Built site for gh-pages

joshwlambert · Jan 30, 2024 · aa565f7 · aa565f7
1 parent 7d1d959
commit aa565f7
Show file tree

Hide file tree

Showing 30 changed files with 2,002 additions and 375 deletions.
diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-53bd91ba
+f8b0f27b
diff --git a/DAISIE.html b/DAISIE.html
diff --git a/DAISIE_files/figure-html/unnamed-chunk-10-1.png b/DAISIE_files/figure-html/unnamed-chunk-10-1.png
diff --git a/DAISIE_files/figure-html/unnamed-chunk-11-1.png b/DAISIE_files/figure-html/unnamed-chunk-11-1.png
diff --git a/DAISIE_files/figure-html/unnamed-chunk-12-1.png b/DAISIE_files/figure-html/unnamed-chunk-12-1.png
diff --git a/DAISIE_files/figure-html/unnamed-chunk-6-1.png b/DAISIE_files/figure-html/unnamed-chunk-6-1.png
diff --git a/DAISIE_files/figure-html/unnamed-chunk-7-1.png b/DAISIE_files/figure-html/unnamed-chunk-7-1.png
diff --git a/DAISIE_files/figure-html/unnamed-chunk-8-1.png b/DAISIE_files/figure-html/unnamed-chunk-8-1.png
diff --git a/DAISIE_files/figure-html/unnamed-chunk-9-1.png b/DAISIE_files/figure-html/unnamed-chunk-9-1.png
diff --git a/DAISIEprep.html b/DAISIEprep.html
diff --git a/assignment.html b/assignment.html
diff --git a/data/Figure_Insula_Tip_states.pdf b/data/Figure_Insula_Tip_states.pdf
diff --git a/data/Insula_checklist.xlsx b/data/Insula_checklist.xlsx
diff --git a/data/galapagos_datalist.Rdata b/data/galapagos_datalist.Rdata
diff --git a/exercise.html b/exercise.html
diff --git a/index.html b/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.3.450">
+<meta name="generator" content="quarto-1.4.549">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,7 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "start",
   "type": "textbox",
-  "limit": 20,
+  "limit": 50,
+  "keyboard-shortcut": [
+    "f",
+    "/",
+    "s"
+  ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -58,6 +64,7 @@
     "search-more-match-text": "more match in this document",
     "search-more-matches-text": "more matches in this document",
     "search-clear-button-title": "Clear",
+    "search-text-placeholder": "",
     "search-detached-cancel-button-title": "Cancel",
     "search-submit-button-title": "Submit",
     "search-label": "Search"
@@ -73,12 +80,12 @@
   <header id="quarto-header" class="headroom fixed-top">
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./index.html"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Welcome</span></a></li></ol></nav>
-      <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
-      </a>
+        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./index.html"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Welcome</span></a></li></ol></nav>
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        </a>
       <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
         <i class="bi bi-search"></i>
       </button>
@@ -88,7 +95,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="pt-lg-2 mt-2 text-left sidebar-header">
     <div class="sidebar-title mb-0 py-0">
       <a href="./">Island Biology DAISIE Practical</a> 
@@ -149,7 +156,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
 
@@ -178,12 +185,14 @@ <h1 class="title">Island Biology DAISIE Practical</h1>
   </div>
 
 
+
 </header>
 
+
 <p>Welcome to the DAISIE computer practical of the Island Biology course. Here you will find the material to learn how to use the DAISIE ecosystem of R packages to analyse the ecology and evolution of island communities. These tools have been developed to answer research questions in island biogeography and macroevolution. We will apply them to a case study of a group of beetles from the Caribbean islands.</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
-<p><img src="images/Figure_Insula_ancestral_state_reconstruction.png" class="img-fluid figure-img" width="400"></p>
+<p><img src="images/Figure_Insula_ancestral_state_reconstruction.png" class="img-fluid quarto-figure quarto-figure-center figure-img" width="400"></p>
 </figure>
 </div>
 
@@ -233,6 +242,33 @@ <h1 class="title">Island Biology DAISIE Practical</h1>
       }
     }
   }
+  const toggleGiscusIfUsed = (isAlternate, darkModeDefault) => {
+    const baseTheme = document.querySelector('#giscus-base-theme')?.value ?? 'light';
+    const alternateTheme = document.querySelector('#giscus-alt-theme')?.value ?? 'dark';
+    let newTheme = '';
+    if(darkModeDefault) {
+      newTheme = isAlternate ? baseTheme : alternateTheme;
+    } else {
+      newTheme = isAlternate ? alternateTheme : baseTheme;
+    }
+    const changeGiscusTheme = () => {
+      // From: https://github.com/giscus/giscus/issues/336
+      const sendMessage = (message) => {
+        const iframe = document.querySelector('iframe.giscus-frame');
+        if (!iframe) return;
+        iframe.contentWindow.postMessage({ giscus: message }, 'https://giscus.app');
+      }
+      sendMessage({
+        setConfig: {
+          theme: newTheme
+        }
+      });
+    }
+    const isGiscussLoaded = window.document.querySelector('iframe.giscus-frame') !== null;
+    if (isGiscussLoaded) {
+      changeGiscusTheme();
+    }
+  }
   const toggleColorMode = (alternate) => {
     // Switch the stylesheets
     const alternateStylesheets = window.document.querySelectorAll('link.quarto-color-scheme.quarto-color-alternate');
@@ -299,13 +335,15 @@ <h1 class="title">Island Biology DAISIE Practical</h1>
       return localAlternateSentinel;
     }
   }
-  let localAlternateSentinel = 'default';
+  const darkModeDefault = false;
+  let localAlternateSentinel = darkModeDefault ? 'alternate' : 'default';
   // Dark / light mode switch
   window.quartoToggleColorScheme = () => {
     // Read the current dark / light value 
     let toAlternate = !hasAlternateSentinel();
     toggleColorMode(toAlternate);
     setStyleSentinel(toAlternate);
+    toggleGiscusIfUsed(toAlternate, darkModeDefault);
   };
   // Ensure there is a toggle, if there isn't float one in the top right
   if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
@@ -384,10 +422,9 @@ <h1 class="title">Island Biology DAISIE Practical</h1>
     // clear code selection
     e.clearSelection();
   });
-  function tippyHover(el, contentFn) {
+  function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
     const config = {
       allowHTML: true,
-      content: contentFn,
       maxWidth: 500,
       delay: 100,
       arrow: false,
@@ -397,8 +434,17 @@ <h1 class="title">Island Biology DAISIE Practical</h1>
       interactive: true,
       interactiveBorder: 10,
       theme: 'quarto',
-      placement: 'bottom-start'
+      placement: 'bottom-start',
     };
+    if (contentFn) {
+      config.content = contentFn;
+    }
+    if (onTriggerFn) {
+      config.onTrigger = onTriggerFn;
+    }
+    if (onUntriggerFn) {
+      config.onUntrigger = onUntriggerFn;
+    }
     window.tippy(el, config); 
   }
   const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
@@ -412,6 +458,125 @@ <h1 class="title">Island Biology DAISIE Practical</h1>
       const note = window.document.getElementById(id);
       return note.innerHTML;
     });
+  }
+  const xrefs = window.document.querySelectorAll('a.quarto-xref');
+  const processXRef = (id, note) => {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    if (id === null || id.startsWith('sec-')) {
+      // Special case sections, only their first couple elements
+      const container = document.createElement("div");
+      if (note.children && note.children.length > 2) {
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
+        }
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(container);
+        }
+        return container.innerHTML
+      } else {
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(note);
+        }
+        return note.innerHTML;
+      }
+    } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      if (window.Quarto?.typesetMath) {
+        window.Quarto.typesetMath(note);
+      }
+      // TODO in 1.5, we should make sure this works without a callout special case
+      if (note.classList.contains("callout")) {
+        return note.outerHTML;
+      } else {
+        return note.innerHTML;
+      }
+    }
+  }
+  for (var i=0; i<xrefs.length; i++) {
+    const xref = xrefs[i];
+    tippyHover(xref, undefined, function(instance) {
+      instance.disable();
+      let url = xref.getAttribute('href');
+      let hash = undefined; 
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
+        }
+      } else {
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
+        .then(res => res.text())
+        .then(html => {
+          const parser = new DOMParser();
+          const htmlDoc = parser.parseFromString(html, "text/html");
+          const note = htmlDoc.querySelector('main.content');
+          if (note !== null) {
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
+            instance.setContent(html);
+          } 
+        }).finally(() => {
+          instance.enable();
+          instance.show();
+        });
+      }
+    }, function(instance) {
+    });
   }
       let selectedAnnoteEl;
       const selectorForAnnotation = ( cell, annotation) => {
@@ -454,6 +619,7 @@ <h1 class="title">Island Biology DAISIE Practical</h1>
             }
             div.style.top = top - 2 + "px";
             div.style.height = height + 4 + "px";
+            div.style.left = 0;
             let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
             if (gutterDiv === null) {
               gutterDiv = window.document.createElement("div");
@@ -479,6 +645,32 @@ <h1 class="title">Island Biology DAISIE Practical</h1>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -542,7 +734,7 @@ <h1 class="title">Island Biology DAISIE Practical</h1>
   <div class="nav-page nav-page-previous">
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./installation.html" class="pagination-link">
+      <a href="./installation.html" class="pagination-link" aria-label="<span class='chapter-number'>2</span>&nbsp; <span class='chapter-title'>Installation</span>">
         <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Installation</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
@@ -551,4 +743,5 @@ <h1 class="title">Island Biology DAISIE Practical</h1>
 
 
 
+
 </body></html>