From e50dc63fa702bcc63c52fbb93db38408914e0b96 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Fri, 5 Jul 2024 12:33:52 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 389c044437119b338f3544b966229d3f3d2acc7c
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-07-05 12:33:31 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 6721f7b49af4753df0d50119deac911029c4a4f6
Branch  : main
Author  : Andree Valle Campos <avallecam@gmail.com>
Time    : 2024-07-05 12:29:10 +0000
Message : fix lintr checks
---
 404.html                                  |  6 +-
 CODE_OF_CONDUCT.html                      |  4 +-
 LICENSE.html                              |  4 +-
 aio.html                                  | 70 ++++++++++-----------
 create-forecast.html                      |  4 +-
 delays-access.html                        |  4 +-
 delays-functions.html                     |  4 +-
 images.html                               |  6 +-
 index.html                                |  6 +-
 instructor-notes.html                     |  6 +-
 instructor/404.html                       |  6 +-
 instructor/CODE_OF_CONDUCT.html           |  4 +-
 instructor/LICENSE.html                   |  4 +-
 instructor/aio.html                       | 74 +++++++++++------------
 instructor/create-forecast.html           |  4 +-
 instructor/delays-access.html             |  4 +-
 instructor/delays-functions.html          |  4 +-
 instructor/images.html                    |  6 +-
 instructor/index.html                     |  6 +-
 instructor/instructor-notes.html          |  6 +-
 instructor/key-points.html                |  6 +-
 instructor/profiles.html                  |  6 +-
 instructor/quantify-transmissibility.html |  4 +-
 instructor/reference.html                 |  4 +-
 instructor/severity-static.html           | 50 +++++++--------
 instructor/superspreading-estimate.html   |  4 +-
 instructor/superspreading-simulate.html   | 26 ++++----
 key-points.html                           |  6 +-
 pkgdown.yml                               |  2 +-
 profiles.html                             |  6 +-
 quantify-transmissibility.html            |  4 +-
 reference.html                            |  4 +-
 renv.lock                                 |  2 +-
 severity-static.html                      | 46 +++++++-------
 superspreading-estimate.html              |  4 +-
 superspreading-simulate.html              | 26 ++++----
 36 files changed, 216 insertions(+), 216 deletions(-)

diff --git a/404.html b/404.html
index d97b9b0a..cc8c9863 100644
--- a/404.html
+++ b/404.html
@@ -340,9 +340,9 @@ <h1>Page not found</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/404.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/404.html",
-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 6534406c..35383308 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -360,9 +360,9 @@ <h1>Contributor Code of Conduct</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/CODE_OF_CONDUCT.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/CODE_OF_CONDUCT.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 154e2aac..744a0e56 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -408,9 +408,9 @@ <h1>Licenses</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/LICENSE.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/LICENSE.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index e9bad5dc..14fabb09 100644
--- a/aio.html
+++ b/aio.html
@@ -5066,7 +5066,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>Inspect the format of the data input.</p>
 <ul>
@@ -5084,7 +5084,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>We read the data input using <code>readr::read_csv()</code>. This
 function recognize that the column <code>date</code> is a
@@ -5169,7 +5169,7 @@ <h3 class="callout-title">Two biases that affect CFR estimation<a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> 1. Preferential ascertainment of severe cases </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>For diseases with a <em>spectrum</em> of clinical presentations,
 those cases that come to the attention of public health authorities and
@@ -5189,7 +5189,7 @@ <h4 class="accordion-header" id="headingSolution2"> 1. Preferential ascertainmen
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> 2. Bias due to delayed reporting of death </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>During an <em>ongoing</em> epidemic, there is a delay between the
 time someone dies and the time their death is reported. Therefore, at
@@ -5213,7 +5213,7 @@ <h4 class="accordion-header" id="headingSolution3"> 2. Bias due to delayed repor
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Case study: Influenza A (H1N1), Mexico, 2009 </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Improving an <em>early</em> epidemiological assessment of a
 delay-adjusted CFR is crucial for determining virulence, shaping the
@@ -5348,7 +5348,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <ul>
 <li>Find the appropriate <code>&lt;epidist&gt;</code> object!</li>
@@ -5362,7 +5362,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <p>We use <code>{epiparameter}</code> to access a delay distribution for
 the SARS-CoV-2 aggregated incidence data:</p>
@@ -5452,7 +5452,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> When to use discrete distributions? </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>For <code>cfr_static()</code> and all the <code>cfr_*()</code> family
 of functions, the most appropriate choice to pass are
@@ -5479,7 +5479,7 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> How does {cfr} works? </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <p>To adjust the CFR, <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006852" class="external-link">Nishiura
 et al., 2009</a> use the case and death incidence data to estimate the
@@ -5687,7 +5687,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Case study: SARS outbreak, Hong Kong, 2003 </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <p>Figures A and B show the cumulative numbers of cases and deaths of
 SARS, and Figure C shows the observed (biased) CFR estimates as a
@@ -5740,7 +5740,7 @@ <h3 class="callout-title">Interpret the early-stage CFR estimate<a class="anchor
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
 <div class="accordion-body">
 <p>We can use either visual inspection or analysis of the output data
 frames.</p>
@@ -5753,7 +5753,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <p>There is almost one month of difference.</p>
 <p>Note that the estimate has considerable uncertainty at the beginning
@@ -5787,7 +5787,7 @@ <h3 class="callout-title">Checklist<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Why the naive and delay-adjusted differ? </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p><a href="https://github.com/epiverse-trace/cfr" class="external-link">cfr</a> method aims to obtain an unbiased estimator “well
 before” observing the entire course of the outbreak. For this,
@@ -5803,7 +5803,7 @@ <h4 class="accordion-header" id="headingSolution7"> Why the naive and delay-adju
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> What is the sampling process? </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <figure><img src="fig/cfr-pone.0006852.g001.png" alt="The population of confirmed cases and sampling process for estimating the unbiased CFR during the course of an outbreak. (Nishiura et al., 2009)" class="figure mx-auto d-block"><div class="figcaption">The population of confirmed cases and sampling
 process for estimating the unbiased CFR during the course of an
@@ -5843,7 +5843,7 @@ <h4 class="accordion-header" id="headingSolution8"> What is the sampling process
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Limitations </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <ul>
 <li>The delay-adjusted CFR does not address all sources of error in data
@@ -5916,7 +5916,7 @@ <h3 class="callout-title">Use incidence2 to rearrange your data<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint4" aria-expanded="false" aria-controls="collapseHint4">
   <h4 class="accordion-header" id="headingHint4"> Give me a hint </h4>
 </button>
-<div id="collapseHint4" class="accordion-collapse collapse" data-bs-parent="#accordionHint4" aria-labelledby="headingHint4">
+<div id="collapseHint4" class="accordion-collapse collapse" aria-labelledby="headingHint4" data-bs-parent="#accordionHint4">
 <div class="accordion-body">
 <p><strong>How to rearrange my input data?</strong></p>
 <p>Rearranging the input data for data analysis can take most of the
@@ -5939,7 +5939,7 @@ <h4 class="accordion-header" id="headingHint4"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution10" aria-expanded="false" aria-controls="collapseSolution10">
   <h4 class="accordion-header" id="headingSolution10"> Show me the solution </h4>
 </button>
-<div id="collapseSolution10" class="accordion-collapse collapse" data-bs-parent="#accordionSolution10" aria-labelledby="headingSolution10">
+<div id="collapseSolution10" class="accordion-collapse collapse" aria-labelledby="headingSolution10" data-bs-parent="#accordionSolution10">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb35">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6112,7 +6112,7 @@ <h3 class="callout-title">Severity heterogeneity<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint5" aria-expanded="false" aria-controls="collapseHint5">
   <h4 class="accordion-header" id="headingHint5"> Give me a hint </h4>
 </button>
-<div id="collapseHint5" class="accordion-collapse collapse" data-bs-parent="#accordionHint5" aria-labelledby="headingHint5">
+<div id="collapseHint5" class="accordion-collapse collapse" aria-labelledby="headingHint5" data-bs-parent="#accordionHint5">
 <div class="accordion-body">
 <p>One way to do a <em>stratified analysis</em> is to apply a model to
 nested data. This <a href="https://tidyr.tidyverse.org/articles/nest.html#nested-data-and-models" class="external-link"><code>{tidyr}</code>
@@ -6128,7 +6128,7 @@ <h4 class="accordion-header" id="headingHint5"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution11" aria-expanded="false" aria-controls="collapseSolution11">
   <h4 class="accordion-header" id="headingSolution11"> Show me the solution </h4>
 </button>
-<div id="collapseSolution11" class="accordion-collapse collapse" data-bs-parent="#accordionSolution11" aria-labelledby="headingSolution11">
+<div id="collapseSolution11" class="accordion-collapse collapse" aria-labelledby="headingSolution11" data-bs-parent="#accordionSolution11">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6291,7 +6291,7 @@ <h3 class="callout-title">More severity measures<a class="anchor" aria-label="an
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution12" aria-expanded="false" aria-controls="collapseSolution12">
   <h4 class="accordion-header" id="headingSolution12"> Infection and Hospitalization fatality risk </h4>
 </button>
-<div id="collapseSolution12" class="accordion-collapse collapse" data-bs-parent="#accordionSolution12" aria-labelledby="headingSolution12">
+<div id="collapseSolution12" class="accordion-collapse collapse" aria-labelledby="headingSolution12" data-bs-parent="#accordionSolution12">
 <div class="accordion-body">
 <p>If for a <em>Case</em> fatality risk (CFR), we require:</p>
 <ul>
@@ -6322,7 +6322,7 @@ <h4 class="accordion-header" id="headingSolution12"> Infection and Hospitalizati
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution13" aria-expanded="false" aria-controls="collapseSolution13">
   <h4 class="accordion-header" id="headingSolution13"> Data sources for more severity measures </h4>
 </button>
-<div id="collapseSolution13" class="accordion-collapse collapse" data-bs-parent="#accordionSolution13" aria-labelledby="headingSolution13">
+<div id="collapseSolution13" class="accordion-collapse collapse" aria-labelledby="headingSolution13" data-bs-parent="#accordionSolution13">
 <div class="accordion-body">
 <p><a href="https://www.nature.com/articles/s41467-020-19238-2/figures/1" class="external-link">Yang
 et al., 2020</a> summarises different definitions and data sources:</p>
@@ -7772,7 +7772,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Poisson and other distributions </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p><code>{epichains}</code> can accept any R function that generates
 random numbers, so the specified arguments will change depending on the
@@ -7818,7 +7818,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> generation time vs serial interval </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <figure><img src="fig/serial-interval-observed.jpeg" alt="A schematic of the relationship of different time periods of transmission between an infector and an infectee in a transmission pair. Exposure window is defined as the time interval having viral exposure, and transmission window is defined as the time interval for onward transmission with respect to the infection time (Chung Lau et al., 2021)." class="figure mx-auto d-block"><div class="figcaption">A schematic of the relationship of different
 time periods of transmission between an infector and an infectee in a
@@ -8092,7 +8092,7 @@ <h3 class="callout-title">Read the epichains output<a class="anchor" aria-label=
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> The epichains object </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Let’s use <code>dplyr::filter()</code> for this:</p>
 <div class="codewrapper sourceCode" id="cb11">
@@ -8150,7 +8150,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> The epichains data frame </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8194,7 +8194,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> An infectee data frame </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>The output data frame collects <strong>infectees</strong> as the
 observation unit:</p>
@@ -8360,7 +8360,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Observed cases vs simulated chains </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <p>Let’s overlap the cumulative number of observed cases using the
 linelist object from the <code>mers_korea_2015</code> dataset of the
@@ -8473,7 +8473,7 @@ <h3 class="callout-title">Monkeypox large outbreak potential<a class="anchor" ar
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>With <code>{epiparameter}</code>, you can access and use offspring
 and delay distributions from previous Ebola outbreaks.</p>
@@ -8533,7 +8533,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8644,7 +8644,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Epidemic Risk assessment accounting for superspreading </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>With <code>{superspreading}</code>, you can get numerical solutions
 to processes that <code>{epichains}</code> solve using branching
@@ -8703,7 +8703,7 @@ <h3 class="callout-title">From a distribution of secondary cases<a class="anchor
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
 <div class="accordion-body">
 <p>Code with the transmission tree data written by <a href="https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(15)70135-0/fulltext" class="external-link">Christian
 Althaus, 2015</a>:</p>
@@ -8734,7 +8734,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb33">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8907,9 +8907,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/aio.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/aio.html",
-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/create-forecast.html b/create-forecast.html
index 77d19be1..1971663a 100644
--- a/create-forecast.html
+++ b/create-forecast.html
@@ -1153,9 +1153,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/create-forecast.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/create-forecast.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/delays-access.html b/delays-access.html
index a07c9811..199c2eeb 100644
--- a/delays-access.html
+++ b/delays-access.html
@@ -1599,9 +1599,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/delays-access.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/delays-access.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/delays-functions.html b/delays-functions.html
index 23369cb0..a3e30192 100644
--- a/delays-functions.html
+++ b/delays-functions.html
@@ -1613,9 +1613,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/delays-functions.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/delays-functions.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 9722abd3..43bd7b07 100644
--- a/images.html
+++ b/images.html
@@ -685,9 +685,9 @@ <h3 id="superspreading-simulate-figure-11">Figure 11</h3>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/images.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/images.html",
-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 7a6ef1ca..b5655a28 100644
--- a/index.html
+++ b/index.html
@@ -746,9 +746,9 @@ <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/index.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/index.html",
-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 95d1e0bf..213d09b7 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -381,9 +381,9 @@ <h1>Instructor Notes</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor-notes.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor-notes.html",
-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 91cac431..cf5a6d99 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -340,9 +340,9 @@ <h1>Page not found</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor/404.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/404.html",
-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 649ccd5f..e5f66e08 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -362,9 +362,9 @@ <h1>Contributor Code of Conduct</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor/CODE_OF_CONDUCT.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/CODE_OF_CONDUCT.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 19150616..6b867242 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -410,9 +410,9 @@ <h1>Licenses</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor/LICENSE.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/LICENSE.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 026db969..e533ddb9 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -5004,7 +5004,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Instructor Note </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
 <div class="accordion-body">
 <p>The periods are relevant: Period 1 – 15 days where CFR is zero to
 indicate this is due to no reported deaths; Period from Mar 15 – Apr 26
@@ -5198,7 +5198,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>Inspect the format of the data input.</p>
 <ul>
@@ -5216,7 +5216,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>We read the data input using <code>readr::read_csv()</code>. This
 function recognize that the column <code>date</code> is a
@@ -5301,7 +5301,7 @@ <h3 class="callout-title">Two biases that affect CFR estimation<a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> 1. Preferential ascertainment of severe cases </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>For diseases with a <em>spectrum</em> of clinical presentations,
 those cases that come to the attention of public health authorities and
@@ -5321,7 +5321,7 @@ <h4 class="accordion-header" id="headingSolution2"> 1. Preferential ascertainmen
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> 2. Bias due to delayed reporting of death </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>During an <em>ongoing</em> epidemic, there is a delay between the
 time someone dies and the time their death is reported. Therefore, at
@@ -5345,7 +5345,7 @@ <h4 class="accordion-header" id="headingSolution3"> 2. Bias due to delayed repor
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Case study: Influenza A (H1N1), Mexico, 2009 </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Improving an <em>early</em> epidemiological assessment of a
 delay-adjusted CFR is crucial for determining virulence, shaping the
@@ -5375,7 +5375,7 @@ <h4 class="accordion-header" id="headingSolution4"> Case study: Influenza A (H1N
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor2" aria-expanded="false" aria-controls="collapseInstructor2">
   <h3 class="accordion-header" id="headingInstructor2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Instructor Note </h3>
 </button>
-<div id="collapseInstructor2" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor2" aria-labelledby="headingInstructor2">
+<div id="collapseInstructor2" class="accordion-collapse collapse" aria-labelledby="headingInstructor2" data-bs-parent="#accordionInstructor2">
 <div class="accordion-body">
 <p>We can showcase this last bias using the <a href="https://epiverse-trace.github.io/cfr/articles/cfr.html#concept-how-reporting-delays-bias-cfr-estimates" class="external-link">concept
 described in this <code>{cfr}</code> vignette</a>.</p>
@@ -5493,7 +5493,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <ul>
 <li>Find the appropriate <code>&lt;epidist&gt;</code> object!</li>
@@ -5507,7 +5507,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <p>We use <code>{epiparameter}</code> to access a delay distribution for
 the SARS-CoV-2 aggregated incidence data:</p>
@@ -5597,7 +5597,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> When to use discrete distributions? </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>For <code>cfr_static()</code> and all the <code>cfr_*()</code> family
 of functions, the most appropriate choice to pass are
@@ -5624,7 +5624,7 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> How does {cfr} works? </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <p>To adjust the CFR, <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006852" class="external-link">Nishiura
 et al., 2009</a> use the case and death incidence data to estimate the
@@ -5832,7 +5832,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Case study: SARS outbreak, Hong Kong, 2003 </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <p>Figures A and B show the cumulative numbers of cases and deaths of
 SARS, and Figure C shows the observed (biased) CFR estimates as a
@@ -5885,7 +5885,7 @@ <h3 class="callout-title">Interpret the early-stage CFR estimate<a class="anchor
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
 <div class="accordion-body">
 <p>We can use either visual inspection or analysis of the output data
 frames.</p>
@@ -5898,7 +5898,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <p>There is almost one month of difference.</p>
 <p>Note that the estimate has considerable uncertainty at the beginning
@@ -5932,7 +5932,7 @@ <h3 class="callout-title">Checklist<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Why the naive and delay-adjusted differ? </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p><a href="https://github.com/epiverse-trace/cfr" class="external-link">cfr</a> method aims to obtain an unbiased estimator “well
 before” observing the entire course of the outbreak. For this,
@@ -5948,7 +5948,7 @@ <h4 class="accordion-header" id="headingSolution7"> Why the naive and delay-adju
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> What is the sampling process? </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <figure><img src="../fig/cfr-pone.0006852.g001.png" alt="The population of confirmed cases and sampling process for estimating the unbiased CFR during the course of an outbreak. (Nishiura et al., 2009)" class="figure mx-auto d-block"><div class="figcaption">The population of confirmed cases and sampling
 process for estimating the unbiased CFR during the course of an
@@ -5988,7 +5988,7 @@ <h4 class="accordion-header" id="headingSolution8"> What is the sampling process
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Limitations </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <ul>
 <li>The delay-adjusted CFR does not address all sources of error in data
@@ -6061,7 +6061,7 @@ <h3 class="callout-title">Use incidence2 to rearrange your data<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint4" aria-expanded="false" aria-controls="collapseHint4">
   <h4 class="accordion-header" id="headingHint4"> Give me a hint </h4>
 </button>
-<div id="collapseHint4" class="accordion-collapse collapse" data-bs-parent="#accordionHint4" aria-labelledby="headingHint4">
+<div id="collapseHint4" class="accordion-collapse collapse" aria-labelledby="headingHint4" data-bs-parent="#accordionHint4">
 <div class="accordion-body">
 <p><strong>How to rearrange my input data?</strong></p>
 <p>Rearranging the input data for data analysis can take most of the
@@ -6084,7 +6084,7 @@ <h4 class="accordion-header" id="headingHint4"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution10" aria-expanded="false" aria-controls="collapseSolution10">
   <h4 class="accordion-header" id="headingSolution10"> Show me the solution </h4>
 </button>
-<div id="collapseSolution10" class="accordion-collapse collapse" data-bs-parent="#accordionSolution10" aria-labelledby="headingSolution10">
+<div id="collapseSolution10" class="accordion-collapse collapse" aria-labelledby="headingSolution10" data-bs-parent="#accordionSolution10">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb35">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6257,7 +6257,7 @@ <h3 class="callout-title">Severity heterogeneity<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint5" aria-expanded="false" aria-controls="collapseHint5">
   <h4 class="accordion-header" id="headingHint5"> Give me a hint </h4>
 </button>
-<div id="collapseHint5" class="accordion-collapse collapse" data-bs-parent="#accordionHint5" aria-labelledby="headingHint5">
+<div id="collapseHint5" class="accordion-collapse collapse" aria-labelledby="headingHint5" data-bs-parent="#accordionHint5">
 <div class="accordion-body">
 <p>One way to do a <em>stratified analysis</em> is to apply a model to
 nested data. This <a href="https://tidyr.tidyverse.org/articles/nest.html#nested-data-and-models" class="external-link"><code>{tidyr}</code>
@@ -6273,7 +6273,7 @@ <h4 class="accordion-header" id="headingHint5"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution11" aria-expanded="false" aria-controls="collapseSolution11">
   <h4 class="accordion-header" id="headingSolution11"> Show me the solution </h4>
 </button>
-<div id="collapseSolution11" class="accordion-collapse collapse" data-bs-parent="#accordionSolution11" aria-labelledby="headingSolution11">
+<div id="collapseSolution11" class="accordion-collapse collapse" aria-labelledby="headingSolution11" data-bs-parent="#accordionSolution11">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6436,7 +6436,7 @@ <h3 class="callout-title">More severity measures<a class="anchor" aria-label="an
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution12" aria-expanded="false" aria-controls="collapseSolution12">
   <h4 class="accordion-header" id="headingSolution12"> Infection and Hospitalization fatality risk </h4>
 </button>
-<div id="collapseSolution12" class="accordion-collapse collapse" data-bs-parent="#accordionSolution12" aria-labelledby="headingSolution12">
+<div id="collapseSolution12" class="accordion-collapse collapse" aria-labelledby="headingSolution12" data-bs-parent="#accordionSolution12">
 <div class="accordion-body">
 <p>If for a <em>Case</em> fatality risk (CFR), we require:</p>
 <ul>
@@ -6467,7 +6467,7 @@ <h4 class="accordion-header" id="headingSolution12"> Infection and Hospitalizati
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution13" aria-expanded="false" aria-controls="collapseSolution13">
   <h4 class="accordion-header" id="headingSolution13"> Data sources for more severity measures </h4>
 </button>
-<div id="collapseSolution13" class="accordion-collapse collapse" data-bs-parent="#accordionSolution13" aria-labelledby="headingSolution13">
+<div id="collapseSolution13" class="accordion-collapse collapse" aria-labelledby="headingSolution13" data-bs-parent="#accordionSolution13">
 <div class="accordion-body">
 <p><a href="https://www.nature.com/articles/s41467-020-19238-2/figures/1" class="external-link">Yang
 et al., 2020</a> summarises different definitions and data sources:</p>
@@ -7919,7 +7919,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Poisson and other distributions </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p><code>{epichains}</code> can accept any R function that generates
 random numbers, so the specified arguments will change depending on the
@@ -7965,7 +7965,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> generation time vs serial interval </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <figure><img src="../fig/serial-interval-observed.jpeg" alt="A schematic of the relationship of different time periods of transmission between an infector and an infectee in a transmission pair. Exposure window is defined as the time interval having viral exposure, and transmission window is defined as the time interval for onward transmission with respect to the infection time (Chung Lau et al., 2021)." class="figure mx-auto d-block"><div class="figcaption">A schematic of the relationship of different
 time periods of transmission between an infector and an infectee in a
@@ -8239,7 +8239,7 @@ <h3 class="callout-title">Read the epichains output<a class="anchor" aria-label=
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> The epichains object </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Let’s use <code>dplyr::filter()</code> for this:</p>
 <div class="codewrapper sourceCode" id="cb11">
@@ -8297,7 +8297,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> The epichains data frame </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8341,7 +8341,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> An infectee data frame </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>The output data frame collects <strong>infectees</strong> as the
 observation unit:</p>
@@ -8507,7 +8507,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Observed cases vs simulated chains </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <p>Let’s overlap the cumulative number of observed cases using the
 linelist object from the <code>mers_korea_2015</code> dataset of the
@@ -8620,7 +8620,7 @@ <h3 class="callout-title">Monkeypox large outbreak potential<a class="anchor" ar
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>With <code>{epiparameter}</code>, you can access and use offspring
 and delay distributions from previous Ebola outbreaks.</p>
@@ -8680,7 +8680,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8791,7 +8791,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Epidemic Risk assessment accounting for superspreading </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>With <code>{superspreading}</code>, you can get numerical solutions
 to processes that <code>{epichains}</code> solve using branching
@@ -8850,7 +8850,7 @@ <h3 class="callout-title">From a distribution of secondary cases<a class="anchor
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
 <div class="accordion-body">
 <p>Code with the transmission tree data written by <a href="https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(15)70135-0/fulltext" class="external-link">Christian
 Althaus, 2015</a>:</p>
@@ -8881,7 +8881,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb33">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -9054,9 +9054,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/create-forecast.html b/instructor/create-forecast.html
index 2e544828..45d9b5ac 100644
--- a/instructor/create-forecast.html
+++ b/instructor/create-forecast.html
@@ -1155,9 +1155,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/create-forecast.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
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diff --git a/instructor/delays-access.html b/instructor/delays-access.html
index c042faee..4d1fd396 100644
--- a/instructor/delays-access.html
+++ b/instructor/delays-access.html
@@ -1662,9 +1662,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor/delays-access.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/delays-access.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/delays-functions.html b/instructor/delays-functions.html
index 460a6677..a5543cff 100644
--- a/instructor/delays-functions.html
+++ b/instructor/delays-functions.html
@@ -1632,9 +1632,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/delays-functions.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index 12d09349..164e9f3b 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -687,9 +687,9 @@ <h3 id="superspreading-simulate-figure-11">Figure 11</h3>
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-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index 21540123..befb1597 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -829,9 +829,9 @@ <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor
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-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 873a152e..ee3e299e 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -482,9 +482,9 @@ <h3 id="severity-static-headingInstructor1">
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-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index 0e74f783..912e88fd 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -436,9 +436,9 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/key-points.html",
-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index ffdeacf5..7546fc46 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -321,9 +321,9 @@ <h1>Learner Profiles</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor/profiles.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/profiles.html",
-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/quantify-transmissibility.html b/instructor/quantify-transmissibility.html
index f3c50635..9454ed88 100644
--- a/instructor/quantify-transmissibility.html
+++ b/instructor/quantify-transmissibility.html
@@ -1344,9 +1344,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor/quantify-transmissibility.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/quantify-transmissibility.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 7c41891c..89e100e0 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -648,9 +648,9 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor/reference.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/reference.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/severity-static.html b/instructor/severity-static.html
index 78c16217..48d3c847 100644
--- a/instructor/severity-static.html
+++ b/instructor/severity-static.html
@@ -392,7 +392,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Instructor Note </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
 <div class="accordion-body">
 <p>The periods are relevant: Period 1 – 15 days where CFR is zero to
 indicate this is due to no reported deaths; Period from Mar 15 – Apr 26
@@ -581,7 +581,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>Inspect the format of the data input.</p>
 <ul><li>Does it contain daily data?</li>
@@ -597,7 +597,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>We read the data input using <code>readr::read_csv()</code>. This
 function recognize that the column <code>date</code> is a
@@ -681,7 +681,7 @@ <h3 class="callout-title">Two biases that affect CFR estimation<a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> 1. Preferential ascertainment of severe cases </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>For diseases with a <em>spectrum</em> of clinical presentations,
 those cases that come to the attention of public health authorities and
@@ -701,7 +701,7 @@ <h4 class="accordion-header" id="headingSolution2"> 1. Preferential ascertainmen
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> 2. Bias due to delayed reporting of death </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>During an <em>ongoing</em> epidemic, there is a delay between the
 time someone dies and the time their death is reported. Therefore, at
@@ -725,7 +725,7 @@ <h4 class="accordion-header" id="headingSolution3"> 2. Bias due to delayed repor
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Case study: Influenza A (H1N1), Mexico, 2009 </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Improving an <em>early</em> epidemiological assessment of a
 delay-adjusted CFR is crucial for determining virulence, shaping the
@@ -755,7 +755,7 @@ <h4 class="accordion-header" id="headingSolution4"> Case study: Influenza A (H1N
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor2" aria-expanded="false" aria-controls="collapseInstructor2">
   <h3 class="accordion-header" id="headingInstructor2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Instructor Note </h3>
 </button>
-<div id="collapseInstructor2" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor2" aria-labelledby="headingInstructor2">
+<div id="collapseInstructor2" class="accordion-collapse collapse" aria-labelledby="headingInstructor2" data-bs-parent="#accordionInstructor2">
 <div class="accordion-body">
 <p>We can showcase this last bias using the <a href="https://epiverse-trace.github.io/cfr/articles/cfr.html#concept-how-reporting-delays-bias-cfr-estimates" class="external-link">concept
 described in this <code>{cfr}</code> vignette</a>.</p>
@@ -868,7 +868,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <ul><li>Find the appropriate <code>&lt;epidist&gt;</code> object!</li>
 </ul></div>
@@ -880,7 +880,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <p>We use <code>{epiparameter}</code> to access a delay distribution for
 the SARS-CoV-2 aggregated incidence data:</p>
@@ -970,7 +970,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> When to use discrete distributions? </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>For <code>cfr_static()</code> and all the <code>cfr_*()</code> family
 of functions, the most appropriate choice to pass are
@@ -997,7 +997,7 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> How does {cfr} works? </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <p>To adjust the CFR, <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006852" class="external-link">Nishiura
 et al., 2009</a> use the case and death incidence data to estimate the
@@ -1202,7 +1202,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Case study: SARS outbreak, Hong Kong, 2003 </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <p>Figures A and B show the cumulative numbers of cases and deaths of
 SARS, and Figure C shows the observed (biased) CFR estimates as a
@@ -1250,7 +1250,7 @@ <h3 class="callout-title">Interpret the early-stage CFR estimate<a class="anchor
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
 <div class="accordion-body">
 <p>We can use either visual inspection or analysis of the output data
 frames.</p>
@@ -1263,7 +1263,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <p>There is almost one month of difference.</p>
 <p>Note that the estimate has considerable uncertainty at the beginning
@@ -1297,7 +1297,7 @@ <h3 class="callout-title">Checklist<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Why the naive and delay-adjusted differ? </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p><a href="https://github.com/epiverse-trace/cfr" class="external-link">cfr</a> method aims to obtain an unbiased estimator “well
 before” observing the entire course of the outbreak. For this,
@@ -1313,7 +1313,7 @@ <h4 class="accordion-header" id="headingSolution7"> Why the naive and delay-adju
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> What is the sampling process? </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <figure><img src="../fig/cfr-pone.0006852.g001.png" alt="The population of confirmed cases and sampling process for estimating the unbiased CFR during the course of an outbreak. (Nishiura et al., 2009)" class="figure mx-auto d-block"><div class="figcaption">The population of confirmed cases and sampling
 process for estimating the unbiased CFR during the course of an
@@ -1353,7 +1353,7 @@ <h4 class="accordion-header" id="headingSolution8"> What is the sampling process
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Limitations </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <ul><li>The delay-adjusted CFR does not address all sources of error in data
 like the underdiagnosis of infected individuals.</li>
@@ -1423,7 +1423,7 @@ <h3 class="callout-title">Use incidence2 to rearrange your data<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint4" aria-expanded="false" aria-controls="collapseHint4">
   <h4 class="accordion-header" id="headingHint4"> Give me a hint </h4>
 </button>
-<div id="collapseHint4" class="accordion-collapse collapse" data-bs-parent="#accordionHint4" aria-labelledby="headingHint4">
+<div id="collapseHint4" class="accordion-collapse collapse" aria-labelledby="headingHint4" data-bs-parent="#accordionHint4">
 <div class="accordion-body">
 <p><strong>How to rearrange my input data?</strong></p>
 <p>Rearranging the input data for data analysis can take most of the
@@ -1446,7 +1446,7 @@ <h4 class="accordion-header" id="headingHint4"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution10" aria-expanded="false" aria-controls="collapseSolution10">
   <h4 class="accordion-header" id="headingSolution10"> Show me the solution </h4>
 </button>
-<div id="collapseSolution10" class="accordion-collapse collapse" data-bs-parent="#accordionSolution10" aria-labelledby="headingSolution10">
+<div id="collapseSolution10" class="accordion-collapse collapse" aria-labelledby="headingSolution10" data-bs-parent="#accordionSolution10">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb35">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1619,7 +1619,7 @@ <h3 class="callout-title">Severity heterogeneity<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint5" aria-expanded="false" aria-controls="collapseHint5">
   <h4 class="accordion-header" id="headingHint5"> Give me a hint </h4>
 </button>
-<div id="collapseHint5" class="accordion-collapse collapse" data-bs-parent="#accordionHint5" aria-labelledby="headingHint5">
+<div id="collapseHint5" class="accordion-collapse collapse" aria-labelledby="headingHint5" data-bs-parent="#accordionHint5">
 <div class="accordion-body">
 <p>One way to do a <em>stratified analysis</em> is to apply a model to
 nested data. This <a href="https://tidyr.tidyverse.org/articles/nest.html#nested-data-and-models" class="external-link"><code>{tidyr}</code>
@@ -1635,7 +1635,7 @@ <h4 class="accordion-header" id="headingHint5"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution11" aria-expanded="false" aria-controls="collapseSolution11">
   <h4 class="accordion-header" id="headingSolution11"> Show me the solution </h4>
 </button>
-<div id="collapseSolution11" class="accordion-collapse collapse" data-bs-parent="#accordionSolution11" aria-labelledby="headingSolution11">
+<div id="collapseSolution11" class="accordion-collapse collapse" aria-labelledby="headingSolution11" data-bs-parent="#accordionSolution11">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1797,7 +1797,7 @@ <h3 class="callout-title">More severity measures<a class="anchor" aria-label="an
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution12" aria-expanded="false" aria-controls="collapseSolution12">
   <h4 class="accordion-header" id="headingSolution12"> Infection and Hospitalization fatality risk </h4>
 </button>
-<div id="collapseSolution12" class="accordion-collapse collapse" data-bs-parent="#accordionSolution12" aria-labelledby="headingSolution12">
+<div id="collapseSolution12" class="accordion-collapse collapse" aria-labelledby="headingSolution12" data-bs-parent="#accordionSolution12">
 <div class="accordion-body">
 <p>If for a <em>Case</em> fatality risk (CFR), we require:</p>
 <ul><li>
@@ -1822,7 +1822,7 @@ <h4 class="accordion-header" id="headingSolution12"> Infection and Hospitalizati
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution13" aria-expanded="false" aria-controls="collapseSolution13">
   <h4 class="accordion-header" id="headingSolution13"> Data sources for more severity measures </h4>
 </button>
-<div id="collapseSolution13" class="accordion-collapse collapse" data-bs-parent="#accordionSolution13" aria-labelledby="headingSolution13">
+<div id="collapseSolution13" class="accordion-collapse collapse" aria-labelledby="headingSolution13" data-bs-parent="#accordionSolution13">
 <div class="accordion-body">
 <p><a href="https://www.nature.com/articles/s41467-020-19238-2/figures/1" class="external-link">Yang
 et al., 2020</a> summarises different definitions and data sources:</p>
@@ -1940,9 +1940,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor/severity-static.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/severity-static.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/superspreading-estimate.html b/instructor/superspreading-estimate.html
index fbcaba1b..4a403bd9 100644
--- a/instructor/superspreading-estimate.html
+++ b/instructor/superspreading-estimate.html
@@ -1499,9 +1499,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor/superspreading-estimate.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/superspreading-estimate.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/instructor/superspreading-simulate.html b/instructor/superspreading-simulate.html
index 9016065e..cc958338 100644
--- a/instructor/superspreading-simulate.html
+++ b/instructor/superspreading-simulate.html
@@ -500,7 +500,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Poisson and other distributions </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p><code>{epichains}</code> can accept any R function that generates
 random numbers, so the specified arguments will change depending on the
@@ -545,7 +545,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> generation time vs serial interval </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <figure><img src="../fig/serial-interval-observed.jpeg" alt="A schematic of the relationship of different time periods of transmission between an infector and an infectee in a transmission pair. Exposure window is defined as the time interval having viral exposure, and transmission window is defined as the time interval for onward transmission with respect to the infection time (Chung Lau et al., 2021)." class="figure mx-auto d-block"><div class="figcaption">A schematic of the relationship of different
 time periods of transmission between an infector and an infectee in a
@@ -809,7 +809,7 @@ <h3 class="callout-title">Read the epichains output<a class="anchor" aria-label=
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> The epichains object </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Let’s use <code>dplyr::filter()</code> for this:</p>
 <div class="codewrapper sourceCode" id="cb11">
@@ -867,7 +867,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> The epichains data frame </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -911,7 +911,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> An infectee data frame </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>The output data frame collects <strong>infectees</strong> as the
 observation unit:</p>
@@ -1072,7 +1072,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Observed cases vs simulated chains </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <p>Let’s overlap the cumulative number of observed cases using the
 linelist object from the <code>mers_korea_2015</code> dataset of the
@@ -1181,7 +1181,7 @@ <h3 class="callout-title">Monkeypox large outbreak potential<a class="anchor" ar
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>With <code>{epiparameter}</code>, you can access and use offspring
 and delay distributions from previous Ebola outbreaks.</p>
@@ -1241,7 +1241,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1352,7 +1352,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Epidemic Risk assessment accounting for superspreading </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>With <code>{superspreading}</code>, you can get numerical solutions
 to processes that <code>{epichains}</code> solve using branching
@@ -1409,7 +1409,7 @@ <h3 class="callout-title">From a distribution of secondary cases<a class="anchor
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
 <div class="accordion-body">
 <p>Code with the transmission tree data written by <a href="https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(15)70135-0/fulltext" class="external-link">Christian
 Althaus, 2015</a>:</p>
@@ -1439,7 +1439,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb33">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1620,9 +1620,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/instructor/superspreading-simulate.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/instructor/superspreading-simulate.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 87c635b6..19b2b6f6 100644
--- a/key-points.html
+++ b/key-points.html
@@ -434,9 +434,9 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/key-points.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/key-points.html",
-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 6eaefef9..f6641364 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-07-02T02:46Z
+last_built: 2024-07-05T12:33Z
 
diff --git a/profiles.html b/profiles.html
index b4a7bf4b..fe6af2dd 100644
--- a/profiles.html
+++ b/profiles.html
@@ -321,9 +321,9 @@ <h1>Learner Profiles</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/profiles.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/profiles.html",
-  "dateCreated": "2024-06-25",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateCreated": "2024-07-05",
+  "dateModified": "2024-07-05",
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/quantify-transmissibility.html b/quantify-transmissibility.html
index 184d5843..ef9b5dcf 100644
--- a/quantify-transmissibility.html
+++ b/quantify-transmissibility.html
@@ -1312,9 +1312,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/quantify-transmissibility.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/quantify-transmissibility.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 0b9841bb..a1197fa6 100644
--- a/reference.html
+++ b/reference.html
@@ -646,9 +646,9 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/reference.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/reference.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/renv.lock b/renv.lock
index b796792f..50793c04 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.4.0",
+    "Version": "4.4.1",
     "Repositories": [
       {
         "Name": "CRAN",
diff --git a/severity-static.html b/severity-static.html
index fd307408..98cf996d 100644
--- a/severity-static.html
+++ b/severity-static.html
@@ -564,7 +564,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>Inspect the format of the data input.</p>
 <ul><li>Does it contain daily data?</li>
@@ -580,7 +580,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>We read the data input using <code>readr::read_csv()</code>. This
 function recognize that the column <code>date</code> is a
@@ -664,7 +664,7 @@ <h3 class="callout-title">Two biases that affect CFR estimation<a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> 1. Preferential ascertainment of severe cases </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>For diseases with a <em>spectrum</em> of clinical presentations,
 those cases that come to the attention of public health authorities and
@@ -684,7 +684,7 @@ <h4 class="accordion-header" id="headingSolution2"> 1. Preferential ascertainmen
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> 2. Bias due to delayed reporting of death </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>During an <em>ongoing</em> epidemic, there is a delay between the
 time someone dies and the time their death is reported. Therefore, at
@@ -708,7 +708,7 @@ <h4 class="accordion-header" id="headingSolution3"> 2. Bias due to delayed repor
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Case study: Influenza A (H1N1), Mexico, 2009 </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Improving an <em>early</em> epidemiological assessment of a
 delay-adjusted CFR is crucial for determining virulence, shaping the
@@ -838,7 +838,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <ul><li>Find the appropriate <code>&lt;epidist&gt;</code> object!</li>
 </ul></div>
@@ -850,7 +850,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <p>We use <code>{epiparameter}</code> to access a delay distribution for
 the SARS-CoV-2 aggregated incidence data:</p>
@@ -940,7 +940,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> When to use discrete distributions? </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>For <code>cfr_static()</code> and all the <code>cfr_*()</code> family
 of functions, the most appropriate choice to pass are
@@ -967,7 +967,7 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> How does {cfr} works? </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <p>To adjust the CFR, <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006852" class="external-link">Nishiura
 et al., 2009</a> use the case and death incidence data to estimate the
@@ -1172,7 +1172,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Case study: SARS outbreak, Hong Kong, 2003 </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <p>Figures A and B show the cumulative numbers of cases and deaths of
 SARS, and Figure C shows the observed (biased) CFR estimates as a
@@ -1220,7 +1220,7 @@ <h3 class="callout-title">Interpret the early-stage CFR estimate<a class="anchor
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
 <div class="accordion-body">
 <p>We can use either visual inspection or analysis of the output data
 frames.</p>
@@ -1233,7 +1233,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <p>There is almost one month of difference.</p>
 <p>Note that the estimate has considerable uncertainty at the beginning
@@ -1267,7 +1267,7 @@ <h3 class="callout-title">Checklist<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Why the naive and delay-adjusted differ? </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p><a href="https://github.com/epiverse-trace/cfr" class="external-link">cfr</a> method aims to obtain an unbiased estimator “well
 before” observing the entire course of the outbreak. For this,
@@ -1283,7 +1283,7 @@ <h4 class="accordion-header" id="headingSolution7"> Why the naive and delay-adju
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> What is the sampling process? </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <figure><img src="fig/cfr-pone.0006852.g001.png" alt="The population of confirmed cases and sampling process for estimating the unbiased CFR during the course of an outbreak. (Nishiura et al., 2009)" class="figure mx-auto d-block"><div class="figcaption">The population of confirmed cases and sampling
 process for estimating the unbiased CFR during the course of an
@@ -1323,7 +1323,7 @@ <h4 class="accordion-header" id="headingSolution8"> What is the sampling process
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Limitations </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <ul><li>The delay-adjusted CFR does not address all sources of error in data
 like the underdiagnosis of infected individuals.</li>
@@ -1393,7 +1393,7 @@ <h3 class="callout-title">Use incidence2 to rearrange your data<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint4" aria-expanded="false" aria-controls="collapseHint4">
   <h4 class="accordion-header" id="headingHint4"> Give me a hint </h4>
 </button>
-<div id="collapseHint4" class="accordion-collapse collapse" data-bs-parent="#accordionHint4" aria-labelledby="headingHint4">
+<div id="collapseHint4" class="accordion-collapse collapse" aria-labelledby="headingHint4" data-bs-parent="#accordionHint4">
 <div class="accordion-body">
 <p><strong>How to rearrange my input data?</strong></p>
 <p>Rearranging the input data for data analysis can take most of the
@@ -1416,7 +1416,7 @@ <h4 class="accordion-header" id="headingHint4"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution10" aria-expanded="false" aria-controls="collapseSolution10">
   <h4 class="accordion-header" id="headingSolution10"> Show me the solution </h4>
 </button>
-<div id="collapseSolution10" class="accordion-collapse collapse" data-bs-parent="#accordionSolution10" aria-labelledby="headingSolution10">
+<div id="collapseSolution10" class="accordion-collapse collapse" aria-labelledby="headingSolution10" data-bs-parent="#accordionSolution10">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb35">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1589,7 +1589,7 @@ <h3 class="callout-title">Severity heterogeneity<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint5" aria-expanded="false" aria-controls="collapseHint5">
   <h4 class="accordion-header" id="headingHint5"> Give me a hint </h4>
 </button>
-<div id="collapseHint5" class="accordion-collapse collapse" data-bs-parent="#accordionHint5" aria-labelledby="headingHint5">
+<div id="collapseHint5" class="accordion-collapse collapse" aria-labelledby="headingHint5" data-bs-parent="#accordionHint5">
 <div class="accordion-body">
 <p>One way to do a <em>stratified analysis</em> is to apply a model to
 nested data. This <a href="https://tidyr.tidyverse.org/articles/nest.html#nested-data-and-models" class="external-link"><code>{tidyr}</code>
@@ -1605,7 +1605,7 @@ <h4 class="accordion-header" id="headingHint5"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution11" aria-expanded="false" aria-controls="collapseSolution11">
   <h4 class="accordion-header" id="headingSolution11"> Show me the solution </h4>
 </button>
-<div id="collapseSolution11" class="accordion-collapse collapse" data-bs-parent="#accordionSolution11" aria-labelledby="headingSolution11">
+<div id="collapseSolution11" class="accordion-collapse collapse" aria-labelledby="headingSolution11" data-bs-parent="#accordionSolution11">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1767,7 +1767,7 @@ <h3 class="callout-title">More severity measures<a class="anchor" aria-label="an
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution12" aria-expanded="false" aria-controls="collapseSolution12">
   <h4 class="accordion-header" id="headingSolution12"> Infection and Hospitalization fatality risk </h4>
 </button>
-<div id="collapseSolution12" class="accordion-collapse collapse" data-bs-parent="#accordionSolution12" aria-labelledby="headingSolution12">
+<div id="collapseSolution12" class="accordion-collapse collapse" aria-labelledby="headingSolution12" data-bs-parent="#accordionSolution12">
 <div class="accordion-body">
 <p>If for a <em>Case</em> fatality risk (CFR), we require:</p>
 <ul><li>
@@ -1792,7 +1792,7 @@ <h4 class="accordion-header" id="headingSolution12"> Infection and Hospitalizati
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution13" aria-expanded="false" aria-controls="collapseSolution13">
   <h4 class="accordion-header" id="headingSolution13"> Data sources for more severity measures </h4>
 </button>
-<div id="collapseSolution13" class="accordion-collapse collapse" data-bs-parent="#accordionSolution13" aria-labelledby="headingSolution13">
+<div id="collapseSolution13" class="accordion-collapse collapse" aria-labelledby="headingSolution13" data-bs-parent="#accordionSolution13">
 <div class="accordion-body">
 <p><a href="https://www.nature.com/articles/s41467-020-19238-2/figures/1" class="external-link">Yang
 et al., 2020</a> summarises different definitions and data sources:</p>
@@ -1910,9 +1910,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/severity-static.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/severity-static.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/superspreading-estimate.html b/superspreading-estimate.html
index b73287a8..0ac45051 100644
--- a/superspreading-estimate.html
+++ b/superspreading-estimate.html
@@ -1497,9 +1497,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/superspreading-estimate.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/superspreading-estimate.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>
diff --git a/superspreading-simulate.html b/superspreading-simulate.html
index d21573bc..f209924e 100644
--- a/superspreading-simulate.html
+++ b/superspreading-simulate.html
@@ -498,7 +498,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Poisson and other distributions </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p><code>{epichains}</code> can accept any R function that generates
 random numbers, so the specified arguments will change depending on the
@@ -543,7 +543,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> generation time vs serial interval </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <figure><img src="fig/serial-interval-observed.jpeg" alt="A schematic of the relationship of different time periods of transmission between an infector and an infectee in a transmission pair. Exposure window is defined as the time interval having viral exposure, and transmission window is defined as the time interval for onward transmission with respect to the infection time (Chung Lau et al., 2021)." class="figure mx-auto d-block"><div class="figcaption">A schematic of the relationship of different
 time periods of transmission between an infector and an infectee in a
@@ -807,7 +807,7 @@ <h3 class="callout-title">Read the epichains output<a class="anchor" aria-label=
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> The epichains object </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Let’s use <code>dplyr::filter()</code> for this:</p>
 <div class="codewrapper sourceCode" id="cb11">
@@ -865,7 +865,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> The epichains data frame </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -909,7 +909,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> An infectee data frame </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>The output data frame collects <strong>infectees</strong> as the
 observation unit:</p>
@@ -1070,7 +1070,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Observed cases vs simulated chains </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <p>Let’s overlap the cumulative number of observed cases using the
 linelist object from the <code>mers_korea_2015</code> dataset of the
@@ -1179,7 +1179,7 @@ <h3 class="callout-title">Monkeypox large outbreak potential<a class="anchor" ar
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>With <code>{epiparameter}</code>, you can access and use offspring
 and delay distributions from previous Ebola outbreaks.</p>
@@ -1239,7 +1239,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1350,7 +1350,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Epidemic Risk assessment accounting for superspreading </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>With <code>{superspreading}</code>, you can get numerical solutions
 to processes that <code>{epichains}</code> solve using branching
@@ -1407,7 +1407,7 @@ <h3 class="callout-title">From a distribution of secondary cases<a class="anchor
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
 <div class="accordion-body">
 <p>Code with the transmission tree data written by <a href="https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(15)70135-0/fulltext" class="external-link">Christian
 Althaus, 2015</a>:</p>
@@ -1437,7 +1437,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb33">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1618,9 +1618,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-middle/superspreading-simulate.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-middle/superspreading-simulate.html",
-  "dateCreated": "2024-06-25",
+  "dateCreated": "2024-07-05",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-05"
 }
 
   </script><script>