diff --git a/docs/01-intro.md b/docs/01-intro.md
index ff4e983a7..3c2673345 100644
--- a/docs/01-intro.md
+++ b/docs/01-intro.md
@@ -1,6 +1,4 @@
 
-
-
 # Introduction
 
 
@@ -32,76 +30,49 @@ devtools::session_info()
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-11-07
+##  date     2024-12-19
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date (UTC) lib source
-##  askpass       1.2.0   2023-09-03 [1] RSPM (R 4.3.0)
 ##  bookdown      0.41    2024-10-16 [1] CRAN (R 4.3.2)
 ##  cachem        1.0.8   2023-05-01 [1] RSPM (R 4.3.0)
-##  chromote      0.3.1   2024-08-30 [1] CRAN (R 4.3.2)
 ##  cli           3.6.2   2023-12-11 [1] RSPM (R 4.3.0)
 ##  devtools      2.4.5   2022-10-11 [1] RSPM (R 4.3.0)
 ##  digest        0.6.34  2024-01-11 [1] RSPM (R 4.3.0)
-##  dplyr         1.1.4   2023-11-17 [1] RSPM (R 4.3.0)
 ##  ellipsis      0.3.2   2021-04-29 [1] RSPM (R 4.3.0)
 ##  evaluate      0.23    2023-11-01 [1] RSPM (R 4.3.0)
-##  fansi         1.0.6   2023-12-08 [1] RSPM (R 4.3.0)
 ##  fastmap       1.1.1   2023-02-24 [1] RSPM (R 4.3.0)
 ##  fs            1.6.3   2023-07-20 [1] RSPM (R 4.3.0)
-##  generics      0.1.3   2022-07-05 [1] RSPM (R 4.3.0)
 ##  glue          1.7.0   2024-01-09 [1] RSPM (R 4.3.0)
-##  hms           1.1.3   2023-03-21 [1] RSPM (R 4.3.0)
 ##  htmltools     0.5.7   2023-11-03 [1] RSPM (R 4.3.0)
 ##  htmlwidgets   1.6.4   2023-12-06 [1] RSPM (R 4.3.0)
 ##  httpuv        1.6.14  2024-01-26 [1] RSPM (R 4.3.0)
-##  httr          1.4.7   2023-08-15 [1] RSPM (R 4.3.0)
-##  janitor       2.2.0   2023-02-02 [1] RSPM (R 4.3.0)
-##  jsonlite      1.8.8   2023-12-04 [1] RSPM (R 4.3.0)
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 ##  later         1.3.2   2023-12-06 [1] RSPM (R 4.3.0)
 ##  lifecycle     1.0.4   2023-11-07 [1] RSPM (R 4.3.0)
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 ##  mime          0.12    2021-09-28 [1] RSPM (R 4.3.0)
 ##  miniUI        0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
-##  openssl       2.1.1   2023-09-25 [1] RSPM (R 4.3.0)
-##  ottrpal       1.3.0   2024-10-23 [1] Github (jhudsl/ottrpal@2e19782)
-##  pillar        1.9.0   2023-03-22 [1] RSPM (R 4.3.0)
 ##  pkgbuild      1.4.3   2023-12-10 [1] RSPM (R 4.3.0)
-##  pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.3.0)
 ##  pkgload       1.3.4   2024-01-16 [1] RSPM (R 4.3.0)
-##  processx      3.8.3   2023-12-10 [1] RSPM (R 4.3.0)
 ##  profvis       0.3.8   2023-05-02 [1] RSPM (R 4.3.0)
 ##  promises      1.2.1   2023-08-10 [1] RSPM (R 4.3.0)
-##  ps            1.7.6   2024-01-18 [1] RSPM (R 4.3.0)
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-##  readr         2.1.5   2024-01-10 [1] RSPM (R 4.3.0)
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 ##  rmarkdown     2.25    2023-09-18 [1] RSPM (R 4.3.0)
-##  rprojroot     2.0.4   2023-11-05 [1] CRAN (R 4.3.2)
 ##  sessioninfo   1.2.2   2021-12-06 [1] RSPM (R 4.3.0)
 ##  shiny         1.8.0   2023-11-17 [1] RSPM (R 4.3.0)
-##  snakecase     0.11.1  2023-08-27 [1] RSPM (R 4.3.0)
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 ##  stringr       1.5.1   2023-11-14 [1] RSPM (R 4.3.0)
-##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.2)
-##  tidyselect    1.2.0   2022-10-10 [1] RSPM (R 4.3.0)
-##  timechange    0.3.0   2024-01-18 [1] RSPM (R 4.3.0)
-##  tzdb          0.4.0   2023-05-12 [1] RSPM (R 4.3.0)
 ##  urlchecker    1.0.1   2021-11-30 [1] RSPM (R 4.3.0)
 ##  usethis       2.2.3   2024-02-19 [1] RSPM (R 4.3.0)
-##  utf8          1.2.4   2023-10-22 [1] RSPM (R 4.3.0)
 ##  vctrs         0.6.5   2023-12-01 [1] RSPM (R 4.3.0)
-##  webshot2      0.1.1   2023-08-11 [1] CRAN (R 4.3.2)
-##  websocket     1.4.2   2024-07-22 [1] CRAN (R 4.3.2)
 ##  xfun          0.48    2024-10-03 [1] CRAN (R 4.3.2)
-##  xml2          1.3.6   2023-12-04 [1] RSPM (R 4.3.0)
 ##  xtable        1.8-4   2019-04-21 [1] RSPM (R 4.3.0)
 ##  yaml          2.3.8   2023-12-11 [1] RSPM (R 4.3.0)
 ## 
diff --git a/docs/02-chapter_of_course.md b/docs/02-chapter_of_course.md
index 964526257..afee494d3 100644
--- a/docs/02-chapter_of_course.md
+++ b/docs/02-chapter_of_course.md
@@ -7,9 +7,6 @@ To see the rendered version of this chapter and the rest of the template, see he
 
 Every chapter needs to start out with this chunk of code:
 
-
-
-
 ## Learning Objectives
 
 Every chapter also needs Learning objectives that will look like this:  
@@ -59,7 +56,7 @@ And make plots too:
 hist_plot <- hist(iris$Sepal.Length)
 ```
 
-![](resources/images/02-chapter_of_course_files/figure-docx/unnamed-chunk-4-1.png)<!-- -->
+![](02-chapter_of_course_files/figure-docx/unnamed-chunk-3-1.png)<!-- -->
 
 You can also save these plots to file:
 
@@ -107,7 +104,7 @@ dev.off()
 How to include a Google slide. It's simplest to use the `ottrpal` package:
 
 
-![](resources/images/02-chapter_of_course_files/figure-docx//1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png){width=100%}
+![](02-chapter_of_course_files/figure-docx//1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png){width=100%}
 
 But if you have the slide or some other image locally downloaded you can also use HTML like this:
 
@@ -303,7 +300,7 @@ devtools::session_info()
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-11-07
+##  date     2024-12-19
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
diff --git a/docs/02-chapter_of_course_files/figure-html/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png b/docs/02-chapter_of_course_files/figure-html/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png
new file mode 100644
index 000000000..b865852d5
Binary files /dev/null and b/docs/02-chapter_of_course_files/figure-html/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png differ
diff --git a/docs/resources/images/02-chapter_of_course_files/figure-html/unnamed-chunk-4-1.png b/docs/02-chapter_of_course_files/figure-html/unnamed-chunk-3-1.png
similarity index 100%
rename from docs/resources/images/02-chapter_of_course_files/figure-html/unnamed-chunk-4-1.png
rename to docs/02-chapter_of_course_files/figure-html/unnamed-chunk-3-1.png
diff --git a/docs/About.md b/docs/About.md
index e21b9258f..7feab79c4 100644
--- a/docs/About.md
+++ b/docs/About.md
@@ -51,7 +51,7 @@ 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     2024-11-07
+##  date     2024-12-19
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
diff --git a/docs/Course_Name.docx b/docs/Course_Name.docx
index f09039d46..b32a9374a 100644
Binary files a/docs/Course_Name.docx and b/docs/Course_Name.docx differ
diff --git a/docs/a-new-chapter.html b/docs/a-new-chapter.html
index 40d63eaf7..6e791bcdc 100644
--- a/docs/a-new-chapter.html
+++ b/docs/a-new-chapter.html
@@ -276,7 +276,7 @@ <h2><span class="header-section-number">2.4</span> Code examples<a href="a-new-c
 <span id="cb4-4"><a href="a-new-chapter.html#cb4-4" tabindex="-1"></a>}</span></code></pre></div>
 <p>And make plots too:</p>
 <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="a-new-chapter.html#cb5-1" tabindex="-1"></a>hist_plot <span class="ot">&lt;-</span> <span class="fu">hist</span>(iris<span class="sc">$</span>Sepal.Length)</span></code></pre></div>
-<p><img src="resources/images/02-chapter_of_course_files/figure-html/unnamed-chunk-4-1.png" width="672" /></p>
+<p><img src="02-chapter_of_course_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p>
 <p>You can also save these plots to file:</p>
 <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="a-new-chapter.html#cb6-1" tabindex="-1"></a><span class="fu">png</span>(<span class="fu">file.path</span>(output_dir, <span class="st">&quot;test_plot.png&quot;</span>))</span>
 <span id="cb6-2"><a href="a-new-chapter.html#cb6-2" tabindex="-1"></a>hist_plot</span></code></pre></div>
@@ -308,7 +308,7 @@ <h2><span class="header-section-number">2.4</span> Code examples<a href="a-new-c
 <div id="image-example" class="section level2 hasAnchor" number="2.5">
 <h2><span class="header-section-number">2.5</span> Image example<a href="a-new-chapter.html#image-example" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>How to include a Google slide. It’s simplest to use the <code>ottrpal</code> package:</p>
-<p><img src="resources/images/02-chapter_of_course_files/figure-html/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png" alt="Major point!! example image" width="100%" style="display: block; margin: auto;" /></p>
+<p><img src="02-chapter_of_course_files/figure-html/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png" alt="Major point!! example image" width="100%" style="display: block; margin: auto;" /></p>
 <p>But if you have the slide or some other image locally downloaded you can also use HTML like this:</p>
 <p><img src="resources/images/02-chapter_of_course_files/figure-html/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png" title="Major point!! example image" alt="Major point!! example image" style="display: block; margin: auto;" /></p>
 </div>
@@ -444,7 +444,7 @@ <h2><span class="header-section-number">2.11</span> Print out session info<a hre
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-11-07
+##  date     2024-12-19
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
diff --git a/docs/about-the-authors.html b/docs/about-the-authors.html
index 7ffb4c0e6..9cfea0a8d 100644
--- a/docs/about-the-authors.html
+++ b/docs/about-the-authors.html
@@ -380,7 +380,7 @@ <h1>About the Authors<a href="about-the-authors.html#about-the-authors" class="a
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-11-07
+##  date     2024-12-19
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
diff --git a/docs/index.html b/docs/index.html
index 1c627058f..321285597 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -240,7 +240,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Course Name</h1>
-<p class="date"><em>November, 2024</em></p>
+<p class="date"><em>December, 2024</em></p>
 </div>
 <div id="about-this-course" class="section level1 unnumbered hasAnchor">
 <h1>About this Course<a href="index.html#about-this-course" class="anchor-section" aria-label="Anchor link to header"></a></h1>
diff --git a/docs/index.md b/docs/index.md
index 273c97297..438ad6983 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,6 +1,6 @@
 ---
 title: "Course Name"
-date: "November, 2024"
+date: "December, 2024"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib]
diff --git a/docs/introduction.html b/docs/introduction.html
index 94dffb823..b3c8391fd 100644
--- a/docs/introduction.html
+++ b/docs/introduction.html
@@ -261,79 +261,53 @@ <h2><span class="header-section-number">1.3</span> Curriculum<a href="introducti
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-11-07
+##  date     2024-12-19
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date (UTC) lib source
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 ##  bookdown      0.41    2024-10-16 [1] CRAN (R 4.3.2)
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 ##  cachem        1.0.8   2023-05-01 [1] RSPM (R 4.3.0)
-##  chromote      0.3.1   2024-08-30 [1] CRAN (R 4.3.2)
 ##  cli           3.6.2   2023-12-11 [1] RSPM (R 4.3.0)
 ##  devtools      2.4.5   2022-10-11 [1] RSPM (R 4.3.0)
 ##  digest        0.6.34  2024-01-11 [1] RSPM (R 4.3.0)
-##  dplyr         1.1.4   2023-11-17 [1] RSPM (R 4.3.0)
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-##  fansi         1.0.6   2023-12-08 [1] RSPM (R 4.3.0)
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 ##  glue          1.7.0   2024-01-09 [1] RSPM (R 4.3.0)
-##  hms           1.1.3   2023-03-21 [1] RSPM (R 4.3.0)
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 ##  httpuv        1.6.14  2024-01-26 [1] RSPM (R 4.3.0)
-##  httr          1.4.7   2023-08-15 [1] RSPM (R 4.3.0)
-##  janitor       2.2.0   2023-02-02 [1] RSPM (R 4.3.0)
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 ##  lifecycle     1.0.4   2023-11-07 [1] RSPM (R 4.3.0)
-##  lubridate     1.9.3   2023-09-27 [1] RSPM (R 4.3.0)
 ##  magrittr      2.0.3   2022-03-30 [1] RSPM (R 4.3.0)
 ##  memoise       2.0.1   2021-11-26 [1] RSPM (R 4.3.0)
 ##  mime          0.12    2021-09-28 [1] RSPM (R 4.3.0)
 ##  miniUI        0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
-##  openssl       2.1.1   2023-09-25 [1] RSPM (R 4.3.0)
-##  ottrpal       1.3.0   2024-10-23 [1] Github (jhudsl/ottrpal@2e19782)
-##  pillar        1.9.0   2023-03-22 [1] RSPM (R 4.3.0)
 ##  pkgbuild      1.4.3   2023-12-10 [1] RSPM (R 4.3.0)
-##  pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.3.0)
 ##  pkgload       1.3.4   2024-01-16 [1] RSPM (R 4.3.0)
-##  processx      3.8.3   2023-12-10 [1] RSPM (R 4.3.0)
 ##  profvis       0.3.8   2023-05-02 [1] RSPM (R 4.3.0)
 ##  promises      1.2.1   2023-08-10 [1] RSPM (R 4.3.0)
-##  ps            1.7.6   2024-01-18 [1] RSPM (R 4.3.0)
 ##  purrr         1.0.2   2023-08-10 [1] RSPM (R 4.3.0)
 ##  R6            2.5.1   2021-08-19 [1] RSPM (R 4.3.0)
 ##  Rcpp          1.0.12  2024-01-09 [1] RSPM (R 4.3.0)
-##  readr         2.1.5   2024-01-10 [1] RSPM (R 4.3.0)
 ##  remotes       2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0)
 ##  rlang         1.1.4   2024-06-04 [1] CRAN (R 4.3.2)
 ##  rmarkdown     2.25    2023-09-18 [1] RSPM (R 4.3.0)
-##  rprojroot     2.0.4   2023-11-05 [1] CRAN (R 4.3.2)
 ##  sass          0.4.8   2023-12-06 [1] RSPM (R 4.3.0)
 ##  sessioninfo   1.2.2   2021-12-06 [1] RSPM (R 4.3.0)
 ##  shiny         1.8.0   2023-11-17 [1] RSPM (R 4.3.0)
-##  snakecase     0.11.1  2023-08-27 [1] RSPM (R 4.3.0)
 ##  stringi       1.8.3   2023-12-11 [1] RSPM (R 4.3.0)
 ##  stringr       1.5.1   2023-11-14 [1] RSPM (R 4.3.0)
-##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.2)
-##  tidyselect    1.2.0   2022-10-10 [1] RSPM (R 4.3.0)
-##  timechange    0.3.0   2024-01-18 [1] RSPM (R 4.3.0)
-##  tzdb          0.4.0   2023-05-12 [1] RSPM (R 4.3.0)
 ##  urlchecker    1.0.1   2021-11-30 [1] RSPM (R 4.3.0)
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-##  utf8          1.2.4   2023-10-22 [1] RSPM (R 4.3.0)
 ##  vctrs         0.6.5   2023-12-01 [1] RSPM (R 4.3.0)
-##  webshot2      0.1.1   2023-08-11 [1] CRAN (R 4.3.2)
-##  websocket     1.4.2   2024-07-22 [1] CRAN (R 4.3.2)
 ##  xfun          0.48    2024-10-03 [1] CRAN (R 4.3.2)
-##  xml2          1.3.6   2023-12-04 [1] RSPM (R 4.3.0)
 ##  xtable        1.8-4   2019-04-21 [1] RSPM (R 4.3.0)
 ##  yaml          2.3.8   2023-12-11 [1] RSPM (R 4.3.0)
 ## 
diff --git a/docs/search_index.json b/docs/search_index.json
index 84f73fa32..b886f2b4a 100644
--- a/docs/search_index.json
+++ b/docs/search_index.json
@@ -1 +1 @@
-[["index.html", "Course Name About this Course 0.1 Available course formats", " Course Name November, 2024 About this Course 0.1 Available course formats This course is available in multiple formats which allows you to take it in the way that best suites your needs. You can take it for certificate which can be for free or fee. The material for this course can be viewed without login requirement on this Bookdown website. This format might be most appropriate for you if you rely on screen-reader technology. This course can be taken for free certification through Leanpub. This course can be taken on Coursera for certification here (but it is not available for free on Coursera). Our courses are open source, you can find the source material for this course on GitHub. "],["introduction.html", "Chapter 1 Introduction 1.1 Motivation 1.2 Target Audience 1.3 Curriculum", " Chapter 1 Introduction 1.1 Motivation 1.2 Target Audience The course is intended for … 1.3 Curriculum The course covers… devtools::session_info() ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-11-07 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## askpass 1.2.0 2023-09-03 [1] RSPM (R 4.3.0) ## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## chromote 0.3.1 2024-08-30 [1] CRAN (R 4.3.2) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## dplyr 1.1.4 2023-11-17 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0) ## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) ## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) ## generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0) ## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) ## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## httr 1.4.7 2023-08-15 [1] RSPM (R 4.3.0) ## janitor 2.2.0 2023-02-02 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) ## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## lubridate 1.9.3 2023-09-27 [1] RSPM (R 4.3.0) ## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) ## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) ## openssl 2.1.1 2023-09-25 [1] RSPM (R 4.3.0) ## ottrpal 1.3.0 2024-10-23 [1] Github (jhudsl/ottrpal@2e19782) ## pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0) ## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) ## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0) ## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) ## processx 3.8.3 2023-12-10 [1] RSPM (R 4.3.0) ## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) ## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) ## ps 1.7.6 2024-01-18 [1] RSPM (R 4.3.0) ## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) ## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## readr 2.1.5 2024-01-10 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) ## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0) ## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.3.2) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) ## snakecase 0.11.1 2023-08-27 [1] RSPM (R 4.3.0) ## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.2) ## tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.3.0) ## timechange 0.3.0 2024-01-18 [1] RSPM (R 4.3.0) ## tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## webshot2 0.1.1 2023-08-11 [1] CRAN (R 4.3.2) ## websocket 1.4.2 2024-07-22 [1] CRAN (R 4.3.2) ## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2) ## xml2 1.3.6 2023-12-04 [1] RSPM (R 4.3.0) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── "],["a-new-chapter.html", "Chapter 2 A new chapter 2.1 Learning Objectives 2.2 Libraries 2.3 Topic of Section 2.4 Code examples 2.5 Image example 2.6 Video examples 2.7 Website Examples 2.8 Citation examples 2.9 Stylized boxes 2.10 Dropdown summaries 2.11 Print out session info", " Chapter 2 A new chapter If you haven’t yet read the getting started Wiki pages; start there. To see the rendered version of this chapter and the rest of the template, see here: https://jhudatascience.org/OTTR_Template/. Every chapter needs to start out with this chunk of code: 2.1 Learning Objectives Every chapter also needs Learning objectives that will look like this: This chapter will cover: {You can use https://tips.uark.edu/using-blooms-taxonomy/ to define some learning objectives here} {Another learning objective} 2.2 Libraries For this chapter, we’ll need the following packages attached: *Remember to add any additional packages you need to your course’s own docker image. library(magrittr) 2.3 Topic of Section You can write all your text in sections like this, using ## to indicate a new header. you can use additional pound symbols to create lower levels of headers. See here for additional general information about how you can format text within R Markdown files. In addition, see here for more in depth and advanced options. 2.3.1 Subtopic Here’s a subheading (using three pound symbols) and some text in this subsection! 2.4 Code examples You can demonstrate code like this: output_dir &lt;- file.path(&quot;resources&quot;, &quot;code_output&quot;) if (!dir.exists(output_dir)) { dir.create(output_dir) } And make plots too: hist_plot &lt;- hist(iris$Sepal.Length) You can also save these plots to file: png(file.path(output_dir, &quot;test_plot.png&quot;)) hist_plot ## $breaks ## [1] 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0 ## ## $counts ## [1] 5 27 27 30 31 18 6 6 ## ## $density ## [1] 0.06666667 0.36000000 0.36000000 0.40000000 0.41333333 0.24000000 0.08000000 ## [8] 0.08000000 ## ## $mids ## [1] 4.25 4.75 5.25 5.75 6.25 6.75 7.25 7.75 ## ## $xname ## [1] &quot;iris$Sepal.Length&quot; ## ## $equidist ## [1] TRUE ## ## attr(,&quot;class&quot;) ## [1] &quot;histogram&quot; dev.off() ## png ## 2 2.5 Image example How to include a Google slide. It’s simplest to use the ottrpal package: But if you have the slide or some other image locally downloaded you can also use HTML like this: 2.6 Video examples You may also want to embed videos in your course. If alternatively, you just want to include a link you can do so like this: Check out this link to a video using markdown syntax. 2.6.1 Using knitr To embed videos in your course, you can use knitr::include_url() like this: Note that you should use echo=FALSE in the code chunk because we don’t want the code part of this to show up. If you are unfamiliar with how R Markdown code chunks work, read this. 2.6.2 Using HTML 2.6.3 Using knitr 2.6.4 Using HTML 2.7 Website Examples Yet again you can use a link to a website like so: A Website You might want to have users open a website in a new tab by default, especially if they need to reference both the course and a resource at once. A Website Or, you can embed some websites. 2.7.1 Using knitr This works: 2.7.2 Using HTML If you’d like the URL to show up in a new tab you can do this: &lt;a href=&quot;https://www.linkedin.com&quot; target=&quot;_blank&quot;&gt;LinkedIn&lt;/a&gt; 2.8 Citation examples We can put citations at the end of a sentence like this (Allaire et al. 2021). Or multiple citations Xie, Allaire, and Grolemund (2018). but they need a ; separator (Allaire et al. 2021; Xie, Allaire, and Grolemund 2018). In text, we can put citations like this Allaire et al. (2021). 2.9 Stylized boxes Occasionally, you might find it useful to emphasize a particular piece of information. To help you do so, we have provided css code and images (no need for you to worry about that!) to create the following stylized boxes. You can use these boxes in your course with either of two options: using HTML code or Pandoc syntax. 2.9.1 Using rmarkdown container syntax The rmarkdown package allows for a different syntax to be converted to the HTML that you just saw and also allows for conversion to LaTeX. See the Bookdown documentation for more information (Xie, Dervieux, and Riederer 2020). Note that Bookdown uses Pandoc. ::: {.notice} Note using rmarkdown syntax. ::: Note using rmarkdown syntax. As an example you might do something like this: Please click on the subsection headers in the left hand navigation bar (e.g., 2.1, 4.3) a second time to expand the table of contents and enable the scroll_highlight feature (see more) 2.9.2 Using HTML To add a warning box like the following use: &lt;div class = &quot;notice&quot;&gt; Followed by the text you want inside &lt;/div&gt; This will create the following: Followed by the text you want inside Here is a &lt;div class = \"warning\"&gt; box: Note text Here is a &lt;div class = \"github\"&gt; box: GitHub text Here is a &lt;div class = \"dictionary\"&gt; box: dictionary text Here is a &lt;div class = \"reflection\"&gt; box: reflection text Here is a &lt;div class = \"wip\"&gt; box: Work in Progress text 2.10 Dropdown summaries You can hide additional information in a dropdown menu Here’s more words that are hidden. 2.11 Print out session info You should print out session info when you have code for reproducibility purposes. devtools::session_info() ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-11-07 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## askpass 1.2.0 2023-09-03 [1] RSPM (R 4.3.0) ## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## chromote 0.3.1 2024-08-30 [1] CRAN (R 4.3.2) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## curl 5.2.0 2023-12-08 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## dplyr 1.1.4 2023-11-17 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0) ## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) ## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) ## generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## highr 0.11 2024-05-26 [1] CRAN (R 4.3.2) ## hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0) ## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) ## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## httr 1.4.7 2023-08-15 [1] RSPM (R 4.3.0) ## janitor 2.2.0 2023-02-02 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) ## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## lubridate 1.9.3 2023-09-27 [1] RSPM (R 4.3.0) ## magrittr * 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) ## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) ## openssl 2.1.1 2023-09-25 [1] RSPM (R 4.3.0) ## ottrpal 1.3.0 2024-10-23 [1] Github (jhudsl/ottrpal@2e19782) ## pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0) ## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) ## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0) ## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) ## processx 3.8.3 2023-12-10 [1] RSPM (R 4.3.0) ## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) ## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) ## ps 1.7.6 2024-01-18 [1] RSPM (R 4.3.0) ## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) ## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## readr 2.1.5 2024-01-10 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) ## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0) ## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.3.2) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) ## snakecase 0.11.1 2023-08-27 [1] RSPM (R 4.3.0) ## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.2) ## tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.3.0) ## timechange 0.3.0 2024-01-18 [1] RSPM (R 4.3.0) ## tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## webshot2 0.1.1 2023-08-11 [1] CRAN (R 4.3.2) ## websocket 1.4.2 2024-07-22 [1] CRAN (R 4.3.2) ## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2) ## xml2 1.3.6 2023-12-04 [1] RSPM (R 4.3.0) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── References "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Pedagogy Lead Content Instructor(s) FirstName LastName Lecturer(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved Delivered the course in some way - video or audio Content Author(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved If any other authors besides lead instructor Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involved Wrote less than a chapter Content Editor(s)/Reviewer(s) Checked your content Content Director(s) Helped guide the content direction Content Consultants (include chapter name/link in parentheses or word “General”) - make new line if more than one chapter involved Gave high level advice on content Acknowledgments Gave small assistance to content but not to the level of consulting Production Content Publisher(s) Helped with publishing platform Content Publishing Reviewer(s) Reviewed overall content and aesthetics on publishing platform Technical Course Publishing Engineer(s) Helped with the code for the technical aspects related to the specific course generation Template Publishing Engineers Candace Savonen, Carrie Wright, Ava Hoffman Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Ava Hoffman, Candace Savonen Package Developers (ottrpal) Candace Savonen, Ava Hoffman, Howard Baek, Kate Isaac, Carrie Wright, John Muschelli Art and Design Illustrator(s) Created graphics for the course Figure Artist(s) Created figures/plots for course Videographer(s) Filmed videos Videography Editor(s) Edited film Audiographer(s) Recorded audio Audiography Editor(s) Edited audio recordings Funding Funder(s) Institution/individual who funded course including grant number Funding Staff Staff members who help with funding   ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-11-07 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) ## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) ## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) ## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) ## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) ## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) ## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) ## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) ## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) ## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) ## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) ## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) ## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── "],["references.html", "Chapter 3 References", " Chapter 3 References "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). 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. "]]
+[["index.html", "Course Name About this Course 0.1 Available course formats", " Course Name December, 2024 About this Course 0.1 Available course formats This course is available in multiple formats which allows you to take it in the way that best suites your needs. You can take it for certificate which can be for free or fee. The material for this course can be viewed without login requirement on this Bookdown website. This format might be most appropriate for you if you rely on screen-reader technology. This course can be taken for free certification through Leanpub. This course can be taken on Coursera for certification here (but it is not available for free on Coursera). Our courses are open source, you can find the source material for this course on GitHub. "],["introduction.html", "Chapter 1 Introduction 1.1 Motivation 1.2 Target Audience 1.3 Curriculum", " Chapter 1 Introduction 1.1 Motivation 1.2 Target Audience The course is intended for … 1.3 Curriculum The course covers… devtools::session_info() ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-12-19 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) ## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) ## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) ## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) ## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) ## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) ## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) ## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) ## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) ## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) ## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) ## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) ## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── "],["a-new-chapter.html", "Chapter 2 A new chapter 2.1 Learning Objectives 2.2 Libraries 2.3 Topic of Section 2.4 Code examples 2.5 Image example 2.6 Video examples 2.7 Website Examples 2.8 Citation examples 2.9 Stylized boxes 2.10 Dropdown summaries 2.11 Print out session info", " Chapter 2 A new chapter If you haven’t yet read the getting started Wiki pages; start there. To see the rendered version of this chapter and the rest of the template, see here: https://jhudatascience.org/OTTR_Template/. Every chapter needs to start out with this chunk of code: 2.1 Learning Objectives Every chapter also needs Learning objectives that will look like this: This chapter will cover: {You can use https://tips.uark.edu/using-blooms-taxonomy/ to define some learning objectives here} {Another learning objective} 2.2 Libraries For this chapter, we’ll need the following packages attached: *Remember to add any additional packages you need to your course’s own docker image. library(magrittr) 2.3 Topic of Section You can write all your text in sections like this, using ## to indicate a new header. you can use additional pound symbols to create lower levels of headers. See here for additional general information about how you can format text within R Markdown files. In addition, see here for more in depth and advanced options. 2.3.1 Subtopic Here’s a subheading (using three pound symbols) and some text in this subsection! 2.4 Code examples You can demonstrate code like this: output_dir &lt;- file.path(&quot;resources&quot;, &quot;code_output&quot;) if (!dir.exists(output_dir)) { dir.create(output_dir) } And make plots too: hist_plot &lt;- hist(iris$Sepal.Length) You can also save these plots to file: png(file.path(output_dir, &quot;test_plot.png&quot;)) hist_plot ## $breaks ## [1] 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0 ## ## $counts ## [1] 5 27 27 30 31 18 6 6 ## ## $density ## [1] 0.06666667 0.36000000 0.36000000 0.40000000 0.41333333 0.24000000 0.08000000 ## [8] 0.08000000 ## ## $mids ## [1] 4.25 4.75 5.25 5.75 6.25 6.75 7.25 7.75 ## ## $xname ## [1] &quot;iris$Sepal.Length&quot; ## ## $equidist ## [1] TRUE ## ## attr(,&quot;class&quot;) ## [1] &quot;histogram&quot; dev.off() ## png ## 2 2.5 Image example How to include a Google slide. It’s simplest to use the ottrpal package: But if you have the slide or some other image locally downloaded you can also use HTML like this: 2.6 Video examples You may also want to embed videos in your course. If alternatively, you just want to include a link you can do so like this: Check out this link to a video using markdown syntax. 2.6.1 Using knitr To embed videos in your course, you can use knitr::include_url() like this: Note that you should use echo=FALSE in the code chunk because we don’t want the code part of this to show up. If you are unfamiliar with how R Markdown code chunks work, read this. 2.6.2 Using HTML 2.6.3 Using knitr 2.6.4 Using HTML 2.7 Website Examples Yet again you can use a link to a website like so: A Website You might want to have users open a website in a new tab by default, especially if they need to reference both the course and a resource at once. A Website Or, you can embed some websites. 2.7.1 Using knitr This works: 2.7.2 Using HTML If you’d like the URL to show up in a new tab you can do this: &lt;a href=&quot;https://www.linkedin.com&quot; target=&quot;_blank&quot;&gt;LinkedIn&lt;/a&gt; 2.8 Citation examples We can put citations at the end of a sentence like this (Allaire et al. 2021). Or multiple citations Xie, Allaire, and Grolemund (2018). but they need a ; separator (Allaire et al. 2021; Xie, Allaire, and Grolemund 2018). In text, we can put citations like this Allaire et al. (2021). 2.9 Stylized boxes Occasionally, you might find it useful to emphasize a particular piece of information. To help you do so, we have provided css code and images (no need for you to worry about that!) to create the following stylized boxes. You can use these boxes in your course with either of two options: using HTML code or Pandoc syntax. 2.9.1 Using rmarkdown container syntax The rmarkdown package allows for a different syntax to be converted to the HTML that you just saw and also allows for conversion to LaTeX. See the Bookdown documentation for more information (Xie, Dervieux, and Riederer 2020). Note that Bookdown uses Pandoc. ::: {.notice} Note using rmarkdown syntax. ::: Note using rmarkdown syntax. As an example you might do something like this: Please click on the subsection headers in the left hand navigation bar (e.g., 2.1, 4.3) a second time to expand the table of contents and enable the scroll_highlight feature (see more) 2.9.2 Using HTML To add a warning box like the following use: &lt;div class = &quot;notice&quot;&gt; Followed by the text you want inside &lt;/div&gt; This will create the following: Followed by the text you want inside Here is a &lt;div class = \"warning\"&gt; box: Note text Here is a &lt;div class = \"github\"&gt; box: GitHub text Here is a &lt;div class = \"dictionary\"&gt; box: dictionary text Here is a &lt;div class = \"reflection\"&gt; box: reflection text Here is a &lt;div class = \"wip\"&gt; box: Work in Progress text 2.10 Dropdown summaries You can hide additional information in a dropdown menu Here’s more words that are hidden. 2.11 Print out session info You should print out session info when you have code for reproducibility purposes. devtools::session_info() ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-12-19 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## askpass 1.2.0 2023-09-03 [1] RSPM (R 4.3.0) ## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## chromote 0.3.1 2024-08-30 [1] CRAN (R 4.3.2) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## curl 5.2.0 2023-12-08 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## dplyr 1.1.4 2023-11-17 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## 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stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.2) ## tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.3.0) ## timechange 0.3.0 2024-01-18 [1] RSPM (R 4.3.0) ## tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## webshot2 0.1.1 2023-08-11 [1] CRAN (R 4.3.2) ## websocket 1.4.2 2024-07-22 [1] CRAN (R 4.3.2) ## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2) ## xml2 1.3.6 2023-12-04 [1] RSPM (R 4.3.0) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── References "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Pedagogy Lead Content Instructor(s) FirstName LastName Lecturer(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved Delivered the course in some way - video or audio Content Author(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved If any other authors besides lead instructor Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involved Wrote less than a chapter Content Editor(s)/Reviewer(s) Checked your content Content Director(s) Helped guide the content direction Content Consultants (include chapter name/link in parentheses or word “General”) - make new line if more than one chapter involved Gave high level advice on content Acknowledgments Gave small assistance to content but not to the level of consulting Production Content Publisher(s) Helped with publishing platform Content Publishing Reviewer(s) Reviewed overall content and aesthetics on publishing platform Technical Course Publishing Engineer(s) Helped with the code for the technical aspects related to the specific course generation Template Publishing Engineers Candace Savonen, Carrie Wright, Ava Hoffman Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Ava Hoffman, Candace Savonen Package Developers (ottrpal) Candace Savonen, Ava Hoffman, Howard Baek, Kate Isaac, Carrie Wright, John Muschelli Art and Design Illustrator(s) Created graphics for the course Figure Artist(s) Created figures/plots for course Videographer(s) Filmed videos Videography Editor(s) Edited film Audiographer(s) Recorded audio Audiography Editor(s) Edited audio recordings Funding Funder(s) Institution/individual who funded course including grant number Funding Staff Staff members who help with funding   ## 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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. "]]