Deploying to gh-pages from @ 83c54ab 🚀

docs/devel/pages/extra_material/add-comm-typing.Rmd

@@ -448,13 +448,13 @@ Samples-cluster assignment probabilities / how probable it is that a sample belo
 to each cluster
 
 ```{r}
-head(DirichletMultinomial::mixture(getBestDMNFit(tse_dmn)))
+DirichletMultinomial::mixture(getBestDMNFit(tse_dmn)) |> head()
 ```
 
 Contribution of each taxa to each component
 
 ```{r}
-head(DirichletMultinomial::fitted(getBestDMNFit(tse_dmn)))
+DirichletMultinomial::fitted(getBestDMNFit(tse_dmn)) |> head()
 ```
 Get the assignment probabilities
 
@@ -480,7 +480,7 @@ bray_pcoa_df <- calculateMDS(tse_dmn, FUN = vegan::vegdist, method = "bray",
 # Convert to data.frame
 bray_pcoa_df <- as.data.frame(bray_pcoa_df)
 colnames(bray_pcoa_df) <- c("pcoa1", "pcoa2")
-head(bray_pcoa_df)
+bray_pcoa_df |> head()
 ```
 
 ```{r}

docs/devel/pages/extra_material/dada2_workflow.Rmd

@@ -52,7 +52,7 @@ names(filtRs) <- sample.names
 out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(240,160),
               maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=TRUE,
               compress=TRUE, multithread=TRUE) # On Windows set multithread=FALSE
-head(out)
+out |> head()
 ```
 
 ```{r dada2_8}
@@ -88,7 +88,7 @@ dadaFs[[1]]
 
 mergers <- mergePairs(dadaFs, filtFs, dadaRs, filtRs, verbose=TRUE)
 # Inspect the merger data.frame from the first sample
-head(mergers[[1]])
+mergers[[1]] |> head()
 ```
 
 ```{r dada2_15}
@@ -122,7 +122,7 @@ track <- cbind(out, sapply(dadaFs, getN), sapply(dadaRs, getN), sapply(mergers,
 # If processing a single sample, remove the sapply calls: e.g. replace sapply(dadaFs, getN) with getN(dadaFs)
 colnames(track) <- c("input", "filtered", "denoisedF", "denoisedR", "merged", "nonchim")
 rownames(track) <- sample.names
-head(track)
+track |> head()
 ```
 
 ```{r dada_20}
@@ -143,7 +143,7 @@ taxa <- addSpecies(taxa, "data/silva_species_assignment_v132.fa.gz")
 ```{r dada2_22}
 taxa.print <- taxa # Removing sequence rownames for display only
 rownames(taxa.print) <- NULL
-head(taxa.print)
+taxa.print |> head()
 ```
 
 ```{r dada2_23}

docs/devel/site_libs/quarto-contrib/glightbox/lightbox.css

@@ -5,6 +5,10 @@ body:not(.glightbox-mobile) div.gslide-description .gslide-desc {
   background-color: var(--quarto-body-bg);
 }
 
+body:not(.glightbox-mobile) div.gslide-media {
+  background-color: var(--quarto-body-bg);
+}
+
 .goverlay {
   background: rgba(0, 0, 0, 0.7);
 }

docs/devel/site_libs/quarto-html/quarto.js

@@ -94,7 +94,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
       if (link.href.indexOf("#") !== -1) {
         const anchor = link.href.split("#")[1];
         const heading = window.document.querySelector(
-          `[data-anchor-id=${anchor}]`
+          `[data-anchor-id="${anchor}"]`
         );
         if (heading) {
           // Add the class
@@ -134,8 +134,10 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
       window.innerHeight + window.pageYOffset >=
       window.document.body.offsetHeight
     ) {
+      // This is the no-scroll case where last section should be the active one
       sectionIndex = 0;
     } else {
+      // This finds the last section visible on screen that should be made active
       sectionIndex = [...sections].reverse().findIndex((section) => {
         if (section) {
           return window.pageYOffset >= section.offsetTop - sectionMargin;
@@ -317,6 +319,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
           for (const child of el.children) {
             child.style.opacity = 0;
             child.style.overflow = "hidden";
+            child.style.pointerEvents = "none";
           }
 
           nexttick(() => {
@@ -358,6 +361,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
 
               const clone = child.cloneNode(true);
               clone.style.opacity = 1;
+              clone.style.pointerEvents = null;
               clone.style.display = null;
               toggleContents.append(clone);
             }
@@ -432,6 +436,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
           for (const child of el.children) {
             child.style.opacity = 1;
             child.style.overflow = null;
+            child.style.pointerEvents = null;
           }
 
           const placeholderEl = window.document.getElementById(
@@ -739,6 +744,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
     // Process the collapse state if this is an UL
     if (el.tagName === "UL") {
       if (tocOpenDepth === -1 && depth > 1) {
+        // toc-expand: false
         el.classList.add("collapse");
       } else if (
         depth <= tocOpenDepth ||
@@ -757,10 +763,9 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
   };
 
   // walk the TOC and expand / collapse any items that should be shown
-
   if (tocEl) {
-    walk(tocEl, 0);
     updateActiveLink();
+    walk(tocEl, 0);
   }
 
   // Throttle the scroll event and walk peridiocally
@@ -779,6 +784,10 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
   window.addEventListener(
     "resize",
     throttle(() => {
+      if (tocEl) {
+        updateActiveLink();
+        walk(tocEl, 0);
+      }
       if (!isReaderMode()) {
         hideOverlappedSidebars();
       }

docs/devel/site_libs/quarto-nav/quarto-nav.js

@@ -5,9 +5,45 @@ const headroomChanged = new CustomEvent("quarto-hrChanged", {
   composed: false,
 });
 
+const announceDismiss = () => {
+  const annEl = window.document.getElementById("quarto-announcement");
+  if (annEl) {
+    annEl.remove();
+
+    const annId = annEl.getAttribute("data-announcement-id");
+    window.localStorage.setItem(`quarto-announce-${annId}`, "true");
+  }
+};
+
+const announceRegister = () => {
+  const annEl = window.document.getElementById("quarto-announcement");
+  if (annEl) {
+    const annId = annEl.getAttribute("data-announcement-id");
+    const isDismissed =
+      window.localStorage.getItem(`quarto-announce-${annId}`) || false;
+    if (isDismissed) {
+      announceDismiss();
+      return;
+    } else {
+      annEl.classList.remove("hidden");
+    }
+
+    const actionEl = annEl.querySelector(".quarto-announcement-action");
+    if (actionEl) {
+      actionEl.addEventListener("click", function (e) {
+        e.preventDefault();
+        // Hide the bar immediately
+        announceDismiss();
+      });
+    }
+  }
+};
+
 window.document.addEventListener("DOMContentLoaded", function () {
   let init = false;
 
+  announceRegister();
+
   // Manage the back to top button, if one is present.
   let lastScrollTop = window.pageYOffset || document.documentElement.scrollTop;
   const scrollDownBuffer = 5;

docs/devel/site_libs/quarto-search/quarto-search.js

@@ -1275,7 +1275,11 @@ async function fuseSearch(query, fuse, fuseOptions) {
 
   // If we don't have a subfuse and the query is long enough, go ahead
   // and create a subfuse to use for subsequent queries
-  if (now - then > kFuseMaxWait && subSearchFuse === undefined) {
+  if (
+    now - then > kFuseMaxWait &&
+    subSearchFuse === undefined &&
+    resultsRaw.length < fuseOptions.limit
+  ) {
     subSearchTerm = query;
     subSearchFuse = new window.Fuse([], kFuseIndexOptions);
     resultsRaw.forEach((rr) => {