Updated to address issue with assignment templates.

_bookdown.yml

@@ -1,16 +1,17 @@
-book_filename: "Module1"
-delete_merged_file: true
-language:
-  ui:
-    chapter_name: "Chapter "
-    before_chapter_script: "rscripts/before_chapter.r"
-rmd_files:
-  - "index.Rmd"
-  - "src/02-CoursePreliminaries.Rmd"
-  - "src/03-InstallingR.Rmd"
-  - "src/04-RProgrammingFundamentals.Rmd"
-  - "src/05-WorkingWithData.Rmd"
-  - "src/06-PerformingEffectiveDataAnalysis.Rmd"
-output_dir: "docs"
-# rmd_subdir: ["src"]  # misses index.Rmd if we use this
-# clean: ["src/book.bib"] # removes book.bib file when cleaned
+book_filename: "Module1"
+delete_merged_file: true
+language:
+  ui:
+    chapter_name: "Chapter "
+    before_chapter_script: "rscripts/before_chapter.r"
+rmd_files:
+  - "index.Rmd"
+  - "src/02-CoursePreliminaries.Rmd"
+  - "src/03-InstallingR.Rmd"
+  - "src/04-RProgrammingFundamentals.Rmd"
+  - "src/05-WorkingWithData.Rmd"
+  - "src/06-PerformingEffectiveDataAnalysis.Rmd"
+output_dir: "docs"
+ignore: ["assignment_templates/*"]
+# rmd_subdir: ["src"]  # misses index.Rmd if we use this
+# clean: ["src/book.bib"] # removes book.bib file when cleaned

docs/index.html

@@ -344,7 +344,7 @@ <h1>
 <h1 class="title">R Module 1</h1>
 <p class="author"><em>Alex Fout<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a></em></p>
 <p class="author"><em>Lane Drew<a href="#fn2" class="footnote-ref" id="fnref2"><sup>2</sup></a></em></p>
-<p class="date"><em>11 Jun, 2024, 12:38 PM</em></p>
+<p class="date"><em>13 Jun, 2024, 10:33 AM</em></p>
 </div>
 <div id="welcome" class="section level1 hasAnchor" number="1">
 <h1><span class="header-section-number">Chapter 1</span> Welcome!<a href="index.html#welcome" class="anchor-section" aria-label="Anchor link to header"></a></h1>

docs/reference-keys 2.txt

@@ -0,0 +1,168 @@
+fig:unnamed-chunk-1
+fig:unnamed-chunk-9
+fig:unnamed-chunk-12
+fig:unnamed-chunk-34
+fig:unnamed-chunk-35
+fig:unnamed-chunk-36
+fig:unnamed-chunk-49
+fig:unnamed-chunk-323
+fig:unnamed-chunk-325
+fig:unnamed-chunk-326
+fig:unnamed-chunk-327
+welcome
+how-to-navigate-this-book
+associated-csu-course
+prelim
+this-textbook
+special-boxes
+how-this-book-displays-code
+next-steps
+course-topics-syllabus
+syllabus
+assignment-templates
+course-policies
+grading-scale
+running-your-first-r-code
+getoutoftheclass
+what-is-r
+r-is-a-programming-language
+r-is-software
+r-is-free
+r-is-open-source
+r-is-an-ecosystem
+r-packages
+r-interfaces
+the-r-community
+places-to-get-help-if-youre-a-student-taking-this-class-for-credit
+places-to-get-help-anyone
+installing-r
+computer-basics
+operating-systems
+files-directory-structures
+downloads-and-installations
+install-r-r-studio
+installing-r-1
+windows
+macos
+linux
+conclusion
+installing-rstudio
+windows-1
+macos-1
+conclusion-1
+successfull-installation
+running-code-in-rstudio
+the-r-console
+r-scripts
+same-examples-on-your-computer
+r-markdown
+workspace-setup
+recommended-settings
+setting-working-directory
+create-rstudio-project-and-directories-for-class
+create-rstudio-project
+create-directory-structure
+video
+set
+some-useful-commands-you-should-know
+r-programming-fundamentals
+programming-preliminaries
+r-commands
+comments
+blank-lines
+case
+section
+section-1
+data-types
+numeric
+integer
+character
+logical
+data-structures
+vectors
+accessing-and-changing-elements
+working-with-vectors
+vectors-of-different-types
+special-numeric-vectors
+another-data-type-factor
+combining-vectors
+type-conversion
+matrices
+lists
+lists-and-vectors
+lists-of-vectors
+data-frames
+r-objects
+everything-is-an-object-in-r
+assigning-objects
+attributes
+null-objects
+removing-objects
+working-with-data
+quick-example
+reading-writing-data
+olympic-athletes-example
+locating-your-data-set
+reading-csv-files
+writing-csv-files
+summary-statistics
+quantitative-variables
+categorical-variables
+saving-an-rdata-file
+data-formatting
+raw-data-vs.-clean-data.
+indexing
+vectors-1
+matrices-1
+lists-1
+data-frames-1
+advanced-indexing
+logical-based-indexing
+negative-indexing
+nested-indexing-13
+visualization
+one-quantitative-variable
+two-quantitative-variables
+one-categorical-variable
+two-categorical-variables
+multiple-plots
+other-types-of-plots
+scatterplot-matrix
+surfaces
+saving-images
+rcode
+rstudio-plot-window
+rmarkdown
+plotting-wrap-up
+vignettes
+flood-analysis-example
+map
+installing-and-using-packages
+downloading-the-data
+explore-the-data-structure
+explore-the-data
+analyze-the-data
+performing-effective-data-analysis
+basic-control-flow
+loops
+nested-loops
+breaking-out-of-for-loops.
+if-statements
+else
+breaking-out-of-for-loops.-1
+formatting-conventions
+writing-functions
+the-components-of-a-function
+writing-a-function
+using-functions-for-data-analysis
+function-scope
+advanced-control-flow
+applying-over-multiple-dimensions
+applying-over-data-frame-groups
+working-with-popular-packages
+what-is-a-package
+how-do-i-use-packages
+finding-and-using-package-help.
+making-beautiful-plots-with-ggplot2
+organizing-your-data-with-dplyr
+working-with-character-strings-with-stringr

docs/vignettes.html

@@ -446,11 +446,11 @@ <h4><span class="header-section-number">5.7.1.5</span> Explore the data<a href="
 <pre class="output-style"><code>      Date                q_cfs        
  Min.   :2010-10-01   Min.   :   1.31  
  1st Qu.:2014-03-04   1st Qu.:  22.90  
- Median :2017-08-05   Median :  62.35  
- Mean   :2017-08-05   Mean   : 222.52  
- 3rd Qu.:2021-01-06   3rd Qu.: 147.00  
- Max.   :2024-06-10   Max.   :7150.00  </code></pre>
-<p>It looks like we have data from 2010 to 2024-06-11 and a range in river
+ Median :2017-08-06   Median :  62.40  
+ Mean   :2017-08-06   Mean   : 222.74  
+ 3rd Qu.:2021-01-08   3rd Qu.: 147.00  
+ Max.   :2024-06-12   Max.   :7150.00  </code></pre>
+<p>It looks like we have data from 2010 to 2024-06-13 and a range in river
 flow (q_cfs) from 2.6 cfs all the way up to 7150 cfs. If you’re a hydrologist,
 hopefully these flow numbers look right, but another way to check to make sure
 is to simply plot the data as we do below.</p>

docs/workspace-setup.html

@@ -453,8 +453,8 @@ <h3><span class="header-section-number">3.5.4</span> Some useful commands you sh
 <div class="sourceCode" id="cb8"><pre class="sourceCode r chunk-style"><code class="sourceCode r"><span id="cb8-1"><a href="workspace-setup.html#cb8-1" tabindex="-1"></a><span class="fu">rm</span>(<span class="at">list =</span> <span class="fu">ls</span>())  <span class="co"># Clear everything in your workspace</span></span>
 <span id="cb8-2"><a href="workspace-setup.html#cb8-2" tabindex="-1"></a><span class="fu">gc</span>()             <span class="co"># Perform garbage collection</span></span></code></pre></div>
 <pre class="output-style"><code>          used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
-Ncells  879268 47.0    1675977 89.6         NA  1322192 70.7
-Vcells 1630663 12.5    8388608 64.0     102400  2584202 19.8</code></pre>
+Ncells  879272 47.0    1676008 89.6         NA  1322144 70.7
+Vcells 1630670 12.5    8388608 64.0     102400  2591288 19.8</code></pre>
 <p>You might also want to clear the R console, which you can do by placing your cursor in the R console and typing <code>&lt;control&gt; l</code> (careful! that’s a lowercase L).</p>
 <div class="bonus">
 <p>

docs/writing-functions.html

@@ -406,15 +406,15 @@ <h3><span class="header-section-number">6.2.1</span> The Components Of A Functio
         stop(&quot;&#39;decreasing&#39; must be a length-1 logical vector.\nDid you intend to set &#39;partial&#39;?&quot;)
     UseMethod(&quot;sort&quot;)
 }
-&lt;bytecode: 0x11a66a380&gt;
+&lt;bytecode: 0x14be3cca8&gt;
 &lt;environment: namespace:base&gt;</code></pre>
 <p>Now, there are some things in this output that may be confusing and that we won’t explain in this book, but at least some of the output should look like R code to you!
 Here’s another example, the <code>mean</code> function:</p>
 <div class="sourceCode" id="cb517"><pre class="sourceCode r chunk-style"><code class="sourceCode r"><span id="cb517-1"><a href="writing-functions.html#cb517-1" tabindex="-1"></a><span class="co"># View the code of the mean function (or so we think)</span></span>
 <span id="cb517-2"><a href="writing-functions.html#cb517-2" tabindex="-1"></a>mean</span></code></pre></div>
 <pre class="output-style"><code>function (x, ...) 
 UseMethod(&quot;mean&quot;)
-&lt;bytecode: 0x11b948678&gt;
+&lt;bytecode: 0x12c8f9c78&gt;
 &lt;environment: namespace:base&gt;</code></pre>
 <p>This example doesn’t seem to have as much R code in it, so where is the code for this function?
 The answer is that both <code>sort</code> and <code>mean</code> (and many other R functions) are written in a <em>different</em> programming language, C, which isn’t human readable once it’s compiled.