diff --git a/.github/ISSUE_TEMPLATE/new-course-add-to-sync.md b/.github/ISSUE_TEMPLATE/new-course-add-to-sync.md
new file mode 100644
index 00000000..22e87ea2
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/new-course-add-to-sync.md
@@ -0,0 +1,14 @@
+---
+name: Add your new course to syncs/OTTR updates
+about: Provide information about your new course (which uses the OTTR template) so that we can enroll it in OTTR updates
+title: ''
+labels: ''
+assignees: cansavvy
+
+---
+
+## What is the name of your new repository?
+<!-- The name of the repo. Ex the name of this repo is OTTR_Template -->
+
+## What username or organization is your new repository associated with?
+<!-- The name of the username or organization where the new repository is located . Ex this repository is part of the jhudsl organization. A personal repository would be associated with a username instead of the organization. -->
diff --git a/.github/ISSUE_TEMPLATE/update-course-info-for-sync.md b/.github/ISSUE_TEMPLATE/update-course-info-for-sync.md
new file mode 100644
index 00000000..80a5065e
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/update-course-info-for-sync.md
@@ -0,0 +1,26 @@
+---
+name: Update your course's info for syncs/OTTR updates
+about: Provide information about your moved/renamed course (which uses the OTTR template) so that it can continue to be enrolled in OTTR updates
+title: ''
+labels: ''
+assignees: cansavvy
+
+---
+
+<!-- Remove headings if they are not applicable to the changes/updates you made for your repo-->
+
+## If the name of your repository was changed ...
+
+### What was the old name?
+<!-- The old/original name of the repo. Ex the name of this repo is OTTR_Template -->
+
+### What is the new name?
+<!-- The new/modified name of the repo. Ex the name of this repo is OTTR_Template -->
+
+## If the repository was moved ...
+
+### What was the original username or organization your repository was associated with?
+<!-- The old/original name of the username or organization where the new repository was located . Ex this repository is part of the jhudsl organization. A personal repository would be associated with a username instead of the organization. -->
+
+### What is the new username or organization your repository was associated with?
+<!-- The new/modified name of the username or organization where the new repository is located . Ex this repository is part of the jhudsl organization. A personal repository would be associated with a username instead of the organization. -->
diff --git a/.github/automatic-issues/update-enrollment.md b/.github/automatic-issues/update-enrollment.md
index 46d64ab7..7e804884 100644
--- a/.github/automatic-issues/update-enrollment.md
+++ b/.github/automatic-issues/update-enrollment.md
@@ -5,3 +5,4 @@ We are working on adding more features and smoothing out bugs as we go.
 If you want to receive updates from the original template to your course template, you will need to enroll this repository to the template updates by adding it to the `sync.yml` file.
 
 - [ ] [Follow these instructions](https://www.ottrproject.org/getting_started.html#9_Enroll_your_repository_for_OTTR_updates) to enroll your course repository to receive these updates.
+  - [ ] Alternatively, [open an issue in the OTTR_Template repo](https://github.com/jhudsl/OTTR_Template/issues/new?assignees=cansavvy&labels=&projects=&template=new-course-add-to-sync.md&title=), providing us with the necessary information to add the course for you.
diff --git a/.github/sync.yml b/.github/sync.yml
index f0e528c0..9510ba27 100755
--- a/.github/sync.yml
+++ b/.github/sync.yml
@@ -58,17 +58,21 @@ group:
       griffithlab/pVACtools_Intro_Course
       griffithlab/CIVIC_SVI_Course
       PracticalGenomics/cogaps-on-sciserver
-      fhdsl/AI_for_software
+      fhdsl/AI_for_Efficient_Programming
       fhdsl/AI_for_Decision_Makers
       griffithlab/Immuno_Workflow_Course
-      fhdsl/S1_Intro_to_R
-      fhdsl/S1_Intro_to_Command_Line
-      fhdsl/S1_Intro_to_Git_GitHub
+      fhdsl/Intro_to_R
+      fhdsl/Intro_to_Command_Line
+      fhdsl/Intro_to_Git_GitHub
       fhdsl/WDL_Workflows_Guide
-      fhdsl/S2-Collaborative-Git-GitHub
+      fhdsl/Intermediate-Git-GitHub
       fhdsl/GitHub_Automation_for_Scientists
       williamtmillsiv/introduction_to_bioinformatics
-      fhdsl/ottr
+      fhdsl/OTTR_Quarto
+      fhdsl/bench_to_bytes
+      fhdsl/Intermediate_R
+      fhdsl/DataViz_Practice
+      fhdsl/DataViz_Considerations
 ###ADD NEW REPO HERE following the format above#
 
 ### These are custom groups for syncing -- not all files needs to be synced
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 0d0a4356..b2e39b2c 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -200,7 +200,7 @@ jobs:
           git push -u origin main || echo "No changes to push"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: needs.yaml-check.outputs.toggle_quiz_check == 'no'
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'no'}}
         run: |
           echo needs.yaml-check.outputs.toggle_make_book_txt == 'yes'
           echo needs.yaml-check.outputs.toggle_make_book_txt
@@ -211,7 +211,7 @@ jobs:
             quiz_dir = NULL)"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: needs.yaml-check.outputs.toggle_quiz_check == 'yes'
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
         run: |
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
diff --git a/.github/workflows/starting-course.yml b/.github/workflows/starting-course.yml
index dc87be4f..144aa3d9 100644
--- a/.github/workflows/starting-course.yml
+++ b/.github/workflows/starting-course.yml
@@ -40,6 +40,8 @@ jobs:
             .github/workflows/starting-course.yml \
             .github/ISSUE_TEMPLATE/course-template-problem-report.md \
             .github/ISSUE_TEMPLATE/course-template-feature-request.md \
+            .github/ISSUE_TEMPLATE/new-course-add-to-sync.md \
+            .github/ISSUE_TEMPLATE/update-course-info-for-sync.md \
             .github/PULL_REQUEST_TEMPLATE/add_to_sync_template.md \
             resources/code_output \
             resources/screenshots \
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index c011e0bb..c71331e0 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -25,6 +25,10 @@ The [OTTR_Template_Website repository](https://github.com/jhudsl/OTTR_Template_W
 
 The [ottr-reports repository](https://github.com/jhudsl/ottr-reports) houses the functionality for reporting the results of the GitHub Action checks on spelling, URLs, and quiz formatting.
 
+#### ottr-docker
+
+The [ottr_docker repository](https://github.com/jhudsl/ottr_docker) holds the Dockerfiles for docker images available for use with OTTR.
+
 #### ottrpal
 
 The [ottrpal repository](https://github.com/jhudsl/ottrpal) provides the functionality to convert an OTTR course to files ready for use in Leanpub and Coursera
@@ -71,6 +75,7 @@ Open an issue describing the bug or feature request for the relevant repository
 | OTTR_Quizzes          | [Open an issue here](https://github.com/jhudsl/OTTR_Quizzes/issues/new/choose)         |
 | OTTR_Template_Website | [Open an issue here](https://github.com/jhudsl/OTTR_Template_Website/issues/new/choose)|
 | ottr-reports          | [Open an issue here](https://github.com/jhudsl/ottr-reports/issues/new/choose)         |
+| ottr-docker           | [Open an issue here](https://github.com/jhudsl/ottr_docker/issues/new/choose)          |
 | ottrpal               | [Open an issue here](https://github.com/jhudsl/ottrpal/issues/new/choose)              |
 | cow                   | [Open an issue here](https://github.com/jhudsl/cow/issues/new/choose)                  |
 | ottrproject.org       | [Open an issue here](https://github.com/jhudsl/ottrpal/issues/new/choose)              |
diff --git a/docs/01-intro.md b/docs/01-intro.md
index ef65fe90..7fe34841 100644
--- a/docs/01-intro.md
+++ b/docs/01-intro.md
@@ -17,77 +17,83 @@ The course covers...
 
 
 
-```r
+``` r
 devtools::session_info()
 ```
 
 ```
 ## ─ Session info ───────────────────────────────────────────────────────────────
-##  setting  value                       
-##  version  R version 4.0.2 (2020-06-22)
-##  os       Ubuntu 20.04.5 LTS          
-##  system   x86_64, linux-gnu           
-##  ui       X11                         
-##  language (EN)                        
-##  collate  en_US.UTF-8                 
-##  ctype    en_US.UTF-8                 
-##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  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     2024-06-26
+##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
-##  package     * version date       lib source                            
-##  askpass       1.1     2019-01-13 [1] RSPM (R 4.0.3)                    
-##  assertthat    0.2.1   2019-03-21 [1] RSPM (R 4.0.5)                    
-##  bookdown      0.24    2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) 
-##  cachem        1.0.8   2023-05-01 [1] CRAN (R 4.0.2)                    
-##  callr         3.5.0   2020-10-08 [1] RSPM (R 4.0.2)                    
-##  cli           3.6.2   2023-12-11 [1] CRAN (R 4.0.2)                    
-##  crayon        1.3.4   2017-09-16 [1] RSPM (R 4.0.0)                    
-##  desc          1.2.0   2018-05-01 [1] RSPM (R 4.0.3)                    
-##  devtools      2.3.2   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  digest        0.6.25  2020-02-23 [1] RSPM (R 4.0.0)                    
-##  ellipsis      0.3.1   2020-05-15 [1] RSPM (R 4.0.3)                    
-##  evaluate      0.23    2023-11-01 [1] CRAN (R 4.0.2)                    
-##  fansi         0.4.1   2020-01-08 [1] RSPM (R 4.0.0)                    
-##  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.0.2)                    
-##  fs            1.5.0   2020-07-31 [1] RSPM (R 4.0.3)                    
-##  glue          1.4.2   2020-08-27 [1] RSPM (R 4.0.5)                    
-##  hms           0.5.3   2020-01-08 [1] RSPM (R 4.0.0)                    
-##  htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.0.2)                    
-##  httr          1.4.2   2020-07-20 [1] RSPM (R 4.0.3)                    
-##  jsonlite      1.7.1   2020-09-07 [1] RSPM (R 4.0.2)                    
-##  knitr         1.33    2024-03-13 [1] Github (yihui/knitr@a1052d1)      
-##  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.0.2)                    
-##  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.0.2)                    
-##  memoise       2.0.1   2021-11-26 [1] CRAN (R 4.0.2)                    
-##  openssl       1.4.3   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  ottrpal       1.2.1   2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44)   
-##  pillar        1.9.0   2023-03-22 [1] CRAN (R 4.0.2)                    
-##  pkgbuild      1.1.0   2020-07-13 [1] RSPM (R 4.0.2)                    
-##  pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.0.3)                    
-##  pkgload       1.1.0   2020-05-29 [1] RSPM (R 4.0.3)                    
-##  prettyunits   1.1.1   2020-01-24 [1] RSPM (R 4.0.3)                    
-##  processx      3.4.4   2020-09-03 [1] RSPM (R 4.0.2)                    
-##  ps            1.4.0   2020-10-07 [1] RSPM (R 4.0.2)                    
-##  R6            2.4.1   2019-11-12 [1] RSPM (R 4.0.0)                    
-##  readr         1.4.0   2020-10-05 [1] RSPM (R 4.0.2)                    
-##  remotes       2.2.0   2020-07-21 [1] RSPM (R 4.0.3)                    
-##  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.0.2)                    
-##  rmarkdown     2.10    2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25)
-##  rprojroot     2.0.4   2023-11-05 [1] CRAN (R 4.0.2)                    
-##  sessioninfo   1.1.1   2018-11-05 [1] RSPM (R 4.0.3)                    
-##  stringi       1.5.3   2020-09-09 [1] RSPM (R 4.0.3)                    
-##  stringr       1.4.0   2019-02-10 [1] RSPM (R 4.0.3)                    
-##  testthat      3.0.1   2024-03-13 [1] Github (R-lib/testthat@e99155a)   
-##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.0.2)                    
-##  usethis       1.6.3   2020-09-17 [1] RSPM (R 4.0.2)                    
-##  utf8          1.1.4   2018-05-24 [1] RSPM (R 4.0.3)                    
-##  vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.0.2)                    
-##  withr         2.3.0   2020-09-22 [1] RSPM (R 4.0.2)                    
-##  xfun          0.26    2024-03-13 [1] Github (yihui/xfun@74c2a66)       
-##  xml2          1.3.2   2020-04-23 [1] RSPM (R 4.0.3)                    
-##  yaml          2.2.1   2020-02-01 [1] RSPM (R 4.0.3)                    
+##  package     * version date (UTC) lib source
+##  askpass       1.2.0   2023-09-03 [1] RSPM (R 4.3.0)
+##  bookdown      0.39.1  2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
+##  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)
+##  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)
+##  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)
+##  jsonlite      1.8.8   2023-12-04 [1] RSPM (R 4.3.0)
+##  knitr         1.47.3  2024-06-11 [1] Github (yihui/knitr@e1edd34)
+##  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)
+##  openssl       2.1.1   2023-09-25 [1] RSPM (R 4.3.0)
+##  ottrpal       1.2.1   2024-06-11 [1] Github (jhudsl/ottrpal@828539f)
+##  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)
+##  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)
+##  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     2.27.1  2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
+##  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)
+##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.2)
+##  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)
+##  xfun          0.44.4  2024-06-11 [1] Github (yihui/xfun@9da62cc)
+##  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
+##  [1] /usr/local/lib/R/site-library
+##  [2] /usr/local/lib/R/library
+## 
+## ──────────────────────────────────────────────────────────────────────────────
 ```
diff --git a/docs/02-chapter_of_course.md b/docs/02-chapter_of_course.md
index ca62190d..49e0cd6a 100644
--- a/docs/02-chapter_of_course.md
+++ b/docs/02-chapter_of_course.md
@@ -26,7 +26,7 @@ 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](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image).
 
 
-```r
+``` r
 library(magrittr)
 ```
 
@@ -45,7 +45,7 @@ Here's a subheading (using three pound symbols) and some text in this subsection
 You can demonstrate code like this:
 
 
-```r
+``` r
 output_dir <- file.path("resources", "code_output")
 if (!dir.exists(output_dir)) {
   dir.create(output_dir)
@@ -55,7 +55,7 @@ if (!dir.exists(output_dir)) {
 And make plots too:
 
 
-```r
+``` r
 hist_plot <- hist(iris$Sepal.Length)
 ```
 
@@ -64,7 +64,7 @@ hist_plot <- hist(iris$Sepal.Length)
 You can also save these plots to file:
 
 
-```r
+``` r
 png(file.path(output_dir, "test_plot.png"))
 hist_plot
 ```
@@ -93,7 +93,7 @@ hist_plot
 ## [1] "histogram"
 ```
 
-```r
+``` r
 dev.off()
 ```
 
@@ -124,7 +124,7 @@ 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](https://rmarkdown.rstudio.com/lesson-3.html).
 
 
-<iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="100%" height="400px"></iframe>
+<iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="100%" height="400px" data-external="1"></iframe>
 
 ### Using HTML
 
@@ -132,7 +132,7 @@ Note that you should use `echo=FALSE` in the code chunk because we don't want th
 
 ### Using `knitr`
 
-<iframe src="https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview" width="100%" height="400px"></iframe>
+<iframe src="https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview" width="100%" height="400px" data-external="1"></iframe>
 
 ### Using HTML
 
@@ -154,7 +154,7 @@ Or, you can embed some websites.
 
 This works:
 
-<iframe src="https://yihui.org" width="100%" height="400px"></iframe>
+<iframe src="https://yihui.org" width="100%" height="400px" data-external="1"></iframe>
 
 
 ### Using HTML
@@ -283,81 +283,87 @@ Here's more words that are hidden.
 You should print out session info when you have code for [reproducibility purposes](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/managing-package-versions.html).
 
 
-```r
+``` r
 devtools::session_info()
 ```
 
 ```
 ## ─ Session info ───────────────────────────────────────────────────────────────
-##  setting  value                       
-##  version  R version 4.0.2 (2020-06-22)
-##  os       Ubuntu 20.04.5 LTS          
-##  system   x86_64, linux-gnu           
-##  ui       X11                         
-##  language (EN)                        
-##  collate  en_US.UTF-8                 
-##  ctype    en_US.UTF-8                 
-##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  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     2024-06-26
+##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
-##  package     * version date       lib source                            
-##  askpass       1.1     2019-01-13 [1] RSPM (R 4.0.3)                    
-##  assertthat    0.2.1   2019-03-21 [1] RSPM (R 4.0.5)                    
-##  bookdown      0.24    2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) 
-##  cachem        1.0.8   2023-05-01 [1] CRAN (R 4.0.2)                    
-##  callr         3.5.0   2020-10-08 [1] RSPM (R 4.0.2)                    
-##  cli           3.6.2   2023-12-11 [1] CRAN (R 4.0.2)                    
-##  crayon        1.3.4   2017-09-16 [1] RSPM (R 4.0.0)                    
-##  curl          5.2.1   2024-03-01 [1] CRAN (R 4.0.2)                    
-##  desc          1.2.0   2018-05-01 [1] RSPM (R 4.0.3)                    
-##  devtools      2.3.2   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  digest        0.6.25  2020-02-23 [1] RSPM (R 4.0.0)                    
-##  ellipsis      0.3.1   2020-05-15 [1] RSPM (R 4.0.3)                    
-##  evaluate      0.23    2023-11-01 [1] CRAN (R 4.0.2)                    
-##  fansi         0.4.1   2020-01-08 [1] RSPM (R 4.0.0)                    
-##  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.0.2)                    
-##  fs            1.5.0   2020-07-31 [1] RSPM (R 4.0.3)                    
-##  glue          1.4.2   2020-08-27 [1] RSPM (R 4.0.5)                    
-##  highr         0.8     2019-03-20 [1] RSPM (R 4.0.3)                    
-##  hms           0.5.3   2020-01-08 [1] RSPM (R 4.0.0)                    
-##  htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.0.2)                    
-##  httr          1.4.2   2020-07-20 [1] RSPM (R 4.0.3)                    
-##  jsonlite      1.7.1   2020-09-07 [1] RSPM (R 4.0.2)                    
-##  knitr         1.33    2024-03-13 [1] Github (yihui/knitr@a1052d1)      
-##  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.0.2)                    
-##  magrittr    * 2.0.3   2022-03-30 [1] CRAN (R 4.0.2)                    
-##  memoise       2.0.1   2021-11-26 [1] CRAN (R 4.0.2)                    
-##  openssl       1.4.3   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  ottrpal       1.2.1   2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44)   
-##  pillar        1.9.0   2023-03-22 [1] CRAN (R 4.0.2)                    
-##  pkgbuild      1.1.0   2020-07-13 [1] RSPM (R 4.0.2)                    
-##  pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.0.3)                    
-##  pkgload       1.1.0   2020-05-29 [1] RSPM (R 4.0.3)                    
-##  prettyunits   1.1.1   2020-01-24 [1] RSPM (R 4.0.3)                    
-##  processx      3.4.4   2020-09-03 [1] RSPM (R 4.0.2)                    
-##  ps            1.4.0   2020-10-07 [1] RSPM (R 4.0.2)                    
-##  R6            2.4.1   2019-11-12 [1] RSPM (R 4.0.0)                    
-##  readr         1.4.0   2020-10-05 [1] RSPM (R 4.0.2)                    
-##  remotes       2.2.0   2020-07-21 [1] RSPM (R 4.0.3)                    
-##  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.0.2)                    
-##  rmarkdown     2.10    2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25)
-##  rprojroot     2.0.4   2023-11-05 [1] CRAN (R 4.0.2)                    
-##  sessioninfo   1.1.1   2018-11-05 [1] RSPM (R 4.0.3)                    
-##  stringi       1.5.3   2020-09-09 [1] RSPM (R 4.0.3)                    
-##  stringr       1.4.0   2019-02-10 [1] RSPM (R 4.0.3)                    
-##  testthat      3.0.1   2024-03-13 [1] Github (R-lib/testthat@e99155a)   
-##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.0.2)                    
-##  usethis       1.6.3   2020-09-17 [1] RSPM (R 4.0.2)                    
-##  utf8          1.1.4   2018-05-24 [1] RSPM (R 4.0.3)                    
-##  vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.0.2)                    
-##  withr         2.3.0   2020-09-22 [1] RSPM (R 4.0.2)                    
-##  xfun          0.26    2024-03-13 [1] Github (yihui/xfun@74c2a66)       
-##  xml2          1.3.2   2020-04-23 [1] RSPM (R 4.0.3)                    
-##  yaml          2.2.1   2020-02-01 [1] RSPM (R 4.0.3)                    
+##  package     * version date (UTC) lib source
+##  askpass       1.2.0   2023-09-03 [1] RSPM (R 4.3.0)
+##  bookdown      0.39.1  2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
+##  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)
+##  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)
+##  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)
+##  glue          1.7.0   2024-01-09 [1] RSPM (R 4.3.0)
+##  highr         0.10    2022-12-22 [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)
+##  jsonlite      1.8.8   2023-12-04 [1] RSPM (R 4.3.0)
+##  knitr         1.47.3  2024-06-11 [1] Github (yihui/knitr@e1edd34)
+##  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)
+##  openssl       2.1.1   2023-09-25 [1] RSPM (R 4.3.0)
+##  ottrpal       1.2.1   2024-06-11 [1] Github (jhudsl/ottrpal@828539f)
+##  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)
+##  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)
+##  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     2.27.1  2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
+##  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)
+##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.2)
+##  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)
+##  xfun          0.44.4  2024-06-11 [1] Github (yihui/xfun@9da62cc)
+##  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
+##  [1] /usr/local/lib/R/site-library
+##  [2] /usr/local/lib/R/library
+## 
+## ──────────────────────────────────────────────────────────────────────────────
 ```
 
 [many links]: https://github.com/jhudsl/OTTR_Template
diff --git a/docs/404.html b/docs/404.html
index 43745b41..4b2d9eae 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -6,12 +6,11 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Page not found | Course Name</title>
   <meta name="description" content="Description about Course/Book." />
-  <meta name="generator" content="bookdown 0.24 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.39.1 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Page not found | Course Name" />
   <meta property="og:type" content="book" />
   
-  
   <meta property="og:description" content="Description about Course/Book." />
   
 
@@ -31,7 +30,6 @@
   <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
 
 
-<script src="libs/header-attrs-2.10/header-attrs.js"></script>
 <script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
 <link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
@@ -49,8 +47,9 @@
 
 
 
-<link href="libs/anchor-sections-1.0.1/anchor-sections.css" rel="stylesheet" />
-<script src="libs/anchor-sections-1.0.1/anchor-sections.js"></script>
+<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
+<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
+<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
 
 
 <style type="text/css">
@@ -91,7 +90,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -104,7 +103,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */
@@ -118,6 +117,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 <style type="text/css">
 /* Used with Pandoc 2.11+ new --citeproc when CSL is used */
 div.csl-bib-body { }
@@ -201,7 +204,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
diff --git a/docs/About.md b/docs/About.md
index aeb8ef19..362165b8 100644
--- a/docs/About.md
+++ b/docs/About.md
@@ -42,58 +42,65 @@ These credits are based on our [course contributors table guidelines](https://ww
 
 ```
 ## ─ Session info ───────────────────────────────────────────────────────────────
-##  setting  value                       
-##  version  R version 4.0.2 (2020-06-22)
-##  os       Ubuntu 20.04.5 LTS          
-##  system   x86_64, linux-gnu           
-##  ui       X11                         
-##  language (EN)                        
-##  collate  en_US.UTF-8                 
-##  ctype    en_US.UTF-8                 
-##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  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     2024-06-26
+##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
-##  package     * version date       lib source                            
-##  assertthat    0.2.1   2019-03-21 [1] RSPM (R 4.0.5)                    
-##  bookdown      0.24    2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) 
-##  cachem        1.0.8   2023-05-01 [1] CRAN (R 4.0.2)                    
-##  callr         3.5.0   2020-10-08 [1] RSPM (R 4.0.2)                    
-##  cli           3.6.2   2023-12-11 [1] CRAN (R 4.0.2)                    
-##  crayon        1.3.4   2017-09-16 [1] RSPM (R 4.0.0)                    
-##  desc          1.2.0   2018-05-01 [1] RSPM (R 4.0.3)                    
-##  devtools      2.3.2   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  digest        0.6.25  2020-02-23 [1] RSPM (R 4.0.0)                    
-##  ellipsis      0.3.1   2020-05-15 [1] RSPM (R 4.0.3)                    
-##  evaluate      0.23    2023-11-01 [1] CRAN (R 4.0.2)                    
-##  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.0.2)                    
-##  fs            1.5.0   2020-07-31 [1] RSPM (R 4.0.3)                    
-##  glue          1.4.2   2020-08-27 [1] RSPM (R 4.0.5)                    
-##  htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.0.2)                    
-##  knitr         1.33    2024-03-13 [1] Github (yihui/knitr@a1052d1)      
-##  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.0.2)                    
-##  memoise       2.0.1   2021-11-26 [1] CRAN (R 4.0.2)                    
-##  pkgbuild      1.1.0   2020-07-13 [1] RSPM (R 4.0.2)                    
-##  pkgload       1.1.0   2020-05-29 [1] RSPM (R 4.0.3)                    
-##  prettyunits   1.1.1   2020-01-24 [1] RSPM (R 4.0.3)                    
-##  processx      3.4.4   2020-09-03 [1] RSPM (R 4.0.2)                    
-##  ps            1.4.0   2020-10-07 [1] RSPM (R 4.0.2)                    
-##  R6            2.4.1   2019-11-12 [1] RSPM (R 4.0.0)                    
-##  remotes       2.2.0   2020-07-21 [1] RSPM (R 4.0.3)                    
-##  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.0.2)                    
-##  rmarkdown     2.10    2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25)
-##  rprojroot     2.0.4   2023-11-05 [1] CRAN (R 4.0.2)                    
-##  sessioninfo   1.1.1   2018-11-05 [1] RSPM (R 4.0.3)                    
-##  stringi       1.5.3   2020-09-09 [1] RSPM (R 4.0.3)                    
-##  stringr       1.4.0   2019-02-10 [1] RSPM (R 4.0.3)                    
-##  testthat      3.0.1   2024-03-13 [1] Github (R-lib/testthat@e99155a)   
-##  usethis       1.6.3   2020-09-17 [1] RSPM (R 4.0.2)                    
-##  withr         2.3.0   2020-09-22 [1] RSPM (R 4.0.2)                    
-##  xfun          0.26    2024-03-13 [1] Github (yihui/xfun@74c2a66)       
-##  yaml          2.2.1   2020-02-01 [1] RSPM (R 4.0.3)                    
+##  package     * version date (UTC) lib source
+##  bookdown      0.39.1  2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
+##  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)
+##  knitr         1.47.3  2024-06-11 [1] Github (yihui/knitr@e1edd34)
+##  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     2.27.1  2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
+##  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          0.44.4  2024-06-11 [1] Github (yihui/xfun@9da62cc)
+##  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
+##  [1] /usr/local/lib/R/site-library
+##  [2] /usr/local/lib/R/library
+## 
+## ──────────────────────────────────────────────────────────────────────────────
 ```
 
 <!-- Author information -->
diff --git a/docs/Course_Name.docx b/docs/Course_Name.docx
index cf4a9b63..57b27a94 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 4c2244ff..eded3b2c 100644
--- a/docs/a-new-chapter.html
+++ b/docs/a-new-chapter.html
@@ -6,12 +6,11 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Chapter 2 A new chapter | Course Name</title>
   <meta name="description" content="Description about Course/Book." />
-  <meta name="generator" content="bookdown 0.24 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.39.1 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Chapter 2 A new chapter | Course Name" />
   <meta property="og:type" content="book" />
   
-  
   <meta property="og:description" content="Description about Course/Book." />
   
 
@@ -31,7 +30,6 @@
   <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="introduction.html"/>
 <link rel="next" href="about-the-authors.html"/>
-<script src="libs/header-attrs-2.10/header-attrs.js"></script>
 <script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
 <link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
@@ -49,8 +47,9 @@
 
 
 
-<link href="libs/anchor-sections-1.0.1/anchor-sections.css" rel="stylesheet" />
-<script src="libs/anchor-sections-1.0.1/anchor-sections.js"></script>
+<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
+<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
+<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
 
 
 <style type="text/css">
@@ -91,7 +90,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -104,7 +103,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */
@@ -118,6 +117,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 <style type="text/css">
 /* Used with Pandoc 2.11+ new --citeproc when CSL is used */
 div.csl-bib-body { }
@@ -201,7 +204,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
@@ -233,13 +237,13 @@ <h1>
 <div class="hero-image-container">
   <img class= "hero-image" src= "https://github.com/jhudsl/OTTR_Template/raw/main/assets/dasl_thin_main_image.png">
 </div>
-<div id="a-new-chapter" class="section level1" number="2">
-<h1><span class="header-section-number">Chapter 2</span> A new chapter</h1>
+<div id="a-new-chapter" class="section level1 hasAnchor" number="2">
+<h1><span class="header-section-number">Chapter 2</span> A new chapter<a href="a-new-chapter.html#a-new-chapter" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p>If you haven’t yet read the getting started Wiki pages; <a href="https://www.ottrproject.org/getting_started.html">start there</a>.</p>
 <p>To see the rendered version of this chapter and the rest of the template, see here: <a href="https://jhudatascience.org/OTTR_Template/" class="uri">https://jhudatascience.org/OTTR_Template/</a>.</p>
 <p>Every chapter needs to start out with this chunk of code:</p>
-<div id="learning-objectives" class="section level2" number="2.1">
-<h2><span class="header-section-number">2.1</span> Learning Objectives</h2>
+<div id="learning-objectives" class="section level2 hasAnchor" number="2.1">
+<h2><span class="header-section-number">2.1</span> Learning Objectives<a href="a-new-chapter.html#learning-objectives" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>Every chapter also needs Learning objectives that will look like this:</p>
 <p>This chapter will cover:</p>
 <ul>
@@ -247,34 +251,34 @@ <h2><span class="header-section-number">2.1</span> Learning Objectives</h2>
 <li>{Another learning objective}</li>
 </ul>
 </div>
-<div id="libraries" class="section level2" number="2.2">
-<h2><span class="header-section-number">2.2</span> Libraries</h2>
+<div id="libraries" class="section level2 hasAnchor" number="2.2">
+<h2><span class="header-section-number">2.2</span> Libraries<a href="a-new-chapter.html#libraries" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>For this chapter, we’ll need the following packages attached:</p>
 <p>*Remember to add <a href="https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image">any additional packages you need to your course’s own docker image</a>.</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="a-new-chapter.html#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(magrittr)</span></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="a-new-chapter.html#cb3-1" tabindex="-1"></a><span class="fu">library</span>(magrittr)</span></code></pre></div>
 </div>
-<div id="topic-of-section" class="section level2" number="2.3">
-<h2><span class="header-section-number">2.3</span> Topic of Section</h2>
+<div id="topic-of-section" class="section level2 hasAnchor" number="2.3">
+<h2><span class="header-section-number">2.3</span> Topic of Section<a href="a-new-chapter.html#topic-of-section" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>You can write all your text in sections like this, using <code>##</code> to indicate a new header. you can use additional pound symbols to create lower levels of headers.</p>
 <p>See <a href="https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf">here</a> for additional general information about how you can format text within R Markdown files. In addition, see <a href="https://pandoc.org/MANUAL.html#pandocs-markdown">here</a> for more in depth and advanced options.</p>
-<div id="subtopic" class="section level3" number="2.3.1">
-<h3><span class="header-section-number">2.3.1</span> Subtopic</h3>
+<div id="subtopic" class="section level3 hasAnchor" number="2.3.1">
+<h3><span class="header-section-number">2.3.1</span> Subtopic<a href="a-new-chapter.html#subtopic" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>Here’s a subheading (using three pound symbols) and some text in this subsection!</p>
 </div>
 </div>
-<div id="code-examples" class="section level2" number="2.4">
-<h2><span class="header-section-number">2.4</span> Code examples</h2>
+<div id="code-examples" class="section level2 hasAnchor" number="2.4">
+<h2><span class="header-section-number">2.4</span> Code examples<a href="a-new-chapter.html#code-examples" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>You can demonstrate code like this:</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="a-new-chapter.html#cb4-1" aria-hidden="true" tabindex="-1"></a>output_dir <span class="ot">&lt;-</span> <span class="fu">file.path</span>(<span class="st">&quot;resources&quot;</span>, <span class="st">&quot;code_output&quot;</span>)</span>
-<span id="cb4-2"><a href="a-new-chapter.html#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">dir.exists</span>(output_dir)) {</span>
-<span id="cb4-3"><a href="a-new-chapter.html#cb4-3" aria-hidden="true" tabindex="-1"></a>  <span class="fu">dir.create</span>(output_dir)</span>
-<span id="cb4-4"><a href="a-new-chapter.html#cb4-4" aria-hidden="true" tabindex="-1"></a>}</span></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="a-new-chapter.html#cb4-1" tabindex="-1"></a>output_dir <span class="ot">&lt;-</span> <span class="fu">file.path</span>(<span class="st">&quot;resources&quot;</span>, <span class="st">&quot;code_output&quot;</span>)</span>
+<span id="cb4-2"><a href="a-new-chapter.html#cb4-2" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">dir.exists</span>(output_dir)) {</span>
+<span id="cb4-3"><a href="a-new-chapter.html#cb4-3" tabindex="-1"></a>  <span class="fu">dir.create</span>(output_dir)</span>
+<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" aria-hidden="true" tabindex="-1"></a>hist_plot <span class="ot">&lt;-</span> <span class="fu">hist</span>(iris<span class="sc">$</span>Sepal.Length)</span></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="a-new-chapter.html#cb5-1" tabindex="-1"></a>hist_plot <span class="ot">&lt;-</span> <span class="fu">hist</span>(iris<span class="sc">$</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>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" aria-hidden="true" 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" aria-hidden="true" tabindex="-1"></a>hist_plot</span></code></pre></div>
+<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>
 <pre><code>## $breaks
 ## [1] 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
 ## 
@@ -296,79 +300,79 @@ <h2><span class="header-section-number">2.4</span> Code examples</h2>
 ## 
 ## attr(,&quot;class&quot;)
 ## [1] &quot;histogram&quot;</code></pre>
-<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="a-new-chapter.html#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="fu">dev.off</span>()</span></code></pre></div>
+<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="a-new-chapter.html#cb8-1" tabindex="-1"></a><span class="fu">dev.off</span>()</span></code></pre></div>
 <pre><code>## png 
 ##   2</code></pre>
 </div>
-<div id="image-example" class="section level2" number="2.5">
-<h2><span class="header-section-number">2.5</span> Image example</h2>
+<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" title="Major point!! example image" alt="Major point!! example image" width="100%" style="display: block; margin: auto;" /></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>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>
-<div id="video-examples" class="section level2" number="2.6">
-<h2><span class="header-section-number">2.6</span> Video examples</h2>
+<div id="video-examples" class="section level2 hasAnchor" number="2.6">
+<h2><span class="header-section-number">2.6</span> Video examples<a href="a-new-chapter.html#video-examples" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>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:</p>
 <p>Check out this <a href="https://www.youtube.com/embed/VOCYL-FNbr0">link to a video</a> using markdown syntax.</p>
-<div id="using-knitr" class="section level3" number="2.6.1">
-<h3><span class="header-section-number">2.6.1</span> Using <code>knitr</code></h3>
+<div id="using-knitr" class="section level3 hasAnchor" number="2.6.1">
+<h3><span class="header-section-number">2.6.1</span> Using <code>knitr</code><a href="a-new-chapter.html#using-knitr" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>To embed videos in your course, you can use <code>knitr::include_url()</code> like this:
 Note that you should use <code>echo=FALSE</code> in the code chunk because we don’t want the code part of this to show up. If you are unfamiliar with <a href="https://rmarkdown.rstudio.com/lesson-3.html">how R Markdown code chunks work, read this</a>.</p>
-<iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="672" height="400px">
+<iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="672" height="400px" data-external="1">
 </iframe>
 </div>
-<div id="using-html" class="section level3" number="2.6.2">
-<h3><span class="header-section-number">2.6.2</span> Using HTML</h3>
+<div id="using-html" class="section level3 hasAnchor" number="2.6.2">
+<h3><span class="header-section-number">2.6.2</span> Using HTML<a href="a-new-chapter.html#using-html" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="672" height="400px">
 </iframe>
 </div>
-<div id="using-knitr-1" class="section level3" number="2.6.3">
-<h3><span class="header-section-number">2.6.3</span> Using <code>knitr</code></h3>
-<iframe src="https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview" width="100%" height="400px">
+<div id="using-knitr-1" class="section level3 hasAnchor" number="2.6.3">
+<h3><span class="header-section-number">2.6.3</span> Using <code>knitr</code><a href="a-new-chapter.html#using-knitr-1" class="anchor-section" aria-label="Anchor link to header"></a></h3>
+<iframe src="https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview" width="100%" height="400px" data-external="1">
 </iframe>
 </div>
-<div id="using-html-1" class="section level3" number="2.6.4">
-<h3><span class="header-section-number">2.6.4</span> Using HTML</h3>
+<div id="using-html-1" class="section level3 hasAnchor" number="2.6.4">
+<h3><span class="header-section-number">2.6.4</span> Using HTML<a href="a-new-chapter.html#using-html-1" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <iframe src="https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview" width="672" height="800px">
 </iframe>
 </div>
 </div>
-<div id="website-examples" class="section level2" number="2.7">
-<h2><span class="header-section-number">2.7</span> Website Examples</h2>
+<div id="website-examples" class="section level2 hasAnchor" number="2.7">
+<h2><span class="header-section-number">2.7</span> Website Examples<a href="a-new-chapter.html#website-examples" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>Yet again you can use a link to a website like so:</p>
 <p><a href="https://yihui.org">A Website</a></p>
 <p>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.</p>
 <p><a href="https://yihui.org" target="_blank">A Website</a></p>
 <p>Or, you can embed some websites.</p>
-<div id="using-knitr-2" class="section level3" number="2.7.1">
-<h3><span class="header-section-number">2.7.1</span> Using <code>knitr</code></h3>
+<div id="using-knitr-2" class="section level3 hasAnchor" number="2.7.1">
+<h3><span class="header-section-number">2.7.1</span> Using <code>knitr</code><a href="a-new-chapter.html#using-knitr-2" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>This works:</p>
-<iframe src="https://yihui.org" width="672" height="400px">
+<iframe src="https://yihui.org" width="672" height="400px" data-external="1">
 </iframe>
 </div>
-<div id="using-html-2" class="section level3" number="2.7.2">
-<h3><span class="header-section-number">2.7.2</span> Using HTML</h3>
+<div id="using-html-2" class="section level3 hasAnchor" number="2.7.2">
+<h3><span class="header-section-number">2.7.2</span> Using HTML<a href="a-new-chapter.html#using-html-2" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <iframe src="https://yihui.org" width="672" height="400px">
 </iframe>
 <p>If you’d like the URL to show up in a new tab you can do this:</p>
 <pre><code>&lt;a href=&quot;https://www.linkedin.com&quot; target=&quot;_blank&quot;&gt;LinkedIn&lt;/a&gt;</code></pre>
 </div>
 </div>
-<div id="citation-examples" class="section level2" number="2.8">
-<h2><span class="header-section-number">2.8</span> Citation examples</h2>
-<p>We can put citations at the end of a sentence like this <span class="citation">(<a href="#ref-rmarkdown2021" role="doc-biblioref">Allaire et al. 2021</a>)</span>.
-Or multiple citations <span class="citation">Xie, Allaire, and Grolemund (<a href="#ref-Xie2018" role="doc-biblioref">2018</a>)</span>.</p>
-<p>but they need a ; separator <span class="citation">(<a href="#ref-rmarkdown2021" role="doc-biblioref">Allaire et al. 2021</a>; <a href="#ref-Xie2018" role="doc-biblioref">Xie, Allaire, and Grolemund 2018</a>)</span>.</p>
-<p>In text, we can put citations like this <span class="citation">Allaire et al. (<a href="#ref-rmarkdown2021" role="doc-biblioref">2021</a>)</span>.</p>
+<div id="citation-examples" class="section level2 hasAnchor" number="2.8">
+<h2><span class="header-section-number">2.8</span> Citation examples<a href="a-new-chapter.html#citation-examples" class="anchor-section" aria-label="Anchor link to header"></a></h2>
+<p>We can put citations at the end of a sentence like this <span class="citation">(<a href="#ref-rmarkdown2021">Allaire et al. 2021</a>)</span>.
+Or multiple citations <span class="citation">Xie, Allaire, and Grolemund (<a href="#ref-Xie2018">2018</a>)</span>.</p>
+<p>but they need a ; separator <span class="citation">(<a href="#ref-rmarkdown2021">Allaire et al. 2021</a>; <a href="#ref-Xie2018">Xie, Allaire, and Grolemund 2018</a>)</span>.</p>
+<p>In text, we can put citations like this <span class="citation">Allaire et al. (<a href="#ref-rmarkdown2021">2021</a>)</span>.</p>
 </div>
-<div id="stylized-boxes" class="section level2" number="2.9">
-<h2><span class="header-section-number">2.9</span> Stylized boxes</h2>
+<div id="stylized-boxes" class="section level2 hasAnchor" number="2.9">
+<h2><span class="header-section-number">2.9</span> Stylized boxes<a href="a-new-chapter.html#stylized-boxes" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>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.</p>
 <p>You can use these boxes in your course with either of two options: using HTML code or Pandoc syntax.</p>
-<div id="using-rmarkdown-container-syntax" class="section level3" number="2.9.1">
-<h3><span class="header-section-number">2.9.1</span> Using <code>rmarkdown</code> container syntax</h3>
-<p>The <code>rmarkdown</code> 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 <a href="https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html">Bookdown</a> documentation for more information <span class="citation">(<a href="#ref-Xie2020" role="doc-biblioref">Xie, Dervieux, and Riederer 2020</a>)</span>. Note that Bookdown uses Pandoc.</p>
+<div id="using-rmarkdown-container-syntax" class="section level3 hasAnchor" number="2.9.1">
+<h3><span class="header-section-number">2.9.1</span> Using <code>rmarkdown</code> container syntax<a href="a-new-chapter.html#using-rmarkdown-container-syntax" class="anchor-section" aria-label="Anchor link to header"></a></h3>
+<p>The <code>rmarkdown</code> 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 <a href="https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html">Bookdown</a> documentation for more information <span class="citation">(<a href="#ref-Xie2020">Xie, Dervieux, and Riederer 2020</a>)</span>. Note that Bookdown uses Pandoc.</p>
 <pre><code>::: {.notice}
 Note using rmarkdown syntax.
 
@@ -384,8 +388,8 @@ <h3><span class="header-section-number">2.9.1</span> Using <code>rmarkdown</code
 (<a href="introduction.html#scroll-highlight">see more</a>)</p>
 </div>
 </div>
-<div id="using-html-3" class="section level3" number="2.9.2">
-<h3><span class="header-section-number">2.9.2</span> Using HTML</h3>
+<div id="using-html-3" class="section level3 hasAnchor" number="2.9.2">
+<h3><span class="header-section-number">2.9.2</span> Using HTML<a href="a-new-chapter.html#using-html-3" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>To add a warning box like the following use:</p>
 <pre><code>&lt;div class = &quot;notice&quot;&gt;
 Followed by the text you want inside
@@ -416,8 +420,8 @@ <h3><span class="header-section-number">2.9.2</span> Using HTML</h3>
 </div>
 </div>
 </div>
-<div id="dropdown-summaries" class="section level2" number="2.10">
-<h2><span class="header-section-number">2.10</span> Dropdown summaries</h2>
+<div id="dropdown-summaries" class="section level2 hasAnchor" number="2.10">
+<h2><span class="header-section-number">2.10</span> Dropdown summaries<a href="a-new-chapter.html#dropdown-summaries" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <details>
 <summary>
 You can hide additional information in a dropdown menu
@@ -425,87 +429,93 @@ <h2><span class="header-section-number">2.10</span> Dropdown summaries</h2>
 Here’s more words that are hidden.
 </details>
 </div>
-<div id="print-out-session-info" class="section level2" number="2.11">
-<h2><span class="header-section-number">2.11</span> Print out session info</h2>
+<div id="print-out-session-info" class="section level2 hasAnchor" number="2.11">
+<h2><span class="header-section-number">2.11</span> Print out session info<a href="a-new-chapter.html#print-out-session-info" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>You should print out session info when you have code for <a href="https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/managing-package-versions.html">reproducibility purposes</a>.</p>
-<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="a-new-chapter.html#cb13-1" aria-hidden="true" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">session_info</span>()</span></code></pre></div>
+<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="a-new-chapter.html#cb13-1" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">session_info</span>()</span></code></pre></div>
 <pre><code>## ─ Session info ───────────────────────────────────────────────────────────────
-##  setting  value                       
-##  version  R version 4.0.2 (2020-06-22)
-##  os       Ubuntu 20.04.5 LTS          
-##  system   x86_64, linux-gnu           
-##  ui       X11                         
-##  language (EN)                        
-##  collate  en_US.UTF-8                 
-##  ctype    en_US.UTF-8                 
-##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  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     2024-06-26
+##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
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-##  askpass       1.1     2019-01-13 [1] RSPM (R 4.0.3)                    
-##  assertthat    0.2.1   2019-03-21 [1] RSPM (R 4.0.5)                    
-##  bookdown      0.24    2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) 
-##  bslib         0.6.1   2023-11-28 [1] CRAN (R 4.0.2)                    
-##  cachem        1.0.8   2023-05-01 [1] CRAN (R 4.0.2)                    
-##  callr         3.5.0   2020-10-08 [1] RSPM (R 4.0.2)                    
-##  cli           3.6.2   2023-12-11 [1] CRAN (R 4.0.2)                    
-##  crayon        1.3.4   2017-09-16 [1] RSPM (R 4.0.0)                    
-##  curl          5.2.1   2024-03-01 [1] CRAN (R 4.0.2)                    
-##  desc          1.2.0   2018-05-01 [1] RSPM (R 4.0.3)                    
-##  devtools      2.3.2   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  digest        0.6.25  2020-02-23 [1] RSPM (R 4.0.0)                    
-##  ellipsis      0.3.1   2020-05-15 [1] RSPM (R 4.0.3)                    
-##  evaluate      0.23    2023-11-01 [1] CRAN (R 4.0.2)                    
-##  fansi         0.4.1   2020-01-08 [1] RSPM (R 4.0.0)                    
-##  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.0.2)                    
-##  fs            1.5.0   2020-07-31 [1] RSPM (R 4.0.3)                    
-##  glue          1.4.2   2020-08-27 [1] RSPM (R 4.0.5)                    
-##  highr         0.8     2019-03-20 [1] RSPM (R 4.0.3)                    
-##  hms           0.5.3   2020-01-08 [1] RSPM (R 4.0.0)                    
-##  htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.0.2)                    
-##  httr          1.4.2   2020-07-20 [1] RSPM (R 4.0.3)                    
-##  jquerylib     0.1.4   2021-04-26 [1] CRAN (R 4.0.2)                    
-##  jsonlite      1.7.1   2020-09-07 [1] RSPM (R 4.0.2)                    
-##  knitr         1.33    2024-03-13 [1] Github (yihui/knitr@a1052d1)      
-##  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.0.2)                    
-##  magrittr    * 2.0.3   2022-03-30 [1] CRAN (R 4.0.2)                    
-##  memoise       2.0.1   2021-11-26 [1] CRAN (R 4.0.2)                    
-##  openssl       1.4.3   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  ottrpal       1.2.1   2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44)   
-##  pillar        1.9.0   2023-03-22 [1] CRAN (R 4.0.2)                    
-##  pkgbuild      1.1.0   2020-07-13 [1] RSPM (R 4.0.2)                    
-##  pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.0.3)                    
-##  pkgload       1.1.0   2020-05-29 [1] RSPM (R 4.0.3)                    
-##  prettyunits   1.1.1   2020-01-24 [1] RSPM (R 4.0.3)                    
-##  processx      3.4.4   2020-09-03 [1] RSPM (R 4.0.2)                    
-##  ps            1.4.0   2020-10-07 [1] RSPM (R 4.0.2)                    
-##  R6            2.4.1   2019-11-12 [1] RSPM (R 4.0.0)                    
-##  readr         1.4.0   2020-10-05 [1] RSPM (R 4.0.2)                    
-##  remotes       2.2.0   2020-07-21 [1] RSPM (R 4.0.3)                    
-##  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.0.2)                    
-##  rmarkdown     2.10    2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25)
-##  rprojroot     2.0.4   2023-11-05 [1] CRAN (R 4.0.2)                    
-##  sass          0.4.8   2023-12-06 [1] CRAN (R 4.0.2)                    
-##  sessioninfo   1.1.1   2018-11-05 [1] RSPM (R 4.0.3)                    
-##  stringi       1.5.3   2020-09-09 [1] RSPM (R 4.0.3)                    
-##  stringr       1.4.0   2019-02-10 [1] RSPM (R 4.0.3)                    
-##  testthat      3.0.1   2024-03-13 [1] Github (R-lib/testthat@e99155a)   
-##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.0.2)                    
-##  usethis       1.6.3   2020-09-17 [1] RSPM (R 4.0.2)                    
-##  utf8          1.1.4   2018-05-24 [1] RSPM (R 4.0.3)                    
-##  vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.0.2)                    
-##  withr         2.3.0   2020-09-22 [1] RSPM (R 4.0.2)                    
-##  xfun          0.26    2024-03-13 [1] Github (yihui/xfun@74c2a66)       
-##  xml2          1.3.2   2020-04-23 [1] RSPM (R 4.0.3)                    
-##  yaml          2.2.1   2020-02-01 [1] RSPM (R 4.0.3)                    
+##  package     * version date (UTC) lib source
+##  askpass       1.2.0   2023-09-03 [1] RSPM (R 4.3.0)
+##  bookdown      0.39.1  2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
+##  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)
+##  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)
+##  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)
+##  glue          1.7.0   2024-01-09 [1] RSPM (R 4.3.0)
+##  highr         0.10    2022-12-22 [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)
+##  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         1.47.3  2024-06-11 [1] Github (yihui/knitr@e1edd34)
+##  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)
+##  openssl       2.1.1   2023-09-25 [1] RSPM (R 4.3.0)
+##  ottrpal       1.2.1   2024-06-11 [1] Github (jhudsl/ottrpal@828539f)
+##  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)
+##  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)
+##  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     2.27.1  2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
+##  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)
+##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.2)
+##  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)
+##  xfun          0.44.4  2024-06-11 [1] Github (yihui/xfun@9da62cc)
+##  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
 ## 
-## [1] /usr/local/lib/R/site-library
-## [2] /usr/local/lib/R/library</code></pre>
+## ──────────────────────────────────────────────────────────────────────────────</code></pre>
 
 </div>
 </div>
-<h3> References</h3>
+<h3> References<a href="references.html#references" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <div id="refs" class="references csl-bib-body hanging-indent">
 <div id="ref-rmarkdown2021" class="csl-entry">
 Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2021. <em>Rmarkdown: Dynamic Documents for r</em>. <a href="https://github.com/rstudio/rmarkdown">https://github.com/rstudio/rmarkdown</a>.
diff --git a/docs/about-the-authors.html b/docs/about-the-authors.html
index 1e67b47a..3fa251e4 100644
--- a/docs/about-the-authors.html
+++ b/docs/about-the-authors.html
@@ -6,12 +6,11 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>About the Authors | Course Name</title>
   <meta name="description" content="Description about Course/Book." />
-  <meta name="generator" content="bookdown 0.24 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.39.1 and GitBook 2.6.7" />
 
   <meta property="og:title" content="About the Authors | Course Name" />
   <meta property="og:type" content="book" />
   
-  
   <meta property="og:description" content="Description about Course/Book." />
   
 
@@ -31,7 +30,6 @@
   <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="a-new-chapter.html"/>
 <link rel="next" href="references.html"/>
-<script src="libs/header-attrs-2.10/header-attrs.js"></script>
 <script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
 <link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
@@ -49,8 +47,9 @@
 
 
 
-<link href="libs/anchor-sections-1.0.1/anchor-sections.css" rel="stylesheet" />
-<script src="libs/anchor-sections-1.0.1/anchor-sections.js"></script>
+<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
+<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
+<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
 
 
 <style type="text/css">
@@ -91,7 +90,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -104,7 +103,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */
@@ -118,6 +117,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 <style type="text/css">
 /* Used with Pandoc 2.11+ new --citeproc when CSL is used */
 div.csl-bib-body { }
@@ -201,7 +204,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
@@ -233,8 +237,8 @@ <h1>
 <div class="hero-image-container">
   <img class= "hero-image" src= "https://github.com/jhudsl/OTTR_Template/raw/main/assets/dasl_thin_main_image.png">
 </div>
-<div id="about-the-authors" class="section level1 unnumbered">
-<h1>About the Authors</h1>
+<div id="about-the-authors" class="section level1 unnumbered hasAnchor">
+<h1>About the Authors<a href="about-the-authors.html#about-the-authors" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p>These credits are based on our <a href="https://www.ottrproject.org/more_features.html#giving-credits-to-contributors">course contributors table guidelines</a>.</p>
 <p> 
  </p>
@@ -366,63 +370,69 @@ <h1>About the Authors</h1>
 </table>
 <p> </p>
 <pre><code>## ─ Session info ───────────────────────────────────────────────────────────────
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-##  ctype    en_US.UTF-8                 
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-##  yaml          2.2.1   2020-02-01 [1] RSPM (R 4.0.3)                    
+##  package     * version date (UTC) lib source
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+##  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)
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+##  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          0.44.4  2024-06-11 [1] Github (yihui/xfun@9da62cc)
+##  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
 ## 
-## [1] /usr/local/lib/R/site-library
-## [2] /usr/local/lib/R/library</code></pre>
+## ──────────────────────────────────────────────────────────────────────────────</code></pre>
 <!-- Author information -->
 <!-- Links -->
 <!-- Fill out this table using these instructions: https://github.com/jhudsl/OTTR_Template/wiki/How-to-give-credits
diff --git a/docs/index.html b/docs/index.html
index 660ee9c8..72c62bdb 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,12 +6,11 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Course Name</title>
   <meta name="description" content="Description about Course/Book." />
-  <meta name="generator" content="bookdown 0.24 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.39.1 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Course Name" />
   <meta property="og:type" content="book" />
   
-  
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@@ -31,7 +30,6 @@
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 <link rel="next" href="introduction.html"/>
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-<link href="libs/anchor-sections-1.0.1/anchor-sections.css" rel="stylesheet" />
-<script src="libs/anchor-sections-1.0.1/anchor-sections.js"></script>
+<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
+<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
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 <style type="text/css">
@@ -91,7 +90,7 @@
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 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
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 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
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@@ -118,6 +117,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 <style type="text/css">
 /* Used with Pandoc 2.11+ new --citeproc when CSL is used */
 div.csl-bib-body { }
@@ -201,7 +204,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
@@ -235,12 +239,12 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Course Name</h1>
-<p class="date"><em>April, 2024</em></p>
+<p class="date"><em>June, 2024</em></p>
 </div>
-<div id="about-this-course" class="section level1 unnumbered">
-<h1>About this Course</h1>
-<div id="available-course-formats" class="section level2" number="0.1">
-<h2><span class="header-section-number">0.1</span> Available course formats</h2>
+<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>
+<div id="available-course-formats" class="section level2 hasAnchor" number="0.1">
+<h2><span class="header-section-number">0.1</span> Available course formats<a href="index.html#available-course-formats" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>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.</p>
 <ul>
 <li>The material for this course can be viewed without login requirement on this <a href="LINK%20HERE">Bookdown website</a>. This format might be most appropriate for you if you rely on screen-reader technology.</li>
diff --git a/docs/index.md b/docs/index.md
index 979d8a2e..4370830d 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,6 +1,6 @@
 ---
 title: "Course Name"
-date: "April, 2024"
+date: "June, 2024"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib]
diff --git a/docs/introduction.html b/docs/introduction.html
index 6ccda75b..98d879bb 100644
--- a/docs/introduction.html
+++ b/docs/introduction.html
@@ -6,12 +6,11 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Chapter 1 Introduction | Course Name</title>
   <meta name="description" content="Description about Course/Book." />
-  <meta name="generator" content="bookdown 0.24 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.39.1 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Chapter 1 Introduction | Course Name" />
   <meta property="og:type" content="book" />
   
-  
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@@ -31,7 +30,6 @@
   <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="index.html"/>
 <link rel="next" href="a-new-chapter.html"/>
-<script src="libs/header-attrs-2.10/header-attrs.js"></script>
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@@ -49,8 +47,9 @@
 
 
 
-<link href="libs/anchor-sections-1.0.1/anchor-sections.css" rel="stylesheet" />
-<script src="libs/anchor-sections-1.0.1/anchor-sections.js"></script>
+<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
+<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
+<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
 
 
 <style type="text/css">
@@ -91,7 +90,7 @@
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 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
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 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
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 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
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@@ -118,6 +117,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 <style type="text/css">
 /* Used with Pandoc 2.11+ new --citeproc when CSL is used */
 div.csl-bib-body { }
@@ -201,7 +204,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
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-<div id="motivation" class="section level2" number="1.1">
-<h2><span class="header-section-number">1.1</span> Motivation</h2>
+<div id="introduction" class="section level1 hasAnchor" number="1">
+<h1><span class="header-section-number">Chapter 1</span> Introduction<a href="introduction.html#introduction" class="anchor-section" aria-label="Anchor link to header"></a></h1>
+<div id="motivation" class="section level2 hasAnchor" number="1.1">
+<h2><span class="header-section-number">1.1</span> Motivation<a href="introduction.html#motivation" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 </div>
-<div id="target-audience" class="section level2" number="1.2">
-<h2><span class="header-section-number">1.2</span> Target Audience</h2>
+<div id="target-audience" class="section level2 hasAnchor" number="1.2">
+<h2><span class="header-section-number">1.2</span> Target Audience<a href="introduction.html#target-audience" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>The course is intended for …</p>
 </div>
-<div id="curriculum" class="section level2" number="1.3">
-<h2><span class="header-section-number">1.3</span> Curriculum</h2>
+<div id="curriculum" class="section level2 hasAnchor" number="1.3">
+<h2><span class="header-section-number">1.3</span> Curriculum<a href="introduction.html#curriculum" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>The course covers…</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="introduction.html#cb1-1" aria-hidden="true" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">session_info</span>()</span></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="introduction.html#cb1-1" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">session_info</span>()</span></code></pre></div>
 <pre><code>## ─ Session info ───────────────────────────────────────────────────────────────
-##  setting  value                       
-##  version  R version 4.0.2 (2020-06-22)
-##  os       Ubuntu 20.04.5 LTS          
-##  system   x86_64, linux-gnu           
-##  ui       X11                         
-##  language (EN)                        
-##  collate  en_US.UTF-8                 
-##  ctype    en_US.UTF-8                 
-##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  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     2024-06-26
+##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
-##  package     * version date       lib source                            
-##  askpass       1.1     2019-01-13 [1] RSPM (R 4.0.3)                    
-##  assertthat    0.2.1   2019-03-21 [1] RSPM (R 4.0.5)                    
-##  bookdown      0.24    2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) 
-##  bslib         0.6.1   2023-11-28 [1] CRAN (R 4.0.2)                    
-##  cachem        1.0.8   2023-05-01 [1] CRAN (R 4.0.2)                    
-##  callr         3.5.0   2020-10-08 [1] RSPM (R 4.0.2)                    
-##  cli           3.6.2   2023-12-11 [1] CRAN (R 4.0.2)                    
-##  crayon        1.3.4   2017-09-16 [1] RSPM (R 4.0.0)                    
-##  desc          1.2.0   2018-05-01 [1] RSPM (R 4.0.3)                    
-##  devtools      2.3.2   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  digest        0.6.25  2020-02-23 [1] RSPM (R 4.0.0)                    
-##  ellipsis      0.3.1   2020-05-15 [1] RSPM (R 4.0.3)                    
-##  evaluate      0.23    2023-11-01 [1] CRAN (R 4.0.2)                    
-##  fansi         0.4.1   2020-01-08 [1] RSPM (R 4.0.0)                    
-##  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.0.2)                    
-##  fs            1.5.0   2020-07-31 [1] RSPM (R 4.0.3)                    
-##  glue          1.4.2   2020-08-27 [1] RSPM (R 4.0.5)                    
-##  hms           0.5.3   2020-01-08 [1] RSPM (R 4.0.0)                    
-##  htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.0.2)                    
-##  httr          1.4.2   2020-07-20 [1] RSPM (R 4.0.3)                    
-##  jquerylib     0.1.4   2021-04-26 [1] CRAN (R 4.0.2)                    
-##  jsonlite      1.7.1   2020-09-07 [1] RSPM (R 4.0.2)                    
-##  knitr         1.33    2024-03-13 [1] Github (yihui/knitr@a1052d1)      
-##  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.0.2)                    
-##  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.0.2)                    
-##  memoise       2.0.1   2021-11-26 [1] CRAN (R 4.0.2)                    
-##  openssl       1.4.3   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  ottrpal       1.2.1   2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44)   
-##  pillar        1.9.0   2023-03-22 [1] CRAN (R 4.0.2)                    
-##  pkgbuild      1.1.0   2020-07-13 [1] RSPM (R 4.0.2)                    
-##  pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.0.3)                    
-##  pkgload       1.1.0   2020-05-29 [1] RSPM (R 4.0.3)                    
-##  prettyunits   1.1.1   2020-01-24 [1] RSPM (R 4.0.3)                    
-##  processx      3.4.4   2020-09-03 [1] RSPM (R 4.0.2)                    
-##  ps            1.4.0   2020-10-07 [1] RSPM (R 4.0.2)                    
-##  R6            2.4.1   2019-11-12 [1] RSPM (R 4.0.0)                    
-##  readr         1.4.0   2020-10-05 [1] RSPM (R 4.0.2)                    
-##  remotes       2.2.0   2020-07-21 [1] RSPM (R 4.0.3)                    
-##  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.0.2)                    
-##  rmarkdown     2.10    2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25)
-##  rprojroot     2.0.4   2023-11-05 [1] CRAN (R 4.0.2)                    
-##  sass          0.4.8   2023-12-06 [1] CRAN (R 4.0.2)                    
-##  sessioninfo   1.1.1   2018-11-05 [1] RSPM (R 4.0.3)                    
-##  stringi       1.5.3   2020-09-09 [1] RSPM (R 4.0.3)                    
-##  stringr       1.4.0   2019-02-10 [1] RSPM (R 4.0.3)                    
-##  testthat      3.0.1   2024-03-13 [1] Github (R-lib/testthat@e99155a)   
-##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.0.2)                    
-##  usethis       1.6.3   2020-09-17 [1] RSPM (R 4.0.2)                    
-##  utf8          1.1.4   2018-05-24 [1] RSPM (R 4.0.3)                    
-##  vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.0.2)                    
-##  withr         2.3.0   2020-09-22 [1] RSPM (R 4.0.2)                    
-##  xfun          0.26    2024-03-13 [1] Github (yihui/xfun@74c2a66)       
-##  xml2          1.3.2   2020-04-23 [1] RSPM (R 4.0.3)                    
-##  yaml          2.2.1   2020-02-01 [1] RSPM (R 4.0.3)                    
+##  package     * version date (UTC) lib source
+##  askpass       1.2.0   2023-09-03 [1] RSPM (R 4.3.0)
+##  bookdown      0.39.1  2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
+##  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)
+##  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)
+##  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)
+##  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         1.47.3  2024-06-11 [1] Github (yihui/knitr@e1edd34)
+##  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)
+##  openssl       2.1.1   2023-09-25 [1] RSPM (R 4.3.0)
+##  ottrpal       1.2.1   2024-06-11 [1] Github (jhudsl/ottrpal@828539f)
+##  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)
+##  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)
+##  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     2.27.1  2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
+##  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)
+##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.2)
+##  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)
+##  xfun          0.44.4  2024-06-11 [1] Github (yihui/xfun@9da62cc)
+##  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
 ## 
-## [1] /usr/local/lib/R/site-library
-## [2] /usr/local/lib/R/library</code></pre>
+## ──────────────────────────────────────────────────────────────────────────────</code></pre>
 
 </div>
 </div>
diff --git a/docs/libs/anchor-sections-1.0.1/anchor-sections.js b/docs/libs/anchor-sections-1.0.1/anchor-sections.js
deleted file mode 100644
index fed21918..00000000
--- a/docs/libs/anchor-sections-1.0.1/anchor-sections.js
+++ /dev/null
@@ -1,33 +0,0 @@
-// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
-document.addEventListener('DOMContentLoaded', function() {
-  // Do nothing if AnchorJS is used
-  if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
-    return;
-  }
-
-  const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
-
-  // Do nothing if sections are already anchored
-  if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
-    return null;
-  }
-
-  // Use section id when pandoc runs with --section-divs
-  const section_id = function(x) {
-    return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
-            ? x.id : '');
-  };
-
-  // Add anchors
-  h.forEach(function(x) {
-    const id = x.id || section_id(x.parentElement);
-    if (id === '' || x.matches(':empty')) {
-      return null;
-    }
-    let anchor = document.createElement('a');
-    anchor.href = '#' + id;
-    anchor.classList = ['anchor-section'];
-    x.classList.add('hasAnchor');
-    x.appendChild(anchor);
-  });
-});
diff --git a/docs/libs/anchor-sections-1.1.0/anchor-sections-hash.css b/docs/libs/anchor-sections-1.1.0/anchor-sections-hash.css
new file mode 100644
index 00000000..b563ec97
--- /dev/null
+++ b/docs/libs/anchor-sections-1.1.0/anchor-sections-hash.css
@@ -0,0 +1,2 @@
+/* Styles for section anchors */
+a.anchor-section::before {content: '#';font-size: 80%;}
diff --git a/docs/libs/anchor-sections-1.0.1/anchor-sections.css b/docs/libs/anchor-sections-1.1.0/anchor-sections.css
similarity index 83%
rename from docs/libs/anchor-sections-1.0.1/anchor-sections.css
rename to docs/libs/anchor-sections-1.1.0/anchor-sections.css
index 4bf387c1..041905f8 100644
--- a/docs/libs/anchor-sections-1.0.1/anchor-sections.css
+++ b/docs/libs/anchor-sections-1.1.0/anchor-sections.css
@@ -1,5 +1,4 @@
 /* Styles for section anchors */
 a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
-a.anchor-section::before {content: '#';}
 .hasAnchor:hover a.anchor-section {visibility: visible;}
 ul > li > .anchor-section {display: none;}
diff --git a/docs/libs/anchor-sections-1.1.0/anchor-sections.js b/docs/libs/anchor-sections-1.1.0/anchor-sections.js
new file mode 100644
index 00000000..fee005d9
--- /dev/null
+++ b/docs/libs/anchor-sections-1.1.0/anchor-sections.js
@@ -0,0 +1,11 @@
+document.addEventListener('DOMContentLoaded', function () {
+  // If section divs is used, we need to put the anchor in the child header
+  const headers = document.querySelectorAll("div.hasAnchor.section[class*='level'] > :first-child")
+
+  headers.forEach(function (x) {
+    // Add to the header node
+    if (!x.classList.contains('hasAnchor')) x.classList.add('hasAnchor')
+    // Remove from the section or div created by Pandoc
+    x.parentElement.classList.remove('hasAnchor')
+  })
+})
diff --git a/docs/libs/gitbook-2.6.7/css/plugin-highlight.css b/docs/libs/gitbook-2.6.7/css/plugin-highlight.css
index 2aabd3de..02c01891 100644
--- a/docs/libs/gitbook-2.6.7/css/plugin-highlight.css
+++ b/docs/libs/gitbook-2.6.7/css/plugin-highlight.css
@@ -133,7 +133,7 @@
 .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code {
   /*
 
-Orginal Style from ethanschoonover.com/solarized (c) Jeremy Hull <sourdrums@gmail.com>
+Original Style from ethanschoonover.com/solarized (c) Jeremy Hull <sourdrums@gmail.com>
 
 */
   /* Solarized Green */
diff --git a/docs/libs/gitbook-2.6.7/css/style.css b/docs/libs/gitbook-2.6.7/css/style.css
index 1b0c622a..cba69b23 100644
--- a/docs/libs/gitbook-2.6.7/css/style.css
+++ b/docs/libs/gitbook-2.6.7/css/style.css
@@ -1,15 +1,13 @@
-/*! normalize.css v2.1.0 | MIT License | git.io/normalize */img,legend{border:0}*,.fa{-webkit-font-smoothing:antialiased}.fa-ul>li,sub,sup{position:relative}.book .book-body .page-wrapper .page-inner section.normal hr:after,.book-langs-index .inner .languages:after,.buttons:after,.dropdown-menu .buttons:after{clear:both}body,html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%}article,aside,details,figcaption,figure,footer,header,hgroup,main,nav,section,summary{display:block}audio,canvas,video{display:inline-block}.hidden,[hidden]{display:none}audio:not([controls]){display:none;height:0}html{font-family:sans-serif}body,figure{margin:0}a:focus{outline:dotted thin}a:active,a:hover{outline:0}h1{font-size:2em;margin:.67em 0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}dfn{font-style:italic}hr{-moz-box-sizing:content-box;box-sizing:content-box;height:0}mark{background:#ff0;color:#000}code,kbd,pre,samp{font-family:monospace,serif;font-size:1em}pre{white-space:pre-wrap}q{quotes:"\201C" "\201D" "\2018" "\2019"}small{font-size:80%}sub,sup{font-size:75%;line-height:0;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}svg:not(:root){overflow:hidden}fieldset{border:1px solid silver;margin:0 2px;padding:.35em .625em .75em}legend{padding:0}button,input,select,textarea{font-family:inherit;font-size:100%;margin:0}button,input{line-height:normal}button,select{text-transform:none}button,html input[type=button],input[type=reset],input[type=submit]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}input[type=checkbox],input[type=radio]{box-sizing:border-box;padding:0}input[type=search]{-webkit-appearance:textfield;-moz-box-sizing:content-box;-webkit-box-sizing:content-box;box-sizing:content-box}input[type=search]::-webkit-search-cancel-button{margin-right:10px;}button::-moz-focus-inner,input::-moz-focus-inner{border:0;padding:0}textarea{overflow:auto;vertical-align:top}table{border-collapse:collapse;border-spacing:0}/*!
+/*! normalize.css v2.1.0 | MIT License | git.io/normalize */img,legend{border:0}*{-webkit-font-smoothing:antialiased}sub,sup{position:relative}.book .book-body .page-wrapper .page-inner section.normal hr:after,.book-langs-index .inner .languages:after,.buttons:after,.dropdown-menu .buttons:after{clear:both}body,html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%}article,aside,details,figcaption,figure,footer,header,hgroup,main,nav,section,summary{display:block}audio,canvas,video{display:inline-block}.hidden,[hidden]{display:none}audio:not([controls]){display:none;height:0}html{font-family:sans-serif}body,figure{margin:0}a:focus{outline:dotted thin}a:active,a:hover{outline:0}h1{font-size:2em;margin:.67em 0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}dfn{font-style:italic}hr{-moz-box-sizing:content-box;box-sizing:content-box;height:0}mark{background:#ff0;color:#000}code,kbd,pre,samp{font-family:monospace,serif;font-size:1em}pre{white-space:pre-wrap}q{quotes:"\201C" "\201D" "\2018" "\2019"}small{font-size:80%}sub,sup{font-size:75%;line-height:0;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}svg:not(:root){overflow:hidden}fieldset{border:1px solid silver;margin:0 2px;padding:.35em .625em .75em}legend{padding:0}button,input,select,textarea{font-family:inherit;font-size:100%;margin:0}button,input{line-height:normal}button,select{text-transform:none}button,html input[type=button],input[type=reset],input[type=submit]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}input[type=checkbox],input[type=radio]{box-sizing:border-box;padding:0}input[type=search]{-webkit-appearance:textfield;-moz-box-sizing:content-box;-webkit-box-sizing:content-box;box-sizing:content-box}input[type=search]::-webkit-search-cancel-button{margin-right:10px;}button::-moz-focus-inner,input::-moz-focus-inner{border:0;padding:0}textarea{overflow:auto;vertical-align:top}table{border-collapse:collapse;border-spacing:0}/*!
  * Preboot v2
  *
  * Open sourced under MIT license by @mdo.
  * Some variables and mixins from Bootstrap (Apache 2 license).
- */.link-inherit,.link-inherit:focus,.link-inherit:hover{color:inherit}.fa,.fa-stack{display:inline-block}/*!
+ */.link-inherit,.link-inherit:focus,.link-inherit:hover{color:inherit}/*!
  *  Font Awesome 4.7.0 by @davegandy - http://fontawesome.io - @fontawesome
  *  License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License)
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.navigation:hover{text-decoration:none;color:#444}.book .book-body .navigation.navigation-next{right:0}.book .book-body .navigation.navigation-prev{left:0}@media (max-width:1240px){.book .book-body .navigation{position:static;top:auto;max-width:50%;width:50%;display:inline-block;float:left}.book .book-body .navigation.navigation-unique{max-width:100%;width:100%}}.book .book-body .page-wrapper .page-inner section.glossary{margin-bottom:40px}.book .book-body .page-wrapper .page-inner section.glossary h2 a,.book .book-body .page-wrapper .page-inner section.glossary h2 a:hover{color:inherit;text-decoration:none}.book .book-body .page-wrapper .page-inner section.glossary .glossary-index{list-style:none;margin:0;padding:0}.book .book-body .page-wrapper .page-inner section.glossary .glossary-index li{display:inline;margin:0 8px;white-space:nowrap}*{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;-webkit-overflow-scrolling:auto;-webkit-tap-highlight-color:transparent;-webkit-text-size-adjust:none;-webkit-touch-callout:none}a{text-decoration:none}body,html{height:100%}html{font-size:62.5%}body{text-rendering:optimizeLegibility;font-smoothing:antialiased;font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:14px;letter-spacing:.2px;text-size-adjust:100%}
 .book .book-summary ul.summary li a span {display:inline;padding:initial;overflow:visible;cursor:auto;opacity:1;}
 /* show arrow before summary tag as in bootstrap */
 details > summary {display:list-item;cursor:pointer;}
-/*add whatsapp icon from FA 5.1.1
-TODO: remove when updating fontawesome*/
-.fa-whatsapp:before{content:"\f232"}
diff --git a/docs/libs/gitbook-2.6.7/js/plugin-clipboard.js b/docs/libs/gitbook-2.6.7/js/plugin-clipboard.js
index 9a7d2e75..f0880be6 100644
--- a/docs/libs/gitbook-2.6.7/js/plugin-clipboard.js
+++ b/docs/libs/gitbook-2.6.7/js/plugin-clipboard.js
@@ -9,7 +9,9 @@ gitbook.require(["gitbook", "jQuery"], function(gitbook, $) {
 
     // the page.change event is thrown twice: before and after the page changes
     if (clipboard) {
-      // clipboard is already defined
+      // clipboard is already defined but we are on the same page
+      if (clipboard._prevPage === window.location.pathname) return;
+      // clipboard is already defined and url path change
       // we can deduct that we are before page changes
       clipboard.destroy(); // destroy the previous events listeners
       clipboard = undefined; // reset the clipboard object
@@ -24,6 +26,8 @@ gitbook.require(["gitbook", "jQuery"], function(gitbook, $) {
       }
     });
 
+    clipboard._prevPage = window.location.pathname
+
   });
 
 });
diff --git a/docs/libs/header-attrs-2.10/header-attrs.js b/docs/libs/header-attrs-2.10/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/libs/header-attrs-2.10/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/no_toc/01-intro.md b/docs/no_toc/01-intro.md
index 278fdb34..88bafbb6 100644
--- a/docs/no_toc/01-intro.md
+++ b/docs/no_toc/01-intro.md
@@ -32,7 +32,7 @@ devtools::session_info()
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  date     2024-05-02                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            
diff --git a/docs/no_toc/02-chapter_of_course.md b/docs/no_toc/02-chapter_of_course.md
index abac0f1a..27370c05 100644
--- a/docs/no_toc/02-chapter_of_course.md
+++ b/docs/no_toc/02-chapter_of_course.md
@@ -298,7 +298,7 @@ devtools::session_info()
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  date     2024-05-02                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            
diff --git a/docs/no_toc/404.html b/docs/no_toc/404.html
index 43745b41..4028031b 100644
--- a/docs/no_toc/404.html
+++ b/docs/no_toc/404.html
@@ -201,7 +201,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
diff --git a/docs/no_toc/About.md b/docs/no_toc/About.md
index aff3c17b..dab8e6b7 100644
--- a/docs/no_toc/About.md
+++ b/docs/no_toc/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     2024-04-12                  
+##  date     2024-05-02                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            
diff --git a/docs/no_toc/a-new-chapter.html b/docs/no_toc/a-new-chapter.html
index 4c2244ff..29aaa786 100644
--- a/docs/no_toc/a-new-chapter.html
+++ b/docs/no_toc/a-new-chapter.html
@@ -201,7 +201,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
@@ -439,7 +440,7 @@ <h2><span class="header-section-number">2.11</span> Print out session info</h2>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  date     2024-05-02                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            
diff --git a/docs/no_toc/about-the-authors.html b/docs/no_toc/about-the-authors.html
index cc051bc7..30e9757f 100644
--- a/docs/no_toc/about-the-authors.html
+++ b/docs/no_toc/about-the-authors.html
@@ -201,7 +201,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
@@ -375,7 +376,7 @@ <h1>About the Authors</h1>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  date     2024-05-02                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            
diff --git a/docs/no_toc/index.html b/docs/no_toc/index.html
index 660ee9c8..1bdedbc3 100644
--- a/docs/no_toc/index.html
+++ b/docs/no_toc/index.html
@@ -201,7 +201,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
@@ -235,7 +236,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Course Name</h1>
-<p class="date"><em>April, 2024</em></p>
+<p class="date"><em>May, 2024</em></p>
 </div>
 <div id="about-this-course" class="section level1 unnumbered">
 <h1>About this Course</h1>
diff --git a/docs/no_toc/index.md b/docs/no_toc/index.md
index 979d8a2e..8322cffa 100644
--- a/docs/no_toc/index.md
+++ b/docs/no_toc/index.md
@@ -1,6 +1,6 @@
 ---
 title: "Course Name"
-date: "April, 2024"
+date: "May, 2024"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib]
diff --git a/docs/no_toc/introduction.html b/docs/no_toc/introduction.html
index 6ccda75b..d7d7eb32 100644
--- a/docs/no_toc/introduction.html
+++ b/docs/no_toc/introduction.html
@@ -201,7 +201,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
@@ -256,7 +257,7 @@ <h2><span class="header-section-number">1.3</span> Curriculum</h2>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  date     2024-05-02                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            
diff --git a/docs/no_toc/references.html b/docs/no_toc/references.html
index d0f33c04..023f7995 100644
--- a/docs/no_toc/references.html
+++ b/docs/no_toc/references.html
@@ -201,7 +201,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
diff --git a/docs/no_toc/search_index.json b/docs/no_toc/search_index.json
index 1648ec62..719289bd 100644
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-[["index.html", "Course Name About this Course 0.1 Available course formats", " Course Name April, 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 4.0.2 (2020-06-22) ## os Ubuntu 20.04.5 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-04-12 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## askpass 1.1 2019-01-13 [1] RSPM (R 4.0.3) ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.5) ## bookdown 0.24 2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) ## bslib 0.6.1 2023-11-28 [1] CRAN (R 4.0.2) ## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.0.2) ## callr 3.5.0 2020-10-08 [1] RSPM (R 4.0.2) ## cli 3.6.2 2023-12-11 [1] CRAN (R 4.0.2) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.23 2023-11-01 [1] CRAN (R 4.0.2) ## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0) ## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.0.2) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.5) ## hms 0.5.3 2020-01-08 [1] RSPM (R 4.0.0) ## htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.0.2) ## httr 1.4.2 2020-07-20 [1] RSPM (R 4.0.3) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## jsonlite 1.7.1 2020-09-07 [1] RSPM (R 4.0.2) ## knitr 1.33 2024-03-13 [1] Github (yihui/knitr@a1052d1) ## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.0.2) ## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.0.2) ## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2) ## openssl 1.4.3 2020-09-18 [1] RSPM (R 4.0.3) ## ottrpal 1.2.1 2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44) ## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.0.2) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.0.3) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.4.0 2020-10-07 [1] RSPM (R 4.0.2) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## readr 1.4.0 2020-10-05 [1] RSPM (R 4.0.2) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 1.1.3 2024-01-10 [1] CRAN (R 4.0.2) ## rmarkdown 2.10 2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.0.2) ## sass 0.4.8 2023-12-06 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2024-03-13 [1] Github (R-lib/testthat@e99155a) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.0.2) ## usethis 1.6.3 2020-09-17 [1] RSPM (R 4.0.2) ## utf8 1.1.4 2018-05-24 [1] RSPM (R 4.0.3) ## vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.0.2) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2024-03-13 [1] Github (yihui/xfun@74c2a66) ## xml2 1.3.2 2020-04-23 [1] RSPM (R 4.0.3) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [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 4.0.2 (2020-06-22) ## os Ubuntu 20.04.5 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-04-12 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## askpass 1.1 2019-01-13 [1] RSPM (R 4.0.3) ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.5) ## bookdown 0.24 2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) ## bslib 0.6.1 2023-11-28 [1] CRAN (R 4.0.2) ## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.0.2) ## callr 3.5.0 2020-10-08 [1] RSPM (R 4.0.2) ## cli 3.6.2 2023-12-11 [1] CRAN (R 4.0.2) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## curl 5.2.1 2024-03-01 [1] CRAN (R 4.0.2) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.23 2023-11-01 [1] CRAN (R 4.0.2) ## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0) ## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.0.2) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.5) ## highr 0.8 2019-03-20 [1] RSPM (R 4.0.3) ## hms 0.5.3 2020-01-08 [1] RSPM (R 4.0.0) ## htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.0.2) ## httr 1.4.2 2020-07-20 [1] RSPM (R 4.0.3) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## jsonlite 1.7.1 2020-09-07 [1] RSPM (R 4.0.2) ## knitr 1.33 2024-03-13 [1] Github (yihui/knitr@a1052d1) ## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.0.2) ## magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.0.2) ## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2) ## openssl 1.4.3 2020-09-18 [1] RSPM (R 4.0.3) ## ottrpal 1.2.1 2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44) ## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.0.2) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.0.3) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.4.0 2020-10-07 [1] RSPM (R 4.0.2) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## readr 1.4.0 2020-10-05 [1] RSPM (R 4.0.2) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 1.1.3 2024-01-10 [1] CRAN (R 4.0.2) ## rmarkdown 2.10 2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.0.2) ## sass 0.4.8 2023-12-06 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2024-03-13 [1] Github (R-lib/testthat@e99155a) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.0.2) ## usethis 1.6.3 2020-09-17 [1] RSPM (R 4.0.2) ## utf8 1.1.4 2018-05-24 [1] RSPM (R 4.0.3) ## vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.0.2) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2024-03-13 [1] Github (yihui/xfun@74c2a66) ## xml2 1.3.2 2020-04-23 [1] RSPM (R 4.0.3) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [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, John Muschelli, Carrie Wright 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 4.0.2 (2020-06-22) ## os Ubuntu 20.04.5 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-04-12 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## askpass 1.1 2019-01-13 [1] RSPM (R 4.0.3) ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.5) ## bookdown 0.24 2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) ## bslib 0.6.1 2023-11-28 [1] CRAN (R 4.0.2) ## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.0.2) ## callr 3.5.0 2020-10-08 [1] RSPM (R 4.0.2) ## cli 3.6.2 2023-12-11 [1] CRAN (R 4.0.2) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.23 2023-11-01 [1] CRAN (R 4.0.2) ## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0) ## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.0.2) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.5) ## hms 0.5.3 2020-01-08 [1] RSPM (R 4.0.0) ## htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.0.2) ## httr 1.4.2 2020-07-20 [1] RSPM (R 4.0.3) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## jsonlite 1.7.1 2020-09-07 [1] RSPM (R 4.0.2) ## knitr 1.33 2024-03-13 [1] Github (yihui/knitr@a1052d1) ## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.0.2) ## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.0.2) ## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2) ## openssl 1.4.3 2020-09-18 [1] RSPM (R 4.0.3) ## ottrpal 1.2.1 2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44) ## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.0.2) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.0.3) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.4.0 2020-10-07 [1] RSPM (R 4.0.2) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## readr 1.4.0 2020-10-05 [1] RSPM (R 4.0.2) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 1.1.3 2024-01-10 [1] CRAN (R 4.0.2) ## rmarkdown 2.10 2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.0.2) ## sass 0.4.8 2023-12-06 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2024-03-13 [1] Github (R-lib/testthat@e99155a) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.0.2) ## usethis 1.6.3 2020-09-17 [1] RSPM (R 4.0.2) ## utf8 1.1.4 2018-05-24 [1] RSPM (R 4.0.3) ## vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.0.2) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2024-03-13 [1] Github (yihui/xfun@74c2a66) ## xml2 1.3.2 2020-04-23 [1] RSPM (R 4.0.3) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [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 May, 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 4.0.2 (2020-06-22) ## os Ubuntu 20.04.5 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-05-02 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## askpass 1.1 2019-01-13 [1] RSPM (R 4.0.3) ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.5) ## bookdown 0.24 2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) ## bslib 0.6.1 2023-11-28 [1] CRAN (R 4.0.2) ## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.0.2) ## callr 3.5.0 2020-10-08 [1] RSPM (R 4.0.2) ## cli 3.6.2 2023-12-11 [1] CRAN (R 4.0.2) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.23 2023-11-01 [1] CRAN (R 4.0.2) ## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0) ## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.0.2) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.5) ## hms 0.5.3 2020-01-08 [1] RSPM (R 4.0.0) ## htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.0.2) ## httr 1.4.2 2020-07-20 [1] RSPM (R 4.0.3) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## jsonlite 1.7.1 2020-09-07 [1] RSPM (R 4.0.2) ## knitr 1.33 2024-03-13 [1] Github (yihui/knitr@a1052d1) ## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.0.2) ## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.0.2) ## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2) ## openssl 1.4.3 2020-09-18 [1] RSPM (R 4.0.3) ## ottrpal 1.2.1 2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44) ## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.0.2) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.0.3) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.4.0 2020-10-07 [1] RSPM (R 4.0.2) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## readr 1.4.0 2020-10-05 [1] RSPM (R 4.0.2) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 1.1.3 2024-01-10 [1] CRAN (R 4.0.2) ## rmarkdown 2.10 2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.0.2) ## sass 0.4.8 2023-12-06 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2024-03-13 [1] Github (R-lib/testthat@e99155a) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.0.2) ## usethis 1.6.3 2020-09-17 [1] RSPM (R 4.0.2) ## utf8 1.1.4 2018-05-24 [1] RSPM (R 4.0.3) ## vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.0.2) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2024-03-13 [1] Github (yihui/xfun@74c2a66) ## xml2 1.3.2 2020-04-23 [1] RSPM (R 4.0.3) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [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 4.0.2 (2020-06-22) ## os Ubuntu 20.04.5 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-05-02 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## askpass 1.1 2019-01-13 [1] RSPM (R 4.0.3) ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.5) ## bookdown 0.24 2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) ## bslib 0.6.1 2023-11-28 [1] CRAN (R 4.0.2) ## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.0.2) ## callr 3.5.0 2020-10-08 [1] RSPM (R 4.0.2) ## cli 3.6.2 2023-12-11 [1] CRAN (R 4.0.2) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## curl 5.2.1 2024-03-01 [1] CRAN (R 4.0.2) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.23 2023-11-01 [1] CRAN (R 4.0.2) ## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0) ## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.0.2) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.5) ## highr 0.8 2019-03-20 [1] RSPM (R 4.0.3) ## hms 0.5.3 2020-01-08 [1] RSPM (R 4.0.0) ## htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.0.2) ## httr 1.4.2 2020-07-20 [1] RSPM (R 4.0.3) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## jsonlite 1.7.1 2020-09-07 [1] RSPM (R 4.0.2) ## knitr 1.33 2024-03-13 [1] Github (yihui/knitr@a1052d1) ## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.0.2) ## magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.0.2) ## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2) ## openssl 1.4.3 2020-09-18 [1] RSPM (R 4.0.3) ## ottrpal 1.2.1 2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44) ## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.0.2) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.0.3) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.4.0 2020-10-07 [1] RSPM (R 4.0.2) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## readr 1.4.0 2020-10-05 [1] RSPM (R 4.0.2) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 1.1.3 2024-01-10 [1] CRAN (R 4.0.2) ## rmarkdown 2.10 2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.0.2) ## sass 0.4.8 2023-12-06 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2024-03-13 [1] Github (R-lib/testthat@e99155a) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.0.2) ## usethis 1.6.3 2020-09-17 [1] RSPM (R 4.0.2) ## utf8 1.1.4 2018-05-24 [1] RSPM (R 4.0.3) ## vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.0.2) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2024-03-13 [1] Github (yihui/xfun@74c2a66) ## xml2 1.3.2 2020-04-23 [1] RSPM (R 4.0.3) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [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, John Muschelli, Carrie Wright 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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 code span.op { color: #666666; } /* Operator */
@@ -118,6 +117,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 <style type="text/css">
 /* Used with Pandoc 2.11+ new --citeproc when CSL is used */
 div.csl-bib-body { }
@@ -201,7 +204,8 @@
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
-<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
+<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
 <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
 <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 </ul>
@@ -233,8 +237,8 @@ <h1>
 <div class="hero-image-container">
   <img class= "hero-image" src= "https://github.com/jhudsl/OTTR_Template/raw/main/assets/dasl_thin_main_image.png">
 </div>
-<div id="references" class="section level1" number="3">
-<h1><span class="header-section-number">Chapter 3</span> References</h1>
+<div id="references" class="section level1 hasAnchor" number="3">
+<h1><span class="header-section-number">Chapter 3</span> References<a href="references.html#references" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 
 <div id="refs" class="references csl-bib-body hanging-indent">
 <div class="csl-entry">
diff --git a/docs/search_index.json b/docs/search_index.json
index 360bf5f4..0d5844bf 100644
--- a/docs/search_index.json
+++ b/docs/search_index.json
@@ -1 +1 @@
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"],["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 4.0.2 (2020-06-22) ## os Ubuntu 20.04.5 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-04-12 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## askpass 1.1 2019-01-13 [1] RSPM (R 4.0.3) ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.5) ## bookdown 0.24 2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) ## bslib 0.6.1 2023-11-28 [1] CRAN (R 4.0.2) ## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.0.2) ## callr 3.5.0 2020-10-08 [1] RSPM (R 4.0.2) ## cli 3.6.2 2023-12-11 [1] CRAN (R 4.0.2) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.23 2023-11-01 [1] CRAN (R 4.0.2) ## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0) ## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.0.2) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.5) ## hms 0.5.3 2020-01-08 [1] RSPM (R 4.0.0) ## htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.0.2) ## httr 1.4.2 2020-07-20 [1] RSPM (R 4.0.3) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## jsonlite 1.7.1 2020-09-07 [1] RSPM (R 4.0.2) ## knitr 1.33 2024-03-13 [1] Github (yihui/knitr@a1052d1) ## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.0.2) ## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.0.2) ## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2) ## openssl 1.4.3 2020-09-18 [1] RSPM (R 4.0.3) ## ottrpal 1.2.1 2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44) ## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.0.2) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.0.3) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.4.0 2020-10-07 [1] RSPM (R 4.0.2) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## readr 1.4.0 2020-10-05 [1] RSPM (R 4.0.2) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 1.1.3 2024-01-10 [1] CRAN (R 4.0.2) ## rmarkdown 2.10 2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.0.2) ## sass 0.4.8 2023-12-06 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2024-03-13 [1] Github (R-lib/testthat@e99155a) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.0.2) ## usethis 1.6.3 2020-09-17 [1] RSPM (R 4.0.2) ## utf8 1.1.4 2018-05-24 [1] RSPM (R 4.0.3) ## vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.0.2) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2024-03-13 [1] Github (yihui/xfun@74c2a66) ## xml2 1.3.2 2020-04-23 [1] RSPM (R 4.0.3) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [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 4.0.2 (2020-06-22) ## os Ubuntu 20.04.5 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-04-12 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## askpass 1.1 2019-01-13 [1] RSPM (R 4.0.3) ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.5) ## bookdown 0.24 2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) ## bslib 0.6.1 2023-11-28 [1] CRAN (R 4.0.2) ## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.0.2) ## callr 3.5.0 2020-10-08 [1] RSPM (R 4.0.2) ## cli 3.6.2 2023-12-11 [1] CRAN (R 4.0.2) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## curl 5.2.1 2024-03-01 [1] CRAN (R 4.0.2) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.23 2023-11-01 [1] CRAN (R 4.0.2) ## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0) ## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.0.2) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.5) ## highr 0.8 2019-03-20 [1] RSPM (R 4.0.3) ## hms 0.5.3 2020-01-08 [1] RSPM (R 4.0.0) ## htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.0.2) ## httr 1.4.2 2020-07-20 [1] RSPM (R 4.0.3) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## jsonlite 1.7.1 2020-09-07 [1] RSPM (R 4.0.2) ## knitr 1.33 2024-03-13 [1] Github (yihui/knitr@a1052d1) ## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.0.2) ## magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.0.2) ## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2) ## openssl 1.4.3 2020-09-18 [1] RSPM (R 4.0.3) ## ottrpal 1.2.1 2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44) ## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.0.2) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.0.3) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.4.0 2020-10-07 [1] RSPM (R 4.0.2) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## readr 1.4.0 2020-10-05 [1] RSPM (R 4.0.2) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 1.1.3 2024-01-10 [1] CRAN (R 4.0.2) ## rmarkdown 2.10 2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.0.2) ## sass 0.4.8 2023-12-06 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2024-03-13 [1] Github (R-lib/testthat@e99155a) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.0.2) ## usethis 1.6.3 2020-09-17 [1] RSPM (R 4.0.2) ## utf8 1.1.4 2018-05-24 [1] RSPM (R 4.0.3) ## vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.0.2) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2024-03-13 [1] Github (yihui/xfun@74c2a66) ## xml2 1.3.2 2020-04-23 [1] RSPM (R 4.0.3) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [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, John Muschelli, Carrie Wright 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 4.0.2 (2020-06-22) ## os Ubuntu 20.04.5 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-04-12 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.5) ## bookdown 0.24 2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) ## bslib 0.6.1 2023-11-28 [1] CRAN (R 4.0.2) ## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.0.2) ## callr 3.5.0 2020-10-08 [1] RSPM (R 4.0.2) ## cli 3.6.2 2023-12-11 [1] CRAN (R 4.0.2) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.23 2023-11-01 [1] CRAN (R 4.0.2) ## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.0.2) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.5) ## htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.0.2) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## jsonlite 1.7.1 2020-09-07 [1] RSPM (R 4.0.2) ## knitr 1.33 2024-03-13 [1] Github (yihui/knitr@a1052d1) ## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.0.2) ## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.0.2) ## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.4.0 2020-10-07 [1] RSPM (R 4.0.2) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 1.1.3 2024-01-10 [1] CRAN (R 4.0.2) ## rmarkdown 2.10 2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.0.2) ## sass 0.4.8 2023-12-06 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2024-03-13 [1] Github (R-lib/testthat@e99155a) ## usethis 1.6.3 2020-09-17 [1] RSPM (R 4.0.2) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2024-03-13 [1] Github (yihui/xfun@74c2a66) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [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 June, 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 2024-06-26 ## 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 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1) ## 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) ## 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) ## 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) ## 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 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34) ## 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) ## openssl 2.1.1 2023-09-25 [1] RSPM (R 4.3.0) ## ottrpal 1.2.1 2024-06-11 [1] Github (jhudsl/ottrpal@828539f) ## 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) ## 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) ## 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 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9) ## 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) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.2) ## 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) ## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc) ## 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 2024-06-26 ## 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 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1) ## 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) ## 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) ## 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) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## highr 0.10 2022-12-22 [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) ## 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 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34) ## 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) ## openssl 2.1.1 2023-09-25 [1] RSPM (R 4.3.0) ## ottrpal 1.2.1 2024-06-11 [1] Github (jhudsl/ottrpal@828539f) ## 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) ## 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) ## 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 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9) ## 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) ## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.2) ## 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) ## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc) ## 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, John Muschelli, Carrie Wright 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 2024-06-26 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1) ## 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 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34) ## 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 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9) ## 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 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc) ## 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. "]]
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