Update projects page to resize on small screens

Previously locked into a two column layout, which is too many when on mobile
arnold-c · Apr 21, 2024 · fc81c65 · fc81c65
1 parent ccfbcff
commit fc81c65
Show file tree

Hide file tree

Showing 27 changed files with 1,727 additions and 175 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/_freeze/.DS_Store b/_freeze/.DS_Store
diff --git a/_freeze/projects/execute-results/html.json b/_freeze/projects/execute-results/html.json
@@ -1,7 +1,8 @@
 {
-  "hash": "d0621187aa1c7584f983d8a1fa065317",
+  "hash": "04574a51c38aabbc6dcaa22ef2f6970c",
   "result": {
-    "markdown": "---\npage-layout: full\nformat:\n    html:\n        toc: false\n---\n\n\n## Research\n\n\n\n::: {.cell}\n\n:::\n\n\n:::: {.grid}\n\n\n::: {.g-col-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">Data4Action (COVID-19 at Penn State)</h2>\n<div class=\"container\">\n<div class=\"btn btn-paper\">\n<p class=\"bi bi-journal\" onclick=\"window.location.href='https://www.nature.com/articles/s41598-022-12499-5'\">Paper</p>\n</div>\n</div>\n\nA longitudinal cohort study, comprising of two geographically related cohorts,  that aims to examine the effect of Penn State University students on the SARS-CoV-2 incidence in the surrounding community.\nWe have recently published a the interim serological results in Nature Scientific Reports, which can be found [here](https://doi.org/10.1038/s41598-022-12499-5).\nThe second part of the project focuses on relating the differential exposures observed in the \nstudent cohort to latent risk profiles, examining the potential impact of interventions to reduce infections.\n\n</div>\n:::\n\n::: {.g-col-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">Measles in the DRC</h2>\n<div class=\"container\">\n<div class=\"btn btn-github bi bi-github\" onclick=\"window.location.href='https://www.github.com/arnold-c/drc-urgepi'\">Code</div>\n</div>\n\nAn ongoing collaboration with Médecin Sans Frontières' (MSF) Epicentre unit to analyze measles seroprevalence in the ex-Katanga region of the Democratic  Republic of Congo (DRC).\nThe intial project examined the role of new laboratory testing facilities on the speed of diagnosis and outbreak response decisions.\nThe second project examines the impact of Supplemental Immunization Activities in the ex-Katanga region; principally, characterizing the spatial and age-specific seronegativity, and examining the relationship between optical density (OD) distributions and seropositivity thresholds using finite mixture models.\n\n</div>\n:::\n\n\n::::\n\n</br>\n\n<details>\n<summary>Click to view prior projects</summary>\n\n:::: {.grid}\n\n\n::: {.g-col-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">Waning Measles Immunity Among Infants in Canada</h2>\n<div class=\"container\">\n<div class=\"btn btn-paper\">\n<p class=\"bi bi-journal\" onclick=\"window.location.href='https://doi.org/10.1542/peds.2019-0630'\">Paper</p>\n</div>\n</div>\nA prospective cross-sectional serology study of Canadian newborns and mothers\nassessing the rate of waning measles, varicella, and mumps antibodies in infants, \nincluding subgroup analysis by vaccination status. A retrospective analysis of \nwaning measles antibody titers (PRNT) in stored sera from a separate cohort of \nCanadian newborns was published as part of the study, and can be found \n[here](https://doi.org/10.1542/peds.2019-0630)\n</div>\n:::\n\n\n::::\n\n</details>\n\n\n## Teaching\n:::: {.grid}\n\n\n::: {.g-col-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">An Introduction to Git and GitHub</h2>\n<div class=\"container\">\n<div class=\"btn btn-website bi bi-browser-chrome\" onclick=\"window.location.href='https://psu-git.callumarnold.com'\">Website</div>\n<div class=\"btn btn-github bi bi-github\" onclick=\"window.location.href='https://www.github.com/arnold-c/psu-intro-to-git'\">Code</div>\n</div>\n\nDesigned and create a 2-hour workshop on the basics of Git and GitHub to graduate students, postdocs, and faculty at the Center for Infectious Disease Dynamics at Penn State University.\nFocusses on building a conceptual understanding of Git and GitHub, and how it can be used to improve research workflows by providing clear examples that are directly relevant to infectious disease researchers.\n\n</div>\n:::\n\n::: {.g-col-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">SISMID Modeling Infectious Diseases</h2>\n<div class=\"container\">\n<div class=\"btn btn-website bi bi-browser-chrome\" onclick=\"window.location.href='https://sismid2023.callumarnold.com'\">Website</div>\n<div class=\"btn btn-github bi bi-github\" onclick=\"window.location.href='https://www.github.com/arnold-c/sismid-module-02_2023'\">Code</div>\n</div>\n\nCreated the website and rewrote the teaching materials for the 2023 SISMID module 2 (Mathematical Models of Infectious Diseases), that introduced students to the basics of mathematical modeling of infectious diseases.\nAdditionally, I wrote and delivered the lecture on understanding heterogeneity in models.\n\n</div>\n:::\n\n::: {.g-col-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">Julia for Epidemiologists</h2>\n<div class=\"container\">\n<div class=\"btn btn-website bi bi-browser-chrome\" onclick=\"window.location.href='https://juliaepibook.callumarnold.com/'\">Website</div>\n<div class=\"btn btn-github bi bi-github\" onclick=\"window.location.href='https://github.com/arnold-c/JuliaEpiHandbook'\">Code</div>\n</div>\n\nI am currently in the process of (slowly) writing a book on using Julia for epidemiological research.\nThe book is aimed at epidemiologists with no prior programming experience, and will cover the basics of Julia, and how to use it for epidemiological research.\nThe [EpiRHandbook](https://epirhandbook.com/en/) is an excellent resource for new and experienced epidemiologists, but Julia has many advantages over R (and certainly some disadvantages), and I hope this book will serve a similar purpose and help epidemiologists thinking about the transition to Julia.\n\n</div>\n:::\n\n\n::::\n",
+    "engine": "knitr",
+    "markdown": "---\npage-layout: full\nformat:\n    html:\n        toc: false\n---\n\n\n## Research\n\n\n\n::: {.cell}\n\n:::\n\n\n:::: {.grid}\n\n\n::: {.g-col-12 .g-col-md-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">Data4Action (COVID-19 at Penn State)</h2>\n<div class=\"container\">\n<div class=\"btn btn-paper\">\n<p class=\"bi bi-journal\" onclick=\"window.location.href='https://www.nature.com/articles/s41598-022-12499-5'\">Paper</p>\n</div>\n</div>\n\nA longitudinal cohort study, comprising of two geographically related cohorts,  that aims to examine the effect of Penn State University students on the SARS-CoV-2 incidence in the surrounding community.\nWe have recently published a the interim serological results in Nature Scientific Reports, which can be found [here](https://doi.org/10.1038/s41598-022-12499-5).\nThe second part of the project focuses on relating the differential exposures observed in the \nstudent cohort to latent risk profiles, examining the potential impact of interventions to reduce infections.\n\n</div>\n:::\n\n::: {.g-col-12 .g-col-md-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">Measles in the DRC</h2>\n<div class=\"container\">\n<div class=\"btn btn-github bi bi-github\" onclick=\"window.location.href='https://www.github.com/arnold-c/drc-urgepi'\">Code</div>\n</div>\n\nAn ongoing collaboration with Médecin Sans Frontières' (MSF) Epicentre unit to analyze measles seroprevalence in the ex-Katanga region of the Democratic  Republic of Congo (DRC).\nThe intial project examined the role of new laboratory testing facilities on the speed of diagnosis and outbreak response decisions.\nThe second project examines the impact of Supplemental Immunization Activities in the ex-Katanga region; principally, characterizing the spatial and age-specific seronegativity, and examining the relationship between optical density (OD) distributions and seropositivity thresholds using finite mixture models.\n\n</div>\n:::\n\n\n::::\n\n</br>\n\n<details>\n<summary>Click to view prior projects</summary>\n\n:::: {.grid}\n\n\n::: {.g-col-12 .g-col-md-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">Waning Measles Immunity Among Infants in Canada</h2>\n<div class=\"container\">\n<div class=\"btn btn-paper\">\n<p class=\"bi bi-journal\" onclick=\"window.location.href='https://doi.org/10.1542/peds.2019-0630'\">Paper</p>\n</div>\n</div>\nA prospective cross-sectional serology study of Canadian newborns and mothers\nassessing the rate of waning measles, varicella, and mumps antibodies in infants, \nincluding subgroup analysis by vaccination status. A retrospective analysis of \nwaning measles antibody titers (PRNT) in stored sera from a separate cohort of \nCanadian newborns was published as part of the study, and can be found \n[here](https://doi.org/10.1542/peds.2019-0630)\n</div>\n:::\n\n\n::::\n\n</details>\n\n\n## Teaching\n:::: {.grid}\n\n\n::: {.g-col-12 .g-col-md-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">An Introduction to Git and GitHub</h2>\n<div class=\"container\">\n<div class=\"btn btn-website bi bi-browser-chrome\" onclick=\"window.location.href='https://psu-git.callumarnold.com'\">Website</div>\n<div class=\"btn btn-github bi bi-github\" onclick=\"window.location.href='https://www.github.com/arnold-c/psu-intro-to-git'\">Code</div>\n</div>\n\nDesigned and create a 2-hour workshop on the basics of Git and GitHub to graduate students, postdocs, and faculty at the Center for Infectious Disease Dynamics at Penn State University.\nFocusses on building a conceptual understanding of Git and GitHub, and how it can be used to improve research workflows by providing clear examples that are directly relevant to infectious disease researchers.\n\n</div>\n:::\n\n::: {.g-col-12 .g-col-md-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">SISMID Modeling Infectious Diseases</h2>\n<div class=\"container\">\n<div class=\"btn btn-website bi bi-browser-chrome\" onclick=\"window.location.href='https://sismid2023.callumarnold.com'\">Website</div>\n<div class=\"btn btn-github bi bi-github\" onclick=\"window.location.href='https://www.github.com/arnold-c/sismid-module-02_2023'\">Code</div>\n</div>\n\nCreated the website and rewrote the teaching materials for the 2023 SISMID module 2 (Mathematical Models of Infectious Diseases), that introduced students to the basics of mathematical modeling of infectious diseases.\nAdditionally, I wrote and delivered the lecture on understanding heterogeneity in models.\n\n</div>\n:::\n\n::: {.g-col-12 .g-col-md-6}\n<div class=\"card card-project h-100\">\n<h2 style=\"font-size: 1.45rem\">Julia for Epidemiologists</h2>\n<div class=\"container\">\n<div class=\"btn btn-website bi bi-browser-chrome\" onclick=\"window.location.href='https://juliaepibook.callumarnold.com/'\">Website</div>\n<div class=\"btn btn-github bi bi-github\" onclick=\"window.location.href='https://github.com/arnold-c/JuliaEpiHandbook'\">Code</div>\n</div>\n\nI am currently in the process of (slowly) writing a book on using Julia for epidemiological research.\nThe book is aimed at epidemiologists with no prior programming experience, and will cover the basics of Julia, and how to use it for epidemiological research.\nThe [EpiRHandbook](https://epirhandbook.com/en/) is an excellent resource for new and experienced epidemiologists, but Julia has many advantages over R (and certainly some disadvantages), and I hope this book will serve a similar purpose and help epidemiologists thinking about the transition to Julia.\n\n</div>\n:::\n\n\n::::\n",
     "supporting": [],
     "filters": [
       "rmarkdown/pagebreak.lua"

diff --git a/_site/index.html b/_site/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-1.4.315">
+<meta name="generator" content="quarto-1.4.551">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -48,12 +48,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "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",
@@ -62,6 +63,7 @@
     "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"
@@ -84,7 +86,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="./index.html">
@@ -161,8 +163,9 @@ <h2 id="toc-title">On this page</h2>
 
 
 
+
 <p><link rel="stylesheet" href="academicons/css/academicons.min.css"></p>
-<div class="quarto-about-jolla">
+<div class="quarto-about-jolla content">
   <img src="img/CA_Headshot-Web.jpg" class="about-image
   round " style="height: 15em; width: 15em;">
  <header id="title-block-header" class="quarto-title-block default">
@@ -467,6 +470,24 @@ <h2 data-anchor-id="research-experience">Research Experience</h2>
     // clear code selection
     e.clearSelection();
   });
+    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+    var mailtoRegex = new RegExp(/^mailto:/);
+      var filterRegex = new RegExp('/' + window.location.host + '/');
+    var isInternal = (href) => {
+        return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
+    }
+    // Inspect non-navigation links and adorn them if external
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+    for (var i=0; i<links.length; i++) {
+      const link = links[i];
+      if (!isInternal(link.href)) {
+        // undo the damage that might have been done by quarto-nav.js in the case of
+        // links that we want to consider external
+        if (link.dataset.originalHref !== undefined) {
+          link.href = link.dataset.originalHref;
+        }
+      }
+    }
   function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
     const config = {
       allowHTML: true,
@@ -501,7 +522,11 @@ <h2 data-anchor-id="research-experience">Research Experience</h2>
       try { href = new URL(href).hash; } catch {}
       const id = href.replace(/^#\/?/, "");
       const note = window.document.getElementById(id);
-      return note.innerHTML;
+      if (note) {
+        return note.innerHTML;
+      } else {
+        return "";
+      }
     });
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
@@ -516,15 +541,28 @@ <h2 data-anchor-id="research-experience">Research Experience</h2>
       }
     }
     stripColumnClz(note)
-    if (id.startsWith('sec-')) {
+    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) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        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 {
@@ -533,7 +571,15 @@ <h2 data-anchor-id="research-experience">Research Experience</h2>
       if (anchorLink) {
         anchorLink.remove();
       }
-      return note.innerHTML;
+      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++) {
@@ -575,6 +621,29 @@ <h2 data-anchor-id="research-experience">Research Experience</h2>
             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) {
     });
@@ -650,7 +719,6 @@ <h2 data-anchor-id="research-experience">Research Experience</h2>
     window.addEventListener(
       "resize",
       throttle(() => {
-        console.log("RESIZE");
         elRect = undefined;
         if (selectedAnnoteEl) {
           selectCodeLines(selectedAnnoteEl);

diff --git a/_site/listings.json b/_site/listings.json
@@ -2,6 +2,7 @@
   {
     "listing": "/posts.html",
     "items": [
+      "/posts/2023-08-13_neovim01/neovim-series_01.html",
       "/posts/2023-05-20_Running-a-workshop/running-a-workshop.html",
       "/posts/2019-08-15-an-introduction-to-reproducible-research/repro-research.html"
     ]