"><a href="../../docs/module_details/day3.html">Day 3</a></td>
 <td align="center">Subsetting Data in R</td>
-<td align="center"><a href="../../modules/Subsetting_Data_in_R/Subsetting_Data_in_R.html">HTML</a>, <a href="../../modules/Subsetting_Data_in_R/Subsetting_Data_in_R.pdf">PDF</a></td>
-<td align="center"><a href="../../modules/Subsetting_Data_in_R/Subsetting_Data_in_R.Rmd">Rmd</a></td>
-<td align="center"><a href="../../modules/Subsetting_Data_in_R/lab/Subsetting_Data_in_R_Lab.Rmd">Lab</a>, <a href="../../modules/Subsetting_Data_in_R/lab/Subsetting_Data_in_R_Lab_Key.Rmd">Key</a>, <a href="../../modules/Subsetting_Data_in_R/lab/Subsetting_Data_in_R_Lab_Key.html">Key HTML</a></td>
+<td align="center"><a href="../../modules/Subsetting_Data_in_R/Subsetting_Data_in_R.html">HTML</a>, <a href="../../modules/Subsetting_Data_in_R/Subsetting_Data_in_R.pdf">PDF</a>, <a href="../../modules/Subsetting_Data_in_R/Subsetting_Data_in_R.Rmd">Rmd</a></td>
+<td align="center"><a href="../../modules/Subsetting_Data_in_R/lab/Subsetting_Data_in_R_Lab.Rmd">Lab Rmd</a>, <a href="../../modules/Subsetting_Data_in_R/lab/Subsetting_Data_in_R_Lab_Key.Rmd">Key</a>, <a href="../../modules/Subsetting_Data_in_R/lab/Subsetting_Data_in_R_Lab_Key.html">Key HTML</a></td>
 <td align="center"><a href="../../modules/cheatsheets/Day-3.pdf">Day 3 Cheatsheet</a></td>
 </tr>
 <tr class="even">
 <td align="center"></td>
 <td align="center">Optional Homework 2</td>
 <td align="center"></td>
-<td align="center"><a href="../../modules/HW/homework2.Rmd">Rmd</a>, <a href="../../modules/HW/homework2.html">HTML</a>, <a href="../../modules/HW/homework2_Key.Rmd">Key</a>, <a href="../../modules/HW/homework2_Key.html">Key HTML</a></td>
-<td align="center"></td>
+<td align="center"><a href="../../modules/HW/homework2.Rmd">HW Rmd</a>, <a href="../../modules/HW/homework2.html">HTML</a>, <a href="../../modules/HW/homework2_Key.Rmd">Key</a>, <a href="../../modules/HW/homework2_Key.html">Key HTML</a></td>
 <td align="center"></td>
 </tr>
 </tbody>

diff --git a/docs/module_details/day4.html b/docs/module_details/day4.html
@@ -183,31 +183,35 @@ <h2>Lectures</h2>
 <div id="material" class="section level2">
 <h2>Material</h2>
 <table>
+<colgroup>
+<col width="8%" />
+<col width="3%" />
+<col width="35%" />
+<col width="42%" />
+<col width="10%" />
+</colgroup>
 <thead>
 <tr class="header">
 <th align="center"><strong>Day</strong></th>
 <th align="center"><strong>Module</strong></th>
-<th align="center"><strong>Slides</strong></th>
-<th align="center"><strong>Code</strong></th>
-<th align="center"><strong>Resource</strong></th>
+<th align="center"><strong>Lecture</strong></th>
+<th align="center"><strong>Activity</strong></th>
 <th align="center"><strong>Cheatsheets/Guides</strong></th>
 </tr>
 </thead>
 <tbody>
 <tr class="odd">
 <td align="center"><a href="../../docs/module_details/day4.html">Day 4</a></td>
 <td align="center">Data Summarization</td>
-<td align="center"><a href="../../modules/Data_Summarization/Data_Summarization.html">HTML</a>, <a href="../../modules/Data_Summarization/Data_Summarization.pdf">PDF</a></td>
-<td align="center"><a href="../../modules/Data_Summarization/Data_Summarization.Rmd">Rmd</a></td>
-<td align="center"><a href="../../modules/Data_Summarization/lab/Data_Summarization_Lab.Rmd">Lab</a>, <a href="../../modules/Data_Summarization/lab/Data_Summarization_Lab_Key.Rmd">Key</a>, <a href="../../modules/Data_Summarization/lab/Data_Summarization_Lab_Key.html">Key HTML</a></td>
+<td align="center"><a href="../../modules/Data_Summarization/Data_Summarization.html">HTML</a>, <a href="../../modules/Data_Summarization/Data_Summarization.pdf">PDF</a>, <a href="../../modules/Data_Summarization/Data_Summarization.Rmd">Rmd</a></td>
+<td align="center"><a href="../../modules/Data_Summarization/lab/Data_Summarization_Lab.Rmd">Lab Rmd</a>, <a href="../../modules/Data_Summarization/lab/Data_Summarization_Lab_Key.Rmd">Key</a>, <a href="../../modules/Data_Summarization/lab/Data_Summarization_Lab_Key.html">Key HTML</a></td>
 <td align="center"><a href="../../modules/cheatsheets/Day-4.pdf">Day 4 Cheatsheet</a></td>
 </tr>
 <tr class="even">
 <td align="center"></td>
 <td align="center">Data Classes</td>
-<td align="center"><a href="../../modules/Data_Classes/Data_Classes.html">HTML</a>, <a href="../../modules/Data_Classes/Data_Classes.pdf">PDF</a></td>
-<td align="center"><a href="../../modules/Data_Classes/Data_Classes.Rmd">Rmd</a></td>
-<td align="center"><a href="../../modules/Data_Classes/lab/Data_Classes_Lab.Rmd">Lab</a>, <a href="../../modules/Data_Classes/lab/Data_Classes_Lab_Key.Rmd">Key</a>, <a href="../../modules/Data_Classes/lab/Data_Classes_Lab_Key.html">Key HTML</a></td>
+<td align="center"><a href="../../modules/Data_Classes/Data_Classes.html">HTML</a>, <a href="../../modules/Data_Classes/Data_Classes.pdf">PDF</a>, <a href="../../modules/Data_Classes/Data_Classes.Rmd">Rmd</a></td>
+<td align="center"><a href="../../modules/Data_Classes/lab/Data_Classes_Lab.Rmd">Lab Rmd</a>, <a href="../../modules/Data_Classes/lab/Data_Classes_Lab_Key.Rmd">Key</a>, <a href="../../modules/Data_Classes/lab/Data_Classes_Lab_Key.html">Key HTML</a></td>
 <td align="center"></td>
 </tr>
 </tbody>

diff --git a/docs/module_details/day5.html b/docs/module_details/day5.html
@@ -184,19 +184,17 @@ <h2>Material</h2>
 <tr class="header">
 <th align="center"><strong>Day</strong></th>
 <th align="center"><strong>Module</strong></th>
-<th align="center"><strong>Slides</strong></th>
-<th align="center"><strong>Code</strong></th>
-<th align="center"><strong>Resource</strong></th>
+<th align="center"><strong>Lecture</strong></th>
+<th align="center"><strong>Activity</strong></th>
 <th align="center"><strong>Cheatsheets/Guides</strong></th>
 </tr>
 </thead>
 <tbody>
 <tr class="odd">
 <td align="center"><a href="../../docs/module_details/day5.html">Day 5</a></td>
 <td align="center">Data Cleaning</td>
-<td align="center"><a href="../../modules/Data_Cleaning/Data_Cleaning.html">HTML</a>,<a href="../../modules/Data_Cleaning/Data_Cleaning.pdf">PDF</a></td>
-<td align="center"><a href="../../modules/Data_Cleaning/Data_Cleaning.Rmd">Rmd</a></td>
-<td align="center"><a href="../../modules/Data_Cleaning/lab/Data_Cleaning_Lab.Rmd">Lab</a>, <a href="../../modules/Data_Cleaning/lab/Data_Cleaning_Lab_Key.Rmd">Key</a>, <a href="../../modules/Data_Cleaning/lab/Data_Cleaning_Lab_Key.html">Key HTML</a></td>
+<td align="center"><a href="../../modules/Data_Cleaning/Data_Cleaning.html">HTML</a>,<a href="../../modules/Data_Cleaning/Data_Cleaning.pdf">PDF</a>, <a href="../../modules/Data_Cleaning/Data_Cleaning.Rmd">Rmd</a></td>
+<td align="center"><a href="../../modules/Data_Cleaning/lab/Data_Cleaning_Lab.Rmd">Lab Rmd</a>, <a href="../../modules/Data_Cleaning/lab/Data_Cleaning_Lab_Key.Rmd">Key</a>, <a href="../../modules/Data_Cleaning/lab/Data_Cleaning_Lab_Key.html">Key HTML</a></td>
 <td align="center"><a href="../../modules/cheatsheets/Day-5.pdf">Day 5 Cheatsheet</a></td>
 </tr>
 </tbody>