Render bookdown

fhdsl · Aug 28, 2024 · 57ae156 · 57ae156
1 parent d2995f5
commit 57ae156
Show file tree

Hide file tree

Showing 17 changed files with 302 additions and 354 deletions.
diff --git 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 | AnVIL Collection</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 | AnVIL Collection" />
   <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/AnVIL_style/anvil_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/[email protected]/dist/fuse.min.js"></script>
 <link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
@@ -49,17 +47,11 @@
 
 
 
-<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>
-  <html>
-
-  <head>
-  <title>Page not found | Title</title>
-  </head>
-
-  <body>
-
-<!-- Google tag (gtag.js) -->
+<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>
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
 <script async src="https://www.googletagmanager.com/gtag/js?id=G-0YKJ92NZK4"></script>
 <script>
   window.dataLayer = window.dataLayer || [];
@@ -68,12 +60,13 @@
 
   gtag('config', 'G-0YKJ92NZK4');
 </script>
-
-  </body>
-  </html>
 
 
 
+<style type="text/css">
+
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 
 <link rel="stylesheet" href="assets/AnVIL_style/style.css" type="text/css" />
 </head>
@@ -119,7 +112,7 @@
 <li class="chapter" data-level="" data-path="contribute.html"><a href="contribute.html#how-often-is-the-collection-updated"><i class="fa fa-check"></i>How often is the Collection updated?</a></li>
 <li class="chapter" data-level="" data-path="contribute.html"><a href="contribute.html#how-can-i-add-my-new-coursecontent-to-the-collection"><i class="fa fa-check"></i>How can I add my new course/content to the Collection?</a></li>
 <li class="chapter" data-level="" data-path="contribute.html"><a href="contribute.html#i-want-to-use-the-raw-collection-data"><i class="fa fa-check"></i>I want to use the raw Collection data!</a></li>
-<li><a href="contribute.html#how-do-i-edit-description-homepage-and-topics">How do I edit <strong>description</strong>, <strong>homepage</strong>, and <strong>topics</strong>?</a></li>
+<li class="chapter" data-level="" data-path="contribute.html"><a href="contribute.html#how-do-i-edit-description-homepage-and-topics"><i class="fa fa-check"></i>How do I edit <strong>description</strong>, <strong>homepage</strong>, and <strong>topics</strong>?</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="contribute.html"><a href="contribute.html#anvil-shorts"><i class="fa fa-check"></i>AnVIL Shorts</a></li>
 </ul></li>

diff --git a/docs/Session-info.md b/docs/Session-info.md
@@ -1,61 +1,72 @@
 
 # Session Info {-}
 
+Below is software version information used to render this collection.
+
 
 ```
 ## ─ Session info ───────────────────────────────────────────────────────────────
-##  setting  value                       
-##  version  R version 4.0.2 (2020-06-22)
-##  os       Ubuntu 20.04.3 LTS          
-##  system   x86_64, linux-gnu           
-##  ui       X11                         
-##  language (EN)                        
-##  collate  en_US.UTF-8                 
-##  ctype    en_US.UTF-8                 
-##  tz       Etc/UTC                     
-##  date     2024-08-28                  
+##  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     2024-08-28
+##  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 4.0.3)                    
-##  bookdown      0.24       2022-02-15 [1] Github (rstudio/bookdown@88bc4ea) 
-##  callr         3.4.4      2020-09-07 [1] RSPM (R 4.0.2)                    
-##  cli           2.0.2      2020-02-28 [1] RSPM (R 4.0.0)                    
-##  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      0.14       2019-05-28 [1] RSPM (R 4.0.3)                    
-##  fansi         0.4.1      2020-01-08 [1] RSPM (R 4.0.0)                    
-##  fs            1.5.0      2020-07-31 [1] RSPM (R 4.0.3)                    
-##  glue          1.6.1      2022-01-22 [1] CRAN (R 4.0.2)                    
-##  htmltools     0.5.0      2020-06-16 [1] RSPM (R 4.0.1)                    
-##  jquerylib     0.1.4      2021-04-26 [1] CRAN (R 4.0.2)                    
-##  knitr         1.33       2022-02-15 [1] Github (yihui/knitr@a1052d1)      
-##  lifecycle     1.0.0      2021-02-15 [1] CRAN (R 4.0.2)                    
-##  magrittr      2.0.2      2022-01-26 [1] CRAN (R 4.0.2)                    
-##  memoise       1.1.0      2017-04-21 [1] RSPM (R 4.0.0)                    
-##  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            1.3.4      2020-08-11 [1] RSPM (R 4.0.2)                    
-##  purrr         0.3.4      2020-04-17 [1] RSPM (R 4.0.3)                    
-##  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         0.4.10     2022-02-15 [1] Github (r-lib/rlang@f0c9be5)      
-##  rmarkdown     2.10       2022-02-15 [1] Github (rstudio/rmarkdown@02d3c25)
-##  rprojroot     2.0.2      2020-11-15 [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      2022-02-15 [1] Github (R-lib/testthat@e99155a)   
-##  usethis       2.1.5.9000 2022-02-15 [1] Github (r-lib/usethis@57b109a)    
-##  withr         2.3.0      2020-09-22 [1] RSPM (R 4.0.2)                    
-##  xfun          0.26       2022-02-15 [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)
+##  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
 ## 
-## [1] /usr/local/lib/R/site-library
-## [2] /usr/local/lib/R/library
+## ──────────────────────────────────────────────────────────────────────────────
 ```
diff --git 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 | AnVIL Collection</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 | AnVIL Collection" />
   <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/AnVIL_style/anvil_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="contribute.html"/>
 <link rel="next" href="session-info.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/[email protected]/dist/fuse.min.js"></script>
 <link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
@@ -49,17 +47,11 @@
 
 
 
-<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>
-  <html>
-
-  <head>
-  <title>About the Authors | Title</title>
-  </head>
-
-  <body>
-
-<!-- Google tag (gtag.js) -->
+<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>
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
 <script async src="https://www.googletagmanager.com/gtag/js?id=G-0YKJ92NZK4"></script>
 <script>
   window.dataLayer = window.dataLayer || [];
@@ -68,12 +60,13 @@
 
   gtag('config', 'G-0YKJ92NZK4');
 </script>
-
-  </body>
-  </html>
 
 
 
+<style type="text/css">
+
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 
 <link rel="stylesheet" href="assets/AnVIL_style/style.css" type="text/css" />
 </head>
@@ -119,7 +112,7 @@
 <li class="chapter" data-level="" data-path="contribute.html"><a href="contribute.html#how-often-is-the-collection-updated"><i class="fa fa-check"></i>How often is the Collection updated?</a></li>
 <li class="chapter" data-level="" data-path="contribute.html"><a href="contribute.html#how-can-i-add-my-new-coursecontent-to-the-collection"><i class="fa fa-check"></i>How can I add my new course/content to the Collection?</a></li>
 <li class="chapter" data-level="" data-path="contribute.html"><a href="contribute.html#i-want-to-use-the-raw-collection-data"><i class="fa fa-check"></i>I want to use the raw Collection data!</a></li>
-<li><a href="contribute.html#how-do-i-edit-description-homepage-and-topics">How do I edit <strong>description</strong>, <strong>homepage</strong>, and <strong>topics</strong>?</a></li>
+<li class="chapter" data-level="" data-path="contribute.html"><a href="contribute.html#how-do-i-edit-description-homepage-and-topics"><i class="fa fa-check"></i>How do I edit <strong>description</strong>, <strong>homepage</strong>, and <strong>topics</strong>?</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="contribute.html"><a href="contribute.html#anvil-shorts"><i class="fa fa-check"></i>AnVIL Shorts</a></li>
 </ul></li>
@@ -160,8 +153,8 @@ <h1>
 <div class="hero-image-container"> 
   <img class= "hero-image" src="assets/AnVIL_style/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://github.com/jhudsl/OTTR_Template/wiki/How-to-give-credits">course contributors table guidelines</a>.</p>
 <p> 
  </p>