Merge branch 'main' of https://github.com/jhudsl/intro_to_r into main

jhudsl · Jun 23, 2023 · 20302b0 · 20302b0
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diff --git a/modules/Basic_R/Basic_R.pdf b/modules/Basic_R/Basic_R.pdf
diff --git a/modules/Basic_R/lab/Basic_R_Lab_Key.html b/modules/Basic_R/lab/Basic_R_Lab_Key.html
@@ -308,16 +308,16 @@ <h1>Part 3</h1>
   replace = TRUE
 )
 my_responses</code></pre>
-<pre><code>##  [1] &quot;Strongly Disagree&quot; &quot;Neutral&quot;           &quot;Neutral&quot;          
-##  [4] &quot;Neutral&quot;           &quot;Strongly Agree&quot;    &quot;Strongly Disagree&quot;
-##  [7] &quot;Neutral&quot;           &quot;Neutral&quot;           &quot;Strongly Disagree&quot;
-## [10] &quot;Neutral&quot;           &quot;Disagree&quot;          &quot;Strongly Agree&quot;   
-## [13] &quot;Neutral&quot;           &quot;Agree&quot;             &quot;Strongly Agree&quot;   
-## [16] &quot;Agree&quot;             &quot;Agree&quot;             &quot;Neutral&quot;          
-## [19] &quot;Disagree&quot;          &quot;Strongly Disagree&quot; &quot;Agree&quot;            
-## [22] &quot;Disagree&quot;          &quot;Strongly Disagree&quot; &quot;Strongly Disagree&quot;
-## [25] &quot;Strongly Disagree&quot; &quot;Strongly Disagree&quot; &quot;Agree&quot;            
-## [28] &quot;Disagree&quot;          &quot;Disagree&quot;          &quot;Strongly Disagree&quot;</code></pre>
+<pre><code>##  [1] &quot;Agree&quot;             &quot;Strongly Agree&quot;    &quot;Strongly Disagree&quot;
+##  [4] &quot;Neutral&quot;           &quot;Strongly Agree&quot;    &quot;Neutral&quot;          
+##  [7] &quot;Neutral&quot;           &quot;Agree&quot;             &quot;Neutral&quot;          
+## [10] &quot;Disagree&quot;          &quot;Disagree&quot;          &quot;Agree&quot;            
+## [13] &quot;Strongly Agree&quot;    &quot;Agree&quot;             &quot;Neutral&quot;          
+## [16] &quot;Strongly Disagree&quot; &quot;Strongly Agree&quot;    &quot;Neutral&quot;          
+## [19] &quot;Strongly Disagree&quot; &quot;Strongly Disagree&quot; &quot;Neutral&quot;          
+## [22] &quot;Neutral&quot;           &quot;Strongly Disagree&quot; &quot;Neutral&quot;          
+## [25] &quot;Disagree&quot;          &quot;Agree&quot;             &quot;Strongly Agree&quot;   
+## [28] &quot;Strongly Disagree&quot; &quot;Disagree&quot;          &quot;Strongly Disagree&quot;</code></pre>
 <p><strong>Bonus / Extra practice</strong>: Let’s say you change your survey so participants can rank their response 1-10 (inclusive). Create a randomly sampled vector of 30 survey responses. (hint use <code>seq()</code> and <code>sample()</code> and set the replace argument to <code>TRUE</code>). Store the output as <code>my_responses_2</code>. Examine the data by typing the name <code>my_responses_2</code> in the Console.</p>
 <pre class="r"><code>my_responses_2 &lt;- sample(
   x = seq(from = 1, to = 10),

diff --git a/modules/Data_Classes/Data_Classes.pdf b/modules/Data_Classes/Data_Classes.pdf
diff --git a/modules/Data_Output/my_environment.RData b/modules/Data_Output/my_environment.RData
diff --git a/modules/Data_Visualization/Data_Visualization.html b/modules/Data_Visualization/Data_Visualization.html
diff --git a/modules/Factors/Factors.html b/modules/Factors/Factors.html
@@ -244,7 +244,7 @@ <h1 data-config-title><!-- populated from slide_config.json --></h1>
 <pre >## [1] yellow red    red    blue   yellow blue  
 ## Levels: blue red yellow</pre>
 
-</article></slide><slide class=""><hgroup><h2>A Factor Example</h2></hgroup><article  id="a-factor-example" class="smaller">
+</article></slide><slide class=""><hgroup><h2>A Factor Example</h2></hgroup><article  class="smaller" id="a-factor-example">
 
 <p>We will use data on student dropouts from the State of California during the 2016-2017 school year. More on this data can be found here: <a href='https://www.cde.ca.gov/ds/ad/filesdropouts.asp' title=''>https://www.cde.ca.gov/ds/ad/filesdropouts.asp</a></p>
 
@@ -422,7 +422,7 @@ <h1 data-config-title><!-- populated from slide_config.json --></h1>
 
 <p>Now that’s more like it! Notice how the data is automatically plotted in the order we would like.</p>
 
-</article></slide><slide class=""><hgroup><h2>What about if we <code>arrange()</code> the data by grade ?</h2></hgroup><article  id="what-about-if-we-arrange-the-data-by-grade" class="smaller">
+</article></slide><slide class=""><hgroup><h2>What about if we <code>arrange()</code> the data by grade ?</h2></hgroup><article  class="smaller" id="what-about-if-we-arrange-the-data-by-grade">
 
 <p>Character data is arranged alphabetically.</p>
 
@@ -446,7 +446,7 @@ <h1 data-config-title><!-- populated from slide_config.json --></h1>
 
 <p>Notice that the order is not what we would hope for!</p>
 
-</article></slide><slide class=""><hgroup><h2>Arranging Factors</h2></hgroup><article  id="arranging-factors" class="smaller">
+</article></slide><slide class=""><hgroup><h2>Arranging Factors</h2></hgroup><article  class="smaller" id="arranging-factors">
 
 <p>Factor data is arranged by level.</p>
 
@@ -502,7 +502,7 @@ <h1 data-config-title><!-- populated from slide_config.json --></h1>
 ## 3 Junior                 2
 ## 4 Senior                13</pre>
 
-</article></slide><slide class=""><hgroup><h2><code>forcats</code> for ordering</h2></hgroup><article  id="forcats-for-ordering" class="smaller">
+</article></slide><slide class=""><hgroup><h2><code>forcats</code> for ordering</h2></hgroup><article  class="smaller" id="forcats-for-ordering">
 
 <p>What if we wanted to order <code>grade</code> by increasing <code>n_dropouts</code>?</p>
 
@@ -517,7 +517,7 @@ <h1 data-config-title><!-- populated from slide_config.json --></h1>
 
 <p>This would be useful for identifying easily which grade to focus on.</p>
 
-</article></slide><slide class=""><hgroup><h2>forcats for ordering</h2></hgroup><article  id="forcats-for-ordering-1" class="smaller">
+</article></slide><slide class=""><hgroup><h2>forcats for ordering</h2></hgroup><article  class="smaller" id="forcats-for-ordering-1">
 
 <p>We can order a factor by another variable by using the <code>fct_reorder()</code> function of the <code>forcats</code> package.</p>
 
@@ -552,7 +552,7 @@ <h1 data-config-title><!-- populated from slide_config.json --></h1>
 ## 5 15633216009179 Junior             0     4
 ## 6 33670330113647 Sophomore          0     0</pre>
 
-</article></slide><slide class=""><hgroup><h2>Plotting new variable</h2></hgroup><article  id="plotting-new-variable" class="smaller">
+</article></slide><slide class=""><hgroup><h2>Plotting new variable</h2></hgroup><article  class="smaller" id="plotting-new-variable">
 
 <p>Now let’s plot each of our variables of interest (n_dropouts and tardy) on the y axis and grade on the x axis. Let’s arrange grade by the amount of each.</p>
 

diff --git a/modules/Factors/Factors.pdf b/modules/Factors/Factors.pdf
diff --git a/modules/Functions/Functions.html b/modules/Functions/Functions.html
@@ -626,7 +626,7 @@ <h1 data-config-title><!-- populated from slide_config.json --></h1>
 10 FORD          2000          0  85000     8000
 # … with 72,973 more rows</pre>
 
-</article></slide><slide class=""><hgroup><h2>Applying functions with <code>across</code> from <code>dplyr</code></h2></hgroup><article  id="applying-functions-with-across-from-dplyr-6" class="smaller">
+</article></slide><slide class=""><hgroup><h2>Applying functions with <code>across</code> from <code>dplyr</code></h2></hgroup><article  class="smaller" id="applying-functions-with-across-from-dplyr-6">
 
 <p>Combining with <code>mutate()</code> - the <code>replace_na</code> function</p>
 
@@ -710,7 +710,7 @@ <h1 data-config-title><!-- populated from slide_config.json --></h1>
 
 </article></slide><slide class="segue dark nobackground level1"><hgroup class = 'auto-fadein'><h2>Multiple Data Frames</h2></hgroup><article  id="multiple-data-frames">
 
-</article></slide><slide class=""><hgroup><h2>Multiple data frames</h2></hgroup><article  id="multiple-data-frames-1" class="smaller">
+</article></slide><slide class=""><hgroup><h2>Multiple data frames</h2></hgroup><article  class="smaller" id="multiple-data-frames-1">
 
 <p>Lists help us work with multiple data frames</p>
 

diff --git a/modules/Functions/Functions.pdf b/modules/Functions/Functions.pdf
diff --git a/modules/Functions/lab/Functions_Lab_Key.html b/modules/Functions/lab/Functions_Lab_Key.html
diff --git a/modules/Manipulating_Data_in_R/Manipulating_Data_in_R.pdf b/modules/Manipulating_Data_in_R/Manipulating_Data_in_R.pdf
diff --git a/modules/Reproducibility/Reproducibility.pdf b/modules/Reproducibility/Reproducibility.pdf
diff --git a/modules/Statistics/Statistics.html b/modules/Statistics/Statistics.html
diff --git a/modules/Subsetting_Data_in_R/Subsetting_Data_in_R.pdf b/modules/Subsetting_Data_in_R/Subsetting_Data_in_R.pdf
diff --git a/modules/Subsetting_Data_in_R/index_withbase.html b/modules/Subsetting_Data_in_R/index_withbase.html
@@ -366,7 +366,7 @@ <h1 data-config-title><!-- populated from slide_config.json --></h1>
 {
     UseMethod(&quot;filter&quot;)
 }
-&lt;bytecode: 0x55f94ff62fe0&gt;
+&lt;bytecode: 0x55f8804c9f70&gt;
 &lt;environment: namespace:dplyr&gt;</pre>
 
 </article></slide><slide class=""><hgroup><h2>Renaming Columns of a <code>data.frame</code>: dplyr</h2></hgroup><article  id="renaming-columns-of-a-data.frame-dplyr-2">

diff --git a/modules/cheatsheets/Day-1.pdf b/modules/cheatsheets/Day-1.pdf
diff --git a/modules/cheatsheets/Day-2.pdf b/modules/cheatsheets/Day-2.pdf
diff --git a/modules/cheatsheets/Day-3.pdf b/modules/cheatsheets/Day-3.pdf
diff --git a/modules/cheatsheets/Day-4.pdf b/modules/cheatsheets/Day-4.pdf
diff --git a/modules/cheatsheets/Day-5.pdf b/modules/cheatsheets/Day-5.pdf
diff --git a/modules/cheatsheets/Day-6.pdf b/modules/cheatsheets/Day-6.pdf
diff --git a/modules/cheatsheets/Day-7.pdf b/modules/cheatsheets/Day-7.pdf
diff --git a/modules/cheatsheets/Day-8.pdf b/modules/cheatsheets/Day-8.pdf
diff --git a/modules/cheatsheets/Day-9.pdf b/modules/cheatsheets/Day-9.pdf
diff --git a/quotes_vs_backticks.html b/quotes_vs_backticks.html
@@ -562,10 +562,10 @@ <h2><code>tibble()</code> for naming variables</h2>
 ##   `Number!` `Var with space` `2022` `2021` typical typical2
 ##       &lt;int&gt; &lt;chr&gt;             &lt;int&gt;  &lt;int&gt;   &lt;int&gt;    &lt;int&gt;
 ## 1         1 A                     1      4       1        1
-## 2         2 B                     4      1       2        2
-## 3         3 C                     3      5       3        3
-## 4         4 D                     2      2       4        4
-## 5         5 E                     5      3       5        5</code></pre>
+## 2         2 B                     2      5       2        2
+## 3         3 C                     4      3       3        3
+## 4         4 D                     5      1       4        4
+## 5         5 E                     3      2       5        5</code></pre>
 <pre class="r"><code># this works
 
 ex_data &lt;- tibble(
@@ -580,11 +580,11 @@ <h2><code>tibble()</code> for naming variables</h2>
 <pre><code>## # A tibble: 5 × 6
 ##   `Number!` `Var with space` `2022` `2021` typical typical2
 ##       &lt;int&gt; &lt;chr&gt;             &lt;int&gt;  &lt;int&gt;   &lt;int&gt;    &lt;int&gt;
-## 1         1 A                     5      5       1        1
+## 1         1 A                     3      4       1        1
 ## 2         2 B                     2      1       2        2
-## 3         3 C                     4      3       3        3
-## 4         4 D                     1      2       4        4
-## 5         5 E                     3      4       5        5</code></pre>
+## 3         3 C                     1      3       3        3
+## 4         4 D                     4      5       4        4
+## 5         5 E                     5      2       5        5</code></pre>
 </div>
 <div id="rename" class="section level2">
 <h2><code>rename()</code></h2>
@@ -594,32 +594,32 @@ <h2><code>rename()</code></h2>
 <pre><code>## # A tibble: 5 × 6
 ##   Number `Var with space` `2022` `2021` typical typical2
 ##    &lt;int&gt; &lt;chr&gt;             &lt;int&gt;  &lt;int&gt;   &lt;int&gt;    &lt;int&gt;
-## 1      1 A                     5      5       1        1
+## 1      1 A                     3      4       1        1
 ## 2      2 B                     2      1       2        2
-## 3      3 C                     4      3       3        3
-## 4      4 D                     1      2       4        4
-## 5      5 E                     3      4       5        5</code></pre>
+## 3      3 C                     1      3       3        3
+## 4      4 D                     4      5       4        4
+## 5      5 E                     5      2       5        5</code></pre>
 <pre class="r"><code>ex_data %&gt;%
   rename(Number = &quot;Number!&quot;)</code></pre>
 <pre><code>## # A tibble: 5 × 6
 ##   Number `Var with space` `2022` `2021` typical typical2
 ##    &lt;int&gt; &lt;chr&gt;             &lt;int&gt;  &lt;int&gt;   &lt;int&gt;    &lt;int&gt;
-## 1      1 A                     5      5       1        1
+## 1      1 A                     3      4       1        1
 ## 2      2 B                     2      1       2        2
-## 3      3 C                     4      3       3        3
-## 4      4 D                     1      2       4        4
-## 5      5 E                     3      4       5        5</code></pre>
+## 3      3 C                     1      3       3        3
+## 4      4 D                     4      5       4        4
+## 5      5 E                     5      2       5        5</code></pre>
 <pre class="r"><code># not necessary but not problematic to put new typical name in quotes
 ex_data %&gt;%
   rename(&quot;Number&quot; = &quot;Number!&quot;)</code></pre>
 <pre><code>## # A tibble: 5 × 6
 ##   Number `Var with space` `2022` `2021` typical typical2
 ##    &lt;int&gt; &lt;chr&gt;             &lt;int&gt;  &lt;int&gt;   &lt;int&gt;    &lt;int&gt;
-## 1      1 A                     5      5       1        1
+## 1      1 A                     3      4       1        1
 ## 2      2 B                     2      1       2        2
-## 3      3 C                     4      3       3        3
-## 4      4 D                     1      2       4        4
-## 5      5 E                     3      4       5        5</code></pre>
+## 3      3 C                     1      3       3        3
+## 4      4 D                     4      5       4        4
+## 5      5 E                     5      2       5        5</code></pre>
 <p>Here is another example…</p>
 <pre class="r"><code># This works because Sepal.Length already exists as a column name. However `new name!` needs backticks because it doesn&#39;t exist yet and R needs to know what it is (not a not equal to conditional for example), as R could interpret it differently.
 
@@ -680,29 +680,29 @@ <h2><code>mutate()</code></h2>
 <pre><code>## # A tibble: 5 × 6
 ##   `Number!` `Var with space` `2022` `2021` typical typical2
 ##       &lt;dbl&gt; &lt;chr&gt;             &lt;int&gt;  &lt;int&gt;   &lt;int&gt;    &lt;int&gt;
-## 1         3 A                     5      5       1        1
+## 1         3 A                     3      4       1        1
 ## 2         4 B                     2      1       2        2
-## 3         5 C                     4      3       3        3
-## 4         6 D                     1      2       4        4
-## 5         7 E                     3      4       5        5</code></pre>
+## 3         5 C                     1      3       3        3
+## 4         6 D                     4      5       4        4
+## 5         7 E                     5      2       5        5</code></pre>
 <pre class="r"><code>ex_data %&gt;% mutate(&quot;Number!&quot; = `Number!` + 2)</code></pre>
 <pre><code>## # A tibble: 5 × 6
 ##   `Number!` `Var with space` `2022` `2021` typical typical2
 ##       &lt;dbl&gt; &lt;chr&gt;             &lt;int&gt;  &lt;int&gt;   &lt;int&gt;    &lt;int&gt;
-## 1         3 A                     5      5       1        1
+## 1         3 A                     3      4       1        1
 ## 2         4 B                     2      1       2        2
-## 3         5 C                     4      3       3        3
-## 4         6 D                     1      2       4        4
-## 5         7 E                     3      4       5        5</code></pre>
+## 3         5 C                     1      3       3        3
+## 4         6 D                     4      5       4        4
+## 5         7 E                     5      2       5        5</code></pre>
 <pre class="r"><code>ex_data %&gt;% mutate(Typical = `Number!` + 2)</code></pre>
 <pre><code>## # A tibble: 5 × 7
 ##   `Number!` `Var with space` `2022` `2021` typical typical2 Typical
 ##       &lt;int&gt; &lt;chr&gt;             &lt;int&gt;  &lt;int&gt;   &lt;int&gt;    &lt;int&gt;   &lt;dbl&gt;
-## 1         1 A                     5      5       1        1       3
+## 1         1 A                     3      4       1        1       3
 ## 2         2 B                     2      1       2        2       4
-## 3         3 C                     4      3       3        3       5
-## 4         4 D                     1      2       4        4       6
-## 5         5 E                     3      4       5        5       7</code></pre>
+## 3         3 C                     1      3       3        3       5
+## 4         4 D                     4      5       4        4       6
+## 5         5 E                     5      2       5        5       7</code></pre>
 </div>
 <div id="readr-expects-quotes-not-backticks" class="section level2">
 <h2><code>readr</code> expects quotes not backticks</h2>

diff --git a/resources/debugging_guide.pdf b/resources/debugging_guide.pdf
diff --git a/resources/good-scientific-coding-practices.pdf b/resources/good-scientific-coding-practices.pdf
diff --git a/resources/rtools_windows.pdf b/resources/rtools_windows.pdf