From 366225092a124e69135f80bfcde1301f80f82972 Mon Sep 17 00:00:00 2001
From: matthewferrari <matthewjferrari@gmail.com>
Date: Tue, 8 Jul 2025 13:58:10 -0400
Subject: [PATCH 1/3] module number

changed module number to 1 on welcome page
---
 index.qmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/index.qmd b/index.qmd
index 70106f0..95950b1 100644
--- a/index.qmd
+++ b/index.qmd
@@ -2,7 +2,7 @@
 
 Hello! 
 
-Welcome to this website that accompanies the [2025 Summer Institute in Modeling for Infectious Diseases (SISMID) Module 2: Mathematical Models of Infectious Diseases](https://sph.emory.edu/SISMID/modules/math-models/index.html).
+Welcome to this website that accompanies the [2025 Summer Institute in Modeling for Infectious Diseases (SISMID) Module 1: Mathematical Models of Infectious Diseases](https://sph.emory.edu/SISMID/modules/math-models/index.html).
 This website contains both the lecture notes, so you can refer back to them at a later date, and the exercises that we will be completing throughout the module.
 
 ## Workshop Pre-Requisites

From 92875add40e14a5d11ca37fef8784f3aa3ef95af Mon Sep 17 00:00:00 2001
From: matthewferrari <matthewjferrari@gmail.com>
Date: Tue, 8 Jul 2025 13:59:05 -0400
Subject: [PATCH 2/3] Module number quarto.yml

changed the module nubmer in quarto.yml
---
 _quarto.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_quarto.yml b/_quarto.yml
index 4a8af1c..c9380fd 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -2,7 +2,7 @@ project:
   type: book
 
 book:
-  title: "SISMID Module 2 Materials (2025)"
+  title: "SISMID Module 1 Materials (2025)"
   subtitle: "Mathematical Models of Infectious Diseases"
   author:
     - name: "Callum Arnold"

From fa439428c368e758ac4b04e2c0660a38107421ee Mon Sep 17 00:00:00 2001
From: matthewferrari <matthewjferrari@gmail.com>
Date: Tue, 8 Jul 2025 14:58:08 -0400
Subject: [PATCH 3/3] Rendered module 1

updated render with module 1
---
 _book/index.html  | 14 +++++++-------
 _book/search.json | 12 ++++++------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/_book/index.html b/_book/index.html
index 7f6782e..2760475 100644
--- a/_book/index.html
+++ b/_book/index.html
@@ -7,9 +7,9 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Callum Arnold">
-<meta name="dcterms.date" content="2025-07-07">
+<meta name="dcterms.date" content="2025-07-08">
 
-<title>SISMID Module 2 Materials (2025)</title>
+<title>SISMID Module 1 Materials (2025)</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -310,7 +310,7 @@
       <img src="././images/sismid2025-logo-blue.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
       </a>
     <div class="sidebar-title mb-0 py-0">
-      <a href="./">SISMID Module 2 Materials (2025)</a> 
+      <a href="./">SISMID Module 1 Materials (2025)</a> 
         <div class="sidebar-tools-main tools-wide">
     <a href="https://github.com/arnold-c/SISMID-Module-02_2025" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
   <a href="" class="quarto-color-scheme-toggle quarto-navigation-tool  px-1" onclick="window.quartoToggleColorScheme(); return false;" title="Toggle dark mode"><i class="bi"></i></a>
@@ -513,7 +513,7 @@ <h2 id="toc-title">Page Items</h2>
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<div class="quarto-title-block"><div><h1 class="title">SISMID Module 2 Materials (2025)</h1><button type="button" class="btn code-tools-button" id="quarto-code-tools-source"><i class="bi"></i> Code</button></div></div>
+<div class="quarto-title-block"><div><h1 class="title">SISMID Module 1 Materials (2025)</h1><button type="button" class="btn code-tools-button" id="quarto-code-tools-source"><i class="bi"></i> Code</button></div></div>
 <p class="subtitle lead">Mathematical Models of Infectious Diseases</p>
 </div>
 
@@ -538,7 +538,7 @@ <h2 id="toc-title">Page Items</h2>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">July 7, 2025</p>
+      <p class="date">July 8, 2025</p>
     </div>
   </div>
   
@@ -553,7 +553,7 @@ <h2 id="toc-title">Page Items</h2>
 <section id="welcome" class="level1 unnumbered">
 <h1 class="unnumbered"><strong>Welcome</strong></h1>
 <p>Hello!</p>
-<p>Welcome to this website that accompanies the <a href="https://sph.emory.edu/SISMID/modules/math-models/index.html">2025 Summer Institute in Modeling for Infectious Diseases (SISMID) Module 2: Mathematical Models of Infectious Diseases</a>. This website contains both the lecture notes, so you can refer back to them at a later date, and the exercises that we will be completing throughout the module.</p>
+<p>Welcome to this website that accompanies the <a href="https://sph.emory.edu/SISMID/modules/math-models/index.html">2025 Summer Institute in Modeling for Infectious Diseases (SISMID) Module 1: Mathematical Models of Infectious Diseases</a>. This website contains both the lecture notes, so you can refer back to them at a later date, and the exercises that we will be completing throughout the module.</p>
 <section id="workshop-pre-requisites" class="level2">
 <h2 class="anchored" data-anchor-id="workshop-pre-requisites">Workshop Pre-Requisites</h2>
 <p>As there is a reasonable amount of material to cover, and a relatively short amount of time to cover it in, there are some pre-requisite tasks to get set up ahead of the workshop.</p>
@@ -1204,7 +1204,7 @@ <h3 style="margin-top:0px; text-align: center" class="anchored">
 <span id="cb1-2"><a href="#cb1-2"></a></span>
 <span id="cb1-3"><a href="#cb1-3"></a>Hello! </span>
 <span id="cb1-4"><a href="#cb1-4"></a></span>
-<span id="cb1-5"><a href="#cb1-5"></a>Welcome to this website that accompanies the <span class="co">[</span><span class="ot">2025 Summer Institute in Modeling for Infectious Diseases (SISMID) Module 2: Mathematical Models of Infectious Diseases</span><span class="co">](https://sph.emory.edu/SISMID/modules/math-models/index.html)</span>.</span>
+<span id="cb1-5"><a href="#cb1-5"></a>Welcome to this website that accompanies the <span class="co">[</span><span class="ot">2025 Summer Institute in Modeling for Infectious Diseases (SISMID) Module 1: Mathematical Models of Infectious Diseases</span><span class="co">](https://sph.emory.edu/SISMID/modules/math-models/index.html)</span>.</span>
 <span id="cb1-6"><a href="#cb1-6"></a>This website contains both the lecture notes, so you can refer back to them at a later date, and the exercises that we will be completing throughout the module.</span>
 <span id="cb1-7"><a href="#cb1-7"></a></span>
 <span id="cb1-8"><a href="#cb1-8"></a><span class="fu">## Workshop Pre-Requisites</span></span>
diff --git a/_book/search.json b/_book/search.json
index d21c7f1..b466fec 100644
--- a/_book/search.json
+++ b/_book/search.json
@@ -2,9 +2,9 @@
   {
     "objectID": "index.html",
     "href": "index.html",
-    "title": "SISMID Module 2 Materials (2025)",
+    "title": "SISMID Module 1 Materials (2025)",
     "section": "",
-    "text": "Welcome\nHello!\nWelcome to this website that accompanies the 2025 Summer Institute in Modeling for Infectious Diseases (SISMID) Module 2: Mathematical Models of Infectious Diseases. This website contains both the lecture notes, so you can refer back to them at a later date, and the exercises that we will be completing throughout the module.",
+    "text": "Welcome\nHello!\nWelcome to this website that accompanies the 2025 Summer Institute in Modeling for Infectious Diseases (SISMID) Module 1: Mathematical Models of Infectious Diseases. This website contains both the lecture notes, so you can refer back to them at a later date, and the exercises that we will be completing throughout the module.",
     "crumbs": [
       "**Welcome**"
     ]
@@ -12,7 +12,7 @@
   {
     "objectID": "index.html#workshop-pre-requisites",
     "href": "index.html#workshop-pre-requisites",
-    "title": "SISMID Module 2 Materials (2025)",
+    "title": "SISMID Module 1 Materials (2025)",
     "section": "Workshop Pre-Requisites",
     "text": "Workshop Pre-Requisites\nAs there is a reasonable amount of material to cover, and a relatively short amount of time to cover it in, there are some pre-requisite tasks to get set up ahead of the workshop.\n\n\n\n\n\n\nImportant\n\n\n\nEveryone should refer to the Exercise Requirements page, particularly the R Packages and Data Files sections to ensure you have the neccessary packages and data files installed for the exercises.\n\n\nFirstly, this workshop requires some prior understanding of the R programming languages, as well as a working installation of R. If you do not have any experience, please refer to the Installing R and Just Enough RStudio & Just Enought R pages of the Pre-Requisites section.\nIt is also highly recommended that you read the Organizing A Project page for how to structure your code as you go through the exercises: we provide some guidelines to make your code easier to understand and navigate, both for yourself, and for others.\nPlease set aside about an hour to go through these materials and get set up. You should be able to do this in about 15 minutes if you are already experienced with R, but as with all things computational, it’s worth including some buffer time in case you run into issues. If you are completely new to R, this could take an hour or so, but is certainly worth the time investment: it will be hard to follow some of the exercises if you do not understand what the code is doing.",
     "crumbs": [
@@ -22,7 +22,7 @@
   {
     "objectID": "index.html#tips-about-the-website",
     "href": "index.html#tips-about-the-website",
-    "title": "SISMID Module 2 Materials (2025)",
+    "title": "SISMID Module 1 Materials (2025)",
     "section": "Tips About the Website",
     "text": "Tips About the Website\nThere are a number of useful features throughout this website to help you.\nFirstly, in sections where there is R code showing, clicking on the text ▶ Code above the code block will hide the code if open (the default), or show the code if hidden.\nSecondly, in the top right corner of each code block, there is a button that looks like a clipboard. Clicking this button will copy the code to your clipboard, so you can paste it into your own R session.\nFinally, within the code blocks (and, in fact, in the regular text like this section), functions (e.g. list(), pivot_longer()) that come from a package (i.e., ones we didn’t write) show up in a different color. In most cases, you can hover your cursor over them (on the part next the the parentheses e.g., ode() from the line deSolve::ode()), and if they become underlined, you can click on them to go to the documentation for that function. This is like searching for the documentation from your R console using ?ode.",
     "crumbs": [
@@ -32,7 +32,7 @@
   {
     "objectID": "index.html#keywords-code-and-other-formatting",
     "href": "index.html#keywords-code-and-other-formatting",
-    "title": "SISMID Module 2 Materials (2025)",
+    "title": "SISMID Module 1 Materials (2025)",
     "section": "Keywords, Code, and Other Formatting",
     "text": "Keywords, Code, and Other Formatting\nThroughout the book, you’ll see some keywords, code, and other points that I’ll try to delineate with the following formatting:\n\n\n\n\n\n\nNote\n\n\n\nThis will be a note, and will be used to highlight important points, or to provide additional information.\n\n\n\n\n\n\n\n\nSET\n\n\n\nThis will be an instruction to set certain parameters or values in the R code, or for the interactive plots.\n\n\n\n\n\n\n\n\nInstruction\n\n\n\nThis will be a general instruction.\n\n\n\n\n\n\n\n\nTip\n\n\n\nThis will be used to highlight a useful tip.\n\n\n\n\n\n\n\n\nWarning\n\n\n\nThis will provide a warning that you may get an unexpected result if you’re not careful.\n\n\nIt is worth noting that some of these callouts may be collapsible. You can tell a callout is collapsible if there is a little &gt; or ⋁ in the top right corner of the callout i.e.,\n\n\n\n\n\n\nNote\n\n\n\n\n\nThis is an example of a collapsible callout that defaults to being collapsed.\n\n\n\n\n\nExercise:\n\nExercises that require you to complete missing sections of code, or answer a question, will be highlighted like this in R Session 2 and R Session 3\n\n\ncode will be used to highlight code.\n{package::function()} will be used to denote a specific package and function, e.g., {dplyr::mutate()} denotes the mutate() function from the {dplyr} package.\n\nOften the function() will be listed without the package, as there are library() calls at the top of each page indicating the packages used in that page, and the majority of functions will not cause conflicts, i.e., there are not packages with functions of the same name.\n\nBold will be used to highlight keywords and phrases, e.g., Git or GitHub.\n\nBold will also be highlighted in this way, e.g., commits or pushed being the result of the code git commit or git push\n\nBold-italics will be used to highlight file names, e.g., README.md or LICENSE.\nItalics will be used for emphasis in certain circumstances, e.g., signifying a question from an interactive terminal command.",
     "crumbs": [
@@ -42,7 +42,7 @@
   {
     "objectID": "index.html#about-the-instructors",
     "href": "index.html#about-the-instructors",
-    "title": "SISMID Module 2 Materials (2025)",
+    "title": "SISMID Module 1 Materials (2025)",
     "section": "About the Instructors",
     "text": "About the Instructors\n\n\n\nDr. Amy Winter\n\n\nDr. Winter is an Assistant Professor of Epidemiology & Biostatistics at the University of Georgia College of Public Health.\nDr. Winter’s research group adopts an interdisciplinary approach to tackle policy-relevant challenges in the transmission and control of infectious diseases within human populations. Her work focuses on understanding the spatiotemporal spread of infectious diseases, particularly through the analysis of serological data, developing predictive models to assess outbreak risks, and using scenario modeling to design effective strategies for disease control.\n\n\n\nDr. Matt Ferrari\n\n\nDr. Ferrari is the Director of the Center for Infectious Disease Dynamics at The Pennsylvania State University.\nDr Ferrari’s lab does research on both the application of quantitative modeling and analysis to inform public health policy and the basic ecology of parasites and infectious diseases at the Center for Infectious Disease Dynamics at The Pennsylvania State University.\n\n\n\nDr. Alpha Forna\n\n\nDr. Forna is a Post-doctoral Researcher Associate in the Drake and Rohani Labs at the University of Georgia.\nDr Forna’s research focuses on the adaptation and application of machine learning methods to biological and epidemiological data, with an aim to positively inform efficient and cost-effective infectious disease prevention and intervention efforts (vaccines and antimicrobials, especially).",
     "crumbs": [