added code for r users to download good-enough-project-template

UtrechtUniversity · Nov 28, 2022 · 32f8fd9 · 32f8fd9
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diff --git a/04-project-management.Rmd b/04-project-management.Rmd
@@ -40,6 +40,17 @@ _NB: You can check the slides for more detail._
 
 * Use the instructions [on this slide](../slides/slides_project-setup.html#6) to clone a template repository of a project folder structure to your computer. Remember to also follow the instructions on removing the .git folder that is downloaded.
 
+* R users can also use the following code:
+
+```{r eval=FALSE, echo=TRUE}
+
+# install.packages("usethis")
+
+usethis::use_zip("https://github.com/bvreede/good-enough-project-template/archive/refs/heads/master.zip",
+                 destdir = getwd())
+```
+
+
 * Place your project files in the right folder.
 
 * Adjust paths in your code, and be sure to use relative paths!

diff --git a/docs/2-acknowledgements.html b/docs/2-acknowledgements.html
diff --git a/docs/3-preparation.html b/docs/3-preparation.html
diff --git a/docs/3.1-data-andor-code.html b/docs/3.1-data-andor-code.html
diff --git a/docs/3.2-terminal.html b/docs/3.2-terminal.html
diff --git a/docs/3.3-git.html b/docs/3.3-git.html
diff --git a/docs/3.4-final-test.html b/docs/3.4-final-test.html
diff --git a/docs/4-introduction.html b/docs/4-introduction.html
diff --git a/docs/4.1-schedule.html b/docs/4.1-schedule.html
diff --git a/docs/4.2-course-materials.html b/docs/4.2-course-materials.html
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/5-project-management.html b/docs/5-project-management.html
diff --git a/docs/5.1-project-setup.html b/docs/5.1-project-setup.html
diff --git a/docs/5.2-version-control.html b/docs/5.2-version-control.html
diff --git a/docs/5.3-publication-licensing.html b/docs/5.3-publication-licensing.html
diff --git a/docs/6-code-quality.html b/docs/6-code-quality.html
diff --git a/docs/6.1-readability.html b/docs/6.1-readability.html
diff --git a/docs/6.2-reusability.html b/docs/6.2-reusability.html
diff --git a/docs/6.3-robustness.html b/docs/6.3-robustness.html
diff --git a/docs/7-documentation.html b/docs/7-documentation.html
diff --git a/docs/7.1-comments-and-docstrings.html b/docs/7.1-comments-and-docstrings.html
diff --git a/docs/7.2-the-readme-page.html b/docs/7.2-the-readme-page.html
diff --git a/docs/8-accessibility-reproducibility.html b/docs/8-accessibility-reproducibility.html
diff --git a/docs/8.1-dependencies.html b/docs/8.1-dependencies.html
diff --git a/docs/8.2-binder.html b/docs/8.2-binder.html
diff --git a/docs/8.3-archiving.html b/docs/8.3-archiving.html
diff --git a/docs/9-references.html b/docs/9-references.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/libs/anchor-sections-1.1.0/anchor-sections-hash.css b/docs/libs/anchor-sections-1.1.0/anchor-sections-hash.css
@@ -0,0 +1,2 @@
+/* Styles for section anchors */
+a.anchor-section::before {content: '#';font-size: 80%;}
diff --git a/docs/libs/anchor-sections-1.1.0/anchor-sections.css b/docs/libs/anchor-sections-1.1.0/anchor-sections.css
@@ -0,0 +1,4 @@
+/* Styles for section anchors */
+a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
+.hasAnchor:hover a.anchor-section {visibility: visible;}
+ul > li > .anchor-section {display: none;}
diff --git a/docs/libs/anchor-sections-1.1.0/anchor-sections.js b/docs/libs/anchor-sections-1.1.0/anchor-sections.js
@@ -0,0 +1,11 @@
+document.addEventListener('DOMContentLoaded', function () {
+  // If section divs is used, we need to put the anchor in the child header
+  const headers = document.querySelectorAll("div.hasAnchor.section[class*='level'] > :first-child")
+
+  headers.forEach(function (x) {
+    // Add to the header node
+    if (!x.classList.contains('hasAnchor')) x.classList.add('hasAnchor')
+    // Remove from the section or div created by Pandoc
+    x.parentElement.classList.remove('hasAnchor')
+  })
+})
diff --git a/docs/libs/gitbook-2.6.7/css/plugin-bookdown.css b/docs/libs/gitbook-2.6.7/css/plugin-bookdown.css
@@ -97,3 +97,9 @@ div.proof>*:last-child:after {
 .header-section-number {
   padding-right: .5em;
 }
+#header .multi-author {
+  margin: 0.5em 0 -0.5em 0;
+}
+#header .date {
+  margin-top: 1.5em;
+}
diff --git a/docs/libs/gitbook-2.6.7/js/plugin-search.js b/docs/libs/gitbook-2.6.7/js/plugin-search.js
@@ -1,9 +1,24 @@
 gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
     var index = null;
+    var fuse = null;
+    var _search = {engine: 'lunr', opts: {}};
     var $searchInput, $searchLabel, $searchForm;
     var $highlighted = [], hi, hiOpts = { className: 'search-highlight' };
     var collapse = false, toc_visible = [];
 
+    function init(config) {
+        // Instantiate search settings
+        _search = gitbook.storage.get("search", {
+            engine: config.search.engine || 'lunr',
+            opts: config.search.options || {},
+        });
+    };
+
+    // Save current search settings
+    function saveSearchSettings() {
+        gitbook.storage.set("search", _search);
+    }
+
     // Use a specific index
     function loadIndex(data) {
         // [Yihui] In bookdown, I use a character matrix to store the chapter
@@ -14,18 +29,36 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
         // lunr cannot handle non-English text very well, e.g. the default
         // tokenizer cannot deal with Chinese text, so we may want to replace
         // lunr with a dumb simple text matching approach.
-        index = lunr(function () {
-          this.ref('url');
-          this.field('title', { boost: 10 });
-          this.field('body');
-        });
-        data.map(function(item) {
-          index.add({
-            url: item[0],
-            title: item[1],
-            body: item[2]
+        if (_search.engine === 'lunr') {
+          index = lunr(function () {
+            this.ref('url');
+            this.field('title', { boost: 10 });
+            this.field('body');
           });
-        });
+          data.map(function(item) {
+            index.add({
+              url: item[0],
+              title: item[1],
+              body: item[2]
+            });
+          });
+          return;
+        }
+        fuse = new Fuse(data.map((_data => {
+            return {
+                url: _data[0],
+                title: _data[1],
+                body: _data[2]
+            };
+        })), Object.assign(
+            {
+                includeScore: true,
+                threshold: 0.1,
+                ignoreLocation: true,
+                keys: ["title", "body"]
+            },
+            _search.opts
+        ));
     }
 
     // Fetch the search index
@@ -36,20 +69,33 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
 
     // Search for a term and return results
     function search(q) {
-        if (!index) return;
-
-        var results = _.chain(index.search(q))
-        .map(function(result) {
-            var parts = result.ref.split("#");
-            return {
-                path: parts[0],
-                hash: parts[1]
-            };
-        })
-        .value();
+        let results = [];
+        switch (_search.engine) {
+            case 'fuse':
+                if (!fuse) return;
+                results = fuse.search(q).map(function(result) {
+                    var parts = result.item.url.split('#');
+                    return {
+                        path: parts[0],
+                        hash: parts[1]
+                    };
+                });
+                break;
+            case 'lunr':
+            default:
+                if (!index) return;
+                results = _.chain(index.search(q)).map(function(result) {
+                    var parts = result.ref.split("#");
+                    return {
+                        path: parts[0],
+                        hash: parts[1]
+                    };
+                })
+                .value();
+        }
 
         // [Yihui] Highlight the search keyword on current page
-        $highlighted = results.length === 0 ? [] : $('.page-inner')
+        $highlighted = $('.page-inner')
           .unhighlight(hiOpts).highlight(q, hiOpts).find('span.search-highlight');
         scrollToHighlighted(0);
 
@@ -172,6 +218,7 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
     gitbook.events.bind("start", function(e, config) {
         // [Yihui] disable search
         if (config.search === false) return;
+        init(config);
         collapse = !config.toc || config.toc.collapse === 'section' ||
           config.toc.collapse === 'subsection';
 

diff --git a/docs/libs/jquery-3.6.0/jquery-3.6.0.min.js b/docs/libs/jquery-3.6.0/jquery-3.6.0.min.js
diff --git a/docs/libs/vembedr-0.1.5/css/vembedr.css b/docs/libs/vembedr-0.1.5/css/vembedr.css
@@ -0,0 +1,14 @@
+.vembedr {
+  margin-bottom: 10px;
+}
+
+.vembedr-rounded {
+  display: inline-block;
+  border-radius: 15px;
+  overflow: hidden;
+}
+
+.vembedr-rounded iframe {
+  display: block;
+  border: none;
+}
diff --git a/docs/search_index.json b/docs/search_index.json
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		/* Styles for section anchors */
		a.anchor-section::before {content: '#';font-size: 80%;}