From 121d64a09df182525f172b6746214acc849f0782 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 6 Aug 2024 21:00:56 +0000 Subject: [PATCH] Render course --- docs/01-intro.md | 99 ++++++ docs/02-chapter_of_course.md | 369 +++++++++++++++++++++ docs/404.html | 326 +++++++++++++++++++ docs/About.md | 125 +++++++ docs/Course_Name.docx | Bin 41352 -> 41356 bytes docs/References.md | 2 + docs/a-new-chapter.html | 610 +++++++++++++++++++++++++++++++++++ docs/about-the-authors.html | 528 ++++++++++++++++++++++++++++++ docs/index.html | 338 +++++++++++++++++++ docs/index.md | 26 ++ docs/introduction.html | 413 ++++++++++++++++++++++++ docs/references.html | 335 +++++++++++++++++++ docs/search_index.json | 2 +- 13 files changed, 3172 insertions(+), 1 deletion(-) create mode 100644 docs/01-intro.md create mode 100644 docs/02-chapter_of_course.md create mode 100644 docs/404.html create mode 100644 docs/About.md create mode 100644 docs/References.md create mode 100644 docs/a-new-chapter.html create mode 100644 docs/about-the-authors.html create mode 100644 docs/index.html create mode 100644 docs/index.md create mode 100644 docs/introduction.html create mode 100644 docs/references.html diff --git a/docs/01-intro.md b/docs/01-intro.md new file mode 100644 index 0000000..6eccb03 --- /dev/null +++ b/docs/01-intro.md @@ -0,0 +1,99 @@ + + + +# Introduction + + +## Motivation + + +## Target Audience + +The course is intended for ... + +## Curriculum + +The course covers... + + + +``` r +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 2024-08-06 +## 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) +## 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 +## +## ────────────────────────────────────────────────────────────────────────────── +``` diff --git a/docs/02-chapter_of_course.md b/docs/02-chapter_of_course.md new file mode 100644 index 0000000..dd25c99 --- /dev/null +++ b/docs/02-chapter_of_course.md @@ -0,0 +1,369 @@ + +# A new chapter + +If you haven't yet read the getting started Wiki pages; [start there](https://www.ottrproject.org/getting_started.html). + +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: + + + + +## 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} + +## 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](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image). + + +``` r +library(magrittr) +``` + +## 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](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf) for additional general information about how you can format text within R Markdown files. In addition, see [here](https://pandoc.org/MANUAL.html#pandocs-markdown) for more in depth and advanced options. + +### Subtopic + +Here's a subheading (using three pound symbols) and some text in this subsection! + +## Code examples + +You can demonstrate code like this: + + +``` r +output_dir <- file.path("resources", "code_output") +if (!dir.exists(output_dir)) { + dir.create(output_dir) +} +``` + +And make plots too: + + +``` r +hist_plot <- hist(iris$Sepal.Length) +``` + +![](resources/images/02-chapter_of_course_files/figure-docx/unnamed-chunk-4-1.png) + +You can also save these plots to file: + + +``` r +png(file.path(output_dir, "test_plot.png")) +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 +## +## $xname +## [1] "iris$Sepal.Length" +## +## $equidist +## [1] TRUE +## +## attr(,"class") +## [1] "histogram" +``` + +``` r +dev.off() +``` + +``` +## png +## 2 +``` + +## Image example + +How to include a Google slide. It's simplest to use the `ottrpal` package: + + +![](resources/images/02-chapter_of_course_files/figure-docx//1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png){width=100%} + +But if you have the slide or some other image locally downloaded you can also use HTML like this: + +Major point!! example image + +## 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](https://www.youtube.com/embed/VOCYL-FNbr0) using markdown syntax. + +### 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](https://rmarkdown.rstudio.com/lesson-3.html). + + + + +### Using HTML + + + +### Using `knitr` + + + +### Using HTML + + + +## Website Examples + +Yet again you can use a link to a website like so: + +[A Website](https://yihui.org) + +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](https://yihui.org){target="_blank"} + +Or, you can embed some websites. + +### Using `knitr` + +This works: + + + + +### Using HTML + + + + +If you'd like the URL to show up in a new tab you can do this: + +``` +LinkedIn +``` + +## Citation examples + +We can put citations at the end of a sentence like this [@rmarkdown2021]. +Or multiple citations [@rmarkdown2021, @Xie2018]. + +but they need a ; separator [@rmarkdown2021; @Xie2018]. + +In text, we can put citations like this @rmarkdown2021. + +## 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. + +### 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](https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html) documentation for more information [@Xie2020]. Note that Bookdown uses Pandoc. + + +``` +::: {.notice} +Note using rmarkdown syntax. + +::: +``` + +::: {.notice} +Note using rmarkdown syntax. + +::: + +As an example you might do something like this: + +::: {.notice} +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](introduction.html#scroll-highlight)) +::: + + +### Using HTML + +To add a warning box like the following use: + +``` +
+Followed by the text you want inside +
+``` + +This will create the following: + +
+ +Followed by the text you want inside + +
+ +Here is a `
` box: + +
+ +Note text + +
+ +Here is a `
` box: + +
+ +GitHub text + +
+ + +Here is a `
` box: + +
+ +dictionary text + +
+ + +Here is a `
` box: + +
+ +reflection text + +
+ + +Here is a `
` box: + +
+ +Work in Progress text + +
+ + +## Dropdown summaries + +
You can hide additional information in a dropdown menu +Here's more words that are hidden. +
+ +## Print out session info + +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 +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 2024-08-06 +## 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) +## 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 +## +## ────────────────────────────────────────────────────────────────────────────── +``` + +[many links]: https://github.com/jhudsl/OTTR_Template diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..6145084 --- /dev/null +++ b/docs/404.html @@ -0,0 +1,326 @@ + + + + + + + Page not found | Course Name + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ All illustrations CC-BY. +
+ All other materials CC-BY unless noted otherwise. +
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+ + + + + + + + + + + + + diff --git a/docs/About.md b/docs/About.md new file mode 100644 index 0000000..a6b8953 --- /dev/null +++ b/docs/About.md @@ -0,0 +1,125 @@ + +# About the Authors {-} + +These credits are based on our [course contributors table guidelines](https://www.ottrproject.org/more_features.html#giving-credits-to-contributors). + +  +  + +|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 2024-08-06 +## 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) +## 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 +## +## ────────────────────────────────────────────────────────────────────────────── +``` + + + +[FirstName LastName]: link to personal website +[John Muschelli]: https://johnmuschelli.com/ +[Candace Savonen]: https://www.cansavvy.com/ +[Carrie Wright]: https://carriewright11.github.io/ +[Ava Hoffman]: https://www.avahoffman.com/ + + + +[ottrpal]: https://github.com/jhudsl/ottrpal + + diff --git a/docs/Course_Name.docx b/docs/Course_Name.docx index 57b27a940b0beadbdec265f7797ab4bd27a29dc8..4167af7f9389abb1dcfdada4d7850bff1eee89b3 100644 GIT binary patch delta 10294 zcmai)V{~Or*RFSL+fF*RosQkHjgD>XprcNQJ9g4>I<~EjZQHg^zi&UE&UeN*Yt)bX zuDNPeja4=4$2DenFZhpMaAajU2uMr-I4mrHuozmq8o3D!@?WC%Hy9!q(!bQOr{l;a zB><37y8|8q1{79$j+mAr2->h~IV-uOH?(A?4JX}9Ry&Sa%clQmFBI+CZOTDB>tU0K z(F>Oj#-*(t-9A)8`|#Na8;A#|Drv1BW&spL#biaywnD%WsjMRsvqn zaIPC6ML$)rzySJ9=v=tcyf7nQ3Ay`^@jGfTE*TB%Ap0`h&mDD{bllN$5!z55HMNrUQ` ztpv0r!(#=O%D40b?RqHCsRQ?&l)J@?zhyenwh?Qy} zCe^g!Z#EXliIgUznr_#cJYzqV(rSjuwp5{H$VQ!i~6#U0cGCm-}%b6w7 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zImkSp=5HOR#DpJFr~m-GE&zb_e{{S-;C#w|{CDS*!ZCxE^J)HJ;lQMDE+BF+_1`o6 zee(Z!N&XYkpNRe!`GAbU)c=?O|CsE8vcXh;oBVes|HsA;G!Lfz$K)AI3XdfP;*ui5 z)>MJ}Gx>j70zuLRq;SR{lY)N(3j4z{f^rM~b@u%aive0Hp!?gIr_h+mFChS+ME0*K l{x>avC<^KRSyHr%wpt diff --git a/docs/References.md b/docs/References.md new file mode 100644 index 0000000..98d65dc --- /dev/null +++ b/docs/References.md @@ -0,0 +1,2 @@ + +# References diff --git a/docs/a-new-chapter.html b/docs/a-new-chapter.html new file mode 100644 index 0000000..c1167ac --- /dev/null +++ b/docs/a-new-chapter.html @@ -0,0 +1,610 @@ + + + + + + + Chapter 2 A new chapter | Course Name + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +
+ +
+ +
+
+ + +
+
+ +
+ + + + + + + + + +
+ +
+
+

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:

+ +
+
+

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 <- file.path("resources", "code_output")
+if (!dir.exists(output_dir)) {
+  dir.create(output_dir)
+}
+

And make plots too:

+
hist_plot <- hist(iris$Sepal.Length)
+

+

You can also save these plots to file:

+
png(file.path(output_dir, "test_plot.png"))
+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
+## 
+## $xname
+## [1] "iris$Sepal.Length"
+## 
+## $equidist
+## [1] TRUE
+## 
+## attr(,"class")
+## [1] "histogram"
+
dev.off()
+
## png 
+##   2
+
+
+

2.5 Image example

+

How to include a Google slide. It’s simplest to use the ottrpal package:

+

Major point!! example image

+

But if you have the slide or some other image locally downloaded you can also use HTML like this:

+

Major point!! example image

+
+
+

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:

+
<a href="https://www.linkedin.com" target="_blank">LinkedIn</a>
+
+
+
+

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:

+
<div class = "notice">
+Followed by the text you want inside
+</div>
+

This will create the following:

+
+

Followed by the text you want inside

+
+

Here is a <div class = "warning"> box:

+
+

Note text

+
+

Here is a <div class = "github"> box:

+
+

GitHub text

+
+

Here is a <div class = "dictionary"> box:

+
+

dictionary text

+
+

Here is a <div class = "reflection"> box:

+
+

reflection text

+
+

Here is a <div class = "wip"> box:

+
+

Work in Progress text

+
+
+
+ + +
+

References

+
+
+Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2021. Rmarkdown: Dynamic Documents for r. https://github.com/rstudio/rmarkdown. +
+
+Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown. +
+
+Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook. +
+
+
+
+
+ All illustrations CC-BY. +
+ All other materials CC-BY unless noted otherwise. +
+
+ +
+ +
+
+
+ + +
+
+ + + + + + + + + + + + + diff --git a/docs/about-the-authors.html b/docs/about-the-authors.html new file mode 100644 index 0000000..3f5abe1 --- /dev/null +++ b/docs/about-the-authors.html @@ -0,0 +1,528 @@ + + + + + + + About the Authors | Course Name + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +
+ +
+ +
+
+ + +
+
+ +
+ + + + + + + + + +
+ +
+
+

About the Authors

+

These credits are based on our course contributors table guidelines.

+

  + 

+ ++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
CreditsNames
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 involvedDelivered 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 involvedIf any other authors besides lead instructor
Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involvedWrote 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 involvedGave high level advice on content
AcknowledgmentsGave 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 EngineersCandace Savonen, Carrie Wright, Ava Hoffman
Publishing Maintenance EngineerCandace Savonen
Technical Publishing StylistsCarrie 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 StaffStaff 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     2024-08-06
+##  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)
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+##  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)
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+##  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
+## 
+## ──────────────────────────────────────────────────────────────────────────────
+ + + + +
+
+
+
+ All illustrations CC-BY. +
+ All other materials CC-BY unless noted otherwise. +
+
+ +
+ +
+
+
+ + +
+
+ + + + + + + + + + + + + diff --git a/docs/index.html b/docs/index.html new file mode 100644 index 0000000..c0d3cd9 --- /dev/null +++ b/docs/index.html @@ -0,0 +1,338 @@ + + + + + + + Course Name + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +
+ +
+ +
+
+ + +
+
+ +
+ + + + + + + + + +
+ +
+ +
+

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.

+ + +
+
+
+
+
+ All illustrations CC-BY. +
+ All other materials CC-BY unless noted otherwise. +
+
+ +
+ +
+
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+ + + + + + + + + + + + + diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..a64dd4a --- /dev/null +++ b/docs/index.md @@ -0,0 +1,26 @@ +--- +title: "Course Name" +date: "August, 2024" +site: bookdown::bookdown_site +documentclass: book +bibliography: [book.bib] +biblio-style: apalike +link-citations: yes +description: "Description about Course/Book." +favicon: assets/dasl_favicon.ico +output: + bookdown::word_document2: + toc: true +--- + +# About this Course {-} + + +## 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](LINK HERE). 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](LINK HERE). +- This course can be taken on [Coursera for certification here](LINK 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](LINK HERE). diff --git a/docs/introduction.html b/docs/introduction.html new file mode 100644 index 0000000..c1f3b2d --- /dev/null +++ b/docs/introduction.html @@ -0,0 +1,413 @@ + + + + + + + Chapter 1 Introduction | Course Name + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

Chapter 1 Introduction

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+

1.1 Motivation

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+

1.2 Target Audience

+

The course is intended for …

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+

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     2024-08-06
+##  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)
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+##  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)
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+##  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)
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+##  stringi       1.8.3   2023-12-11 [1] RSPM (R 4.3.0)
+##  stringr       1.5.1   2023-11-14 [1] RSPM (R 4.3.0)
+##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.2)
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+##  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
+## 
+## ──────────────────────────────────────────────────────────────────────────────
+ +
+
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+
+ All illustrations CC-BY. +
+ All other materials CC-BY unless noted otherwise. +
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+ +
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+ + + + + + + + + + + + + diff --git a/docs/references.html b/docs/references.html new file mode 100644 index 0000000..1fd91bd --- /dev/null +++ b/docs/references.html @@ -0,0 +1,335 @@ + + + + + + + Chapter 3 References | Course Name + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

Chapter 3 References

+ +
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+Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2021. Rmarkdown: Dynamic Documents for r. https://github.com/rstudio/rmarkdown. +
+
+Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown. +
+
+Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook. +
+
+
+
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+ All illustrations CC-BY. +
+ All other materials CC-BY unless noted otherwise. +
+
+ +
+ +
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+ + +
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+ + + + + + + + + + + + + diff --git a/docs/search_index.json b/docs/search_index.json index 0d5844b..69bcfef 100644 --- a/docs/search_index.json +++ b/docs/search_index.json @@ -1 +1 @@ -[["index.html", "Course Name About this Course 0.1 Available course formats", " Course Name 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 <- file.path("resources", "code_output") if (!dir.exists(output_dir)) { dir.create(output_dir) } And make plots too: hist_plot <- hist(iris$Sepal.Length) You can also save these plots to file: png(file.path(output_dir, "test_plot.png")) 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 ## ## $xname ## [1] "iris$Sepal.Length" ## ## $equidist ## [1] TRUE ## ## attr(,"class") ## [1] "histogram" 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: <a href="https://www.linkedin.com" target="_blank">LinkedIn</a> 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: <div class = "notice"> Followed by the text you want inside </div> This will create the following: Followed by the text you want inside Here is a <div class = \"warning\"> box: Note text Here is a <div class = \"github\"> box: GitHub text Here is a <div class = \"dictionary\"> box: dictionary text Here is a <div class = \"reflection\"> box: reflection text Here is a <div class = \"wip\"> 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. "]] +[["index.html", "Course Name About this Course 0.1 Available course formats", " Course Name August, 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 2024-08-06 ## 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 <- file.path("resources", "code_output") if (!dir.exists(output_dir)) { dir.create(output_dir) } And make plots too: hist_plot <- hist(iris$Sepal.Length) You can also save these plots to file: png(file.path(output_dir, "test_plot.png")) 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 ## ## $xname ## [1] "iris$Sepal.Length" ## ## $equidist ## [1] TRUE ## ## attr(,"class") ## [1] "histogram" 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: <a href="https://www.linkedin.com" target="_blank">LinkedIn</a> 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: <div class = "notice"> Followed by the text you want inside </div> This will create the following: Followed by the text you want inside Here is a <div class = \"warning\"> box: Note text Here is a <div class = \"github\"> box: GitHub text Here is a <div class = \"dictionary\"> box: dictionary text Here is a <div class = \"reflection\"> box: reflection text Here is a <div class = \"wip\"> 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 2024-08-06 ## 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 2024-08-06 ## 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. "]]