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diff --git a/‎docs/class0.html
Lines changed: 20 additions & 31 deletions b/‎docs/class0.html
Lines changed: 20 additions & 31 deletions
diff --git a/‎docs/class1.html
Lines changed: 20 additions & 31 deletions b/‎docs/class1.html
Lines changed: 20 additions & 31 deletions
@@ -10,7 +10,10 @@ format:
 For this lesson, we will be using a .bed file of genetic variants from <https://marianattestad.com/blog>. We will need to read in this data using the `read.table()` function, then rename the columns with the `name()` function:
 
 ```{r}
-variants <- read.table("data/DataVizDay1-files/variants_from_assembly.bed", sep="\t", quote='', stringsAsFactors=TRUE,header=FALSE)
+# Specify the URL of the dataset
+url <- "https://raw.githubusercontent.com/How-to-Learn-to-Code/Rclass-DataScience/main/data/DataVizDay1-files/variants_from_assembly.bed"
+
+variants <- read.table(url, sep="\t", quote='', stringsAsFactors=TRUE,header=FALSE)
 names(variants) <- c("chrom","start","stop","name","size","strand","type","ref.dist","query.dist")
 
 ```
 
@@ -0,0 +1 @@
+ggplot2
@@ -5,15 +5,14 @@ author: "Brian Gural, Lorrie He, JP Flores"
 format: 
   html: 
     toc: true
-execute: 
-  freeze: true
+
 ---
 
 ```{r, echo=FALSE}
-options(digits = 3)
 renv::restore()
 library(tidyverse)
 library(ggplot2)
+options(digits = 3)
 ```
 
 ## Objectives of Data Wrangling: Class 2
@@ -43,7 +42,7 @@ Take a moment to talk among yourselves about this/any ideas you had since last c
 
 ```{r}
 # Load the data. The sample IDs were stored as the first row, so lets make those the row.names
-cell_props <- read.table("data/wrangling-files/cellProportions.csv",
+cell_props <- read.table("https://raw.githubusercontent.com/How-to-Learn-to-Code/Rclass-DataScience/main/data/wrangling-files/cellProportions.csv",
                        row.names = 1, header = TRUE, sep = ",")
 
 head(cell_props)
@@ -70,7 +69,7 @@ Raw RNA-seq matrices should go up to 100,000s. So if you only see small numbers
 We also have the phenotypes for the samples in a separate file:
 
 ```{r}
-cell_phenos <- read.table("data/wrangling-files/cellPhenotypes.csv",
+cell_phenos <- read.table("https://raw.githubusercontent.com/How-to-Learn-to-Code/Rclass-DataScience/main/data/wrangling-files/cellPhenotypes.csv",
                         row.names = 1,sep = ",",header = TRUE)
 
 str(cell_phenos)
 
@@ -0,0 +1,10 @@
+tidyverse
+ggplot2
+tibble
+tidyr
+readr
+purrr
+dplyr
+stringr
+forcats
+lubridate
@@ -1,7 +1,7 @@
 ---
 title: "Running a Reproducible Analysis"
 subtitle: "Project Management, Day 1"
-author: "Brian Gural"
+author: "Brian Gural, Justin Landis"
 format: 
   html:
     number-sections: true
 
@@ -2,12 +2,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.38">
+<meta name="generator" content="quarto-1.4.553">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>How To Learn to Code for Data Science in R – Welcome to How to Learn to Code!</title>
+<title>How To Learn to Code : R for Data Science - Welcome to How to Learn to Code!</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -33,7 +33,7 @@
 }
 @media print {
 pre > code.sourceCode { white-space: pre-wrap; }
-pre > code.sourceCode > span { display: inline-block; text-indent: -5em; padding-left: 5em; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
 }
 pre.numberSource code
   { counter-reset: source-line 0; }
@@ -117,7 +117,7 @@
     </a>
   </div>
             <div id="quarto-search" class="" title="Search"></div>
-          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" role="menu" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
   <span class="navbar-toggler-icon"></span>
 </button>
           <div class="collapse navbar-collapse" id="navbarCollapse">
@@ -129,17 +129,17 @@
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
-            <div class="quarto-navbar-tools">
+          <div class="quarto-navbar-tools">
 </div>
       </div> <!-- /container-fluid -->
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" role="button" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./class0.html"><span class="chapter-title">Welcome to How to Learn to Code!</span></a></li></ol></nav>
-        <a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -465,7 +465,18 @@ <h2 class="anchored" data-anchor-id="bonus-installing-r-studio-on-your-personal-
     }
     return false;
   }
-  const onCopySuccess = function(e) {
+  const clipboard = new window.ClipboardJS('.code-copy-button', {
+    text: function(trigger) {
+      const codeEl = trigger.previousElementSibling.cloneNode(true);
+      for (const childEl of codeEl.children) {
+        if (isCodeAnnotation(childEl)) {
+          childEl.remove();
+        }
+      }
+      return codeEl.innerText;
+    }
+  });
+  clipboard.on('success', function(e) {
     // button target
     const button = e.trigger;
     // don't keep focus
@@ -497,37 +508,15 @@ <h2 class="anchored" data-anchor-id="bonus-installing-r-studio-on-your-personal-
     }, 1000);
     // clear code selection
     e.clearSelection();
-  }
-  const getTextToCopy = function(trigger) {
-      const codeEl = trigger.previousElementSibling.cloneNode(true);
-      for (const childEl of codeEl.children) {
-        if (isCodeAnnotation(childEl)) {
-          childEl.remove();
-        }
-      }
-      return codeEl.innerText;
-  }
-  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
-    text: getTextToCopy
   });
-  clipboard.on('success', onCopySuccess);
-  if (window.document.getElementById('quarto-embedded-source-code-modal')) {
-    // For code content inside modals, clipBoardJS needs to be initialized with a container option
-    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
-    const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
-      text: getTextToCopy,
-      container: window.document.getElementById('quarto-embedded-source-code-modal')
-    });
-    clipboardModal.on('success', onCopySuccess);
-  }
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
       var filterRegex = new RegExp("https:\/\/h2l2cR\.com");
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
     // Inspect non-navigation links and adorn them if external
- 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
     for (var i=0; i<links.length; i++) {
       const link = links[i];
       if (!isInternal(link.href)) {
 
@@ -2,13 +2,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.38">
+<meta name="generator" content="quarto-1.4.553">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Matthew Sutcliffe, Madeline Gillman, JP Flores">
 
-<title>How To Learn to Code for Data Science in R – R Coding Basics</title>
+<title>How To Learn to Code : R for Data Science - R Coding Basics</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -34,7 +34,7 @@
 }
 @media print {
 pre > code.sourceCode { white-space: pre-wrap; }
-pre > code.sourceCode > span { display: inline-block; text-indent: -5em; padding-left: 5em; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
 }
 pre.numberSource code
   { counter-reset: source-line 0; }
@@ -118,7 +118,7 @@
     </a>
   </div>
             <div id="quarto-search" class="" title="Search"></div>
-          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" role="menu" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
   <span class="navbar-toggler-icon"></span>
 </button>
           <div class="collapse navbar-collapse" id="navbarCollapse">
@@ -130,17 +130,17 @@
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
-            <div class="quarto-navbar-tools">
+          <div class="quarto-navbar-tools">
 </div>
       </div> <!-- /container-fluid -->
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" role="button" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./class1.html"><span class="chapter-title">R Coding Basics</span></a></li></ol></nav>
-        <a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -751,7 +751,18 @@ <h2 class="anchored" data-anchor-id="i-already-need-help">I already need help!</
     }
     return false;
   }
-  const onCopySuccess = function(e) {
+  const clipboard = new window.ClipboardJS('.code-copy-button', {
+    text: function(trigger) {
+      const codeEl = trigger.previousElementSibling.cloneNode(true);
+      for (const childEl of codeEl.children) {
+        if (isCodeAnnotation(childEl)) {
+          childEl.remove();
+        }
+      }
+      return codeEl.innerText;
+    }
+  });
+  clipboard.on('success', function(e) {
     // button target
     const button = e.trigger;
     // don't keep focus
@@ -783,37 +794,15 @@ <h2 class="anchored" data-anchor-id="i-already-need-help">I already need help!</
     }, 1000);
     // clear code selection
     e.clearSelection();
-  }
-  const getTextToCopy = function(trigger) {
-      const codeEl = trigger.previousElementSibling.cloneNode(true);
-      for (const childEl of codeEl.children) {
-        if (isCodeAnnotation(childEl)) {
-          childEl.remove();
-        }
-      }
-      return codeEl.innerText;
-  }
-  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
-    text: getTextToCopy
   });
-  clipboard.on('success', onCopySuccess);
-  if (window.document.getElementById('quarto-embedded-source-code-modal')) {
-    // For code content inside modals, clipBoardJS needs to be initialized with a container option
-    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
-    const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
-      text: getTextToCopy,
-      container: window.document.getElementById('quarto-embedded-source-code-modal')
-    });
-    clipboardModal.on('success', onCopySuccess);
-  }
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
       var filterRegex = new RegExp("https:\/\/h2l2cR\.com");
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
     // Inspect non-navigation links and adorn them if external
- 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
     for (var i=0; i<links.length; i++) {
       const link = links[i];
       if (!isInternal(link.href)) {
-Original file line number
+Diff line change
@@ @@ -0,0 +1,10 @@ @@
 +tidyverse
 +ggplot2
 +tibble
 +tidyr
 +readr
 +purrr
 +dplyr
 +stringr
 +forcats
 +lubridate