diff --git a/404.html b/404.html
index b3a82ec..a30b39f 100644
--- a/404.html
+++ b/404.html
@@ -55,7 +55,7 @@
       <a href="articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="articles/model.html">Model</a>
+      <a href="articles/model.html">Summary of the Stan Model</a>
     </li>
   </ul>
 </li>
diff --git a/LICENSE.html b/LICENSE.html
index ad501d8..493973e 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -38,7 +38,7 @@
       <a href="articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="articles/model.html">Model</a>
+      <a href="articles/model.html">Summary of the Stan Model</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
diff --git a/articles/biokinetics.html b/articles/biokinetics.html
index 52d4113..c44c5d7 100644
--- a/articles/biokinetics.html
+++ b/articles/biokinetics.html
@@ -55,7 +55,7 @@
       <a href="../articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="../articles/model.html">Model</a>
+      <a href="../articles/model.html">Summary of the Stan Model</a>
     </li>
   </ul>
 </li>
@@ -120,9 +120,9 @@ <h2 id="figure-2">Figure 2<a class="anchor" aria-label="anchor" href="#figure-2"
 population trajectories using the fitted population parameters.</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">res</span> <span class="op">&lt;-</span> <span class="va">mod</span><span class="op">$</span><span class="fu">simulate_population_trajectories</span><span class="op">(</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:32] Summarising fits</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:35] Adjusting by regression coefficients</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:38] Summarising into quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:25] Summarising fits</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:29] Adjusting by regression coefficients</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:31] Summarising into quantiles</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">res</span><span class="op">)</span></span>
 <span><span class="co">#&gt;    time_since_last_exp       me        lo       hi titre_type infection_history</span></span>
 <span><span class="co">#&gt;                  &lt;int&gt;    &lt;num&gt;     &lt;num&gt;    &lt;num&gt;     &lt;char&gt;            &lt;char&gt;</span></span>
@@ -191,11 +191,11 @@ <h2 id="figure-4">Figure 4<a class="anchor" aria-label="anchor" href="#figure-4"
 simulate estimates for these from the fitted model:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">res</span> <span class="op">&lt;-</span> <span class="va">mod</span><span class="op">$</span><span class="fu">population_stationary_points</span><span class="op">(</span>n_draws <span class="op">=</span> <span class="fl">2000</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:39] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:39] Adjusting by covariates</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:39] Calculating peak and switch titre values</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:39] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:39] Calculating medians</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:32] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:33] Adjusting by covariates</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:33] Calculating peak and switch titre values</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:33] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:33] Calculating medians</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">res</span><span class="op">)</span></span>
 <span><span class="co">#&gt;    infection_history titre_type     mu_p     mu_s rel_drop_me  mu_p_me  mu_s_me</span></span>
 <span><span class="co">#&gt;               &lt;char&gt;     &lt;char&gt;    &lt;num&gt;    &lt;num&gt;       &lt;num&gt;    &lt;num&gt;    &lt;num&gt;</span></span>
@@ -261,15 +261,15 @@ <h2 id="figure-5">Figure 5<a class="anchor" aria-label="anchor" href="#figure-5"
 maximum number of draws to just 250 for speed.</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">res</span> <span class="op">&lt;-</span> <span class="va">mod</span><span class="op">$</span><span class="fu">simulate_individual_trajectories</span><span class="op">(</span>n_draws <span class="op">=</span> <span class="fl">250</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:40] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:44] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:48] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:49] Calculating exposure days. Adjusting exposures by 0 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:39:52] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:34] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:38] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:42] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:42] Calculating exposure days. Adjusting exposures by 0 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:45] Resampling</span></span>
 <span><span class="co">#&gt; Registered S3 method overwritten by 'mosaic':</span></span>
 <span><span class="co">#&gt;   method                           from   </span></span>
 <span><span class="co">#&gt;   fortify.SpatialPolygonsDataFrame ggplot2</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:02] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:55] Summarising into population quantiles</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">res</span><span class="op">)</span></span>
 <span><span class="co">#&gt;    calendar_day titre_type       me       lo       hi time_shift</span></span>
 <span><span class="co">#&gt;          &lt;IDat&gt;     &lt;char&gt;    &lt;num&gt;    &lt;num&gt;    &lt;num&gt;      &lt;num&gt;</span></span>
@@ -348,72 +348,72 @@ <h2 id="figure-5">Figure 5<a class="anchor" aria-label="anchor" href="#figure-5"
 <span>  <span class="va">shift</span> <span class="op">&lt;-</span> <span class="va">time_shift_values</span><span class="op">[</span><span class="va">index</span><span class="op">]</span></span>
 <span>  <span class="va">mod</span><span class="op">$</span><span class="fu">simulate_individual_trajectories</span><span class="op">(</span>n_draws <span class="op">=</span> <span class="fl">50</span>, time_shift <span class="op">=</span> <span class="va">shift</span><span class="op">)</span></span>
 <span><span class="op">}</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:03] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:06] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:07] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:07] Calculating exposure days. Adjusting exposures by -75 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:08] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:10] Summarising into population quantiles</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:10] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:14] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:14] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:14] Calculating exposure days. Adjusting exposures by -60 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:15] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:17] Summarising into population quantiles</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:17] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:21] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:21] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:21] Calculating exposure days. Adjusting exposures by -45 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:22] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:23] Summarising into population quantiles</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:24] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:27] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:28] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:28] Calculating exposure days. Adjusting exposures by -30 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:28] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:30] Summarising into population quantiles</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:31] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:34] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:35] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:35] Calculating exposure days. Adjusting exposures by -15 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:35] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:37] Summarising into population quantiles</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:38] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:41] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:42] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:42] Calculating exposure days. Adjusting exposures by 0 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:43] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:45] Summarising into population quantiles</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:45] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:49] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:49] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:49] Calculating exposure days. Adjusting exposures by 15 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:50] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:52] Summarising into population quantiles</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:53] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:56] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:57] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:57] Calculating exposure days. Adjusting exposures by 30 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:57] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:40:59] Summarising into population quantiles</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:00] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:03] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:04] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:04] Calculating exposure days. Adjusting exposures by 45 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:04] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:06] Summarising into population quantiles</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:07] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:10] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:11] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:11] Calculating exposure days. Adjusting exposures by 60 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:11] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:13] Summarising into population quantiles</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:14] Extracting parameters</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:17] Simulating individual trajectories</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:18] Recovering covariate names</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:18] Calculating exposure days. Adjusting exposures by 75 days</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:18] Resampling</span></span>
-<span><span class="co">#&gt; INFO [2024-10-23 12:41:20] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:38:56] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:00] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:01] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:01] Calculating exposure days. Adjusting exposures by -75 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:01] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:03] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:04] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:07] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:08] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:08] Calculating exposure days. Adjusting exposures by -60 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:08] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:10] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:11] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:14] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:15] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:15] Calculating exposure days. Adjusting exposures by -45 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:15] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:17] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:18] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:21] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:22] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:22] Calculating exposure days. Adjusting exposures by -30 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:22] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:24] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:24] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:28] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:28] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:29] Calculating exposure days. Adjusting exposures by -15 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:29] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:31] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:32] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:35] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:36] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:36] Calculating exposure days. Adjusting exposures by 0 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:36] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:38] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:39] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:42] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:43] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:43] Calculating exposure days. Adjusting exposures by 15 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:43] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:45] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:46] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:50] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:50] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:50] Calculating exposure days. Adjusting exposures by 30 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:51] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:53] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:53] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:57] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:57] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:57] Calculating exposure days. Adjusting exposures by 45 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:39:58] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:00] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:00] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:03] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:04] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:04] Calculating exposure days. Adjusting exposures by 60 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:05] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:07] Summarising into population quantiles</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:07] Extracting parameters</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:10] Simulating individual trajectories</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:11] Recovering covariate names</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:11] Calculating exposure days. Adjusting exposures by 75 days</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:12] Resampling</span></span>
+<span><span class="co">#&gt; INFO [2024-10-24 14:40:13] Summarising into population quantiles</span></span>
 <span></span>
 <span><span class="va">combined_data</span> <span class="op">&lt;-</span> <span class="fu">data.table</span><span class="fu">::</span><span class="fu"><a href="https://rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table</a></span><span class="op">(</span><span class="fu">data.table</span><span class="fu">::</span><span class="fu"><a href="https://rdatatable.gitlab.io/data.table/reference/rbindlist.html" class="external-link">rbindlist</a></span><span class="op">(</span><span class="va">results_list</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p>Plotting the median values:</p>
diff --git a/articles/data.html b/articles/data.html
index fd8d3f2..4b49a31 100644
--- a/articles/data.html
+++ b/articles/data.html
@@ -55,7 +55,7 @@
       <a href="../articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="../articles/model.html">Model</a>
+      <a href="../articles/model.html">Summary of the Stan Model</a>
     </li>
   </ul>
 </li>
diff --git a/articles/index.html b/articles/index.html
index 442c1d4..6797c4c 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -38,7 +38,7 @@
       <a href="../articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="../articles/model.html">Model</a>
+      <a href="../articles/model.html">Summary of the Stan Model</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
@@ -61,7 +61,7 @@ <h3>All vignettes</h3>
         <dd>
         </dd><dt><a href="data.html">A guide to model input and output data</a></dt>
         <dd>
-        </dd><dt><a href="model.html">Model</a></dt>
+        </dd><dt><a href="model.html">Summary of the Stan Model</a></dt>
         <dd>
       </dd></dl></div>
   </div>
diff --git a/articles/model.html b/articles/model.html
index 5427383..64fbbf9 100644
--- a/articles/model.html
+++ b/articles/model.html
@@ -5,13 +5,13 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Model • epikinetics</title>
+<title>Summary of the Stan Model • epikinetics</title>
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-<script src="../pkgdown.js"></script><meta property="og:title" content="Model">
+<script src="../pkgdown.js"></script><meta property="og:title" content="Summary of the Stan Model">
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@@ -55,7 +55,7 @@
       <a href="../articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="../articles/model.html">Model</a>
+      <a href="../articles/model.html">Summary of the Stan Model</a>
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 </li>
@@ -73,7 +73,7 @@
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
-      <h1 data-toc-skip>Model</h1>
+      <h1 data-toc-skip>Summary of the Stan Model</h1>
             
       
 
@@ -83,8 +83,321 @@ <h1 data-toc-skip>Model</h1>
 
     
     
-<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">epikinetics</span><span class="op">)</span></span></code></pre></div>
+<div class="section level2">
+<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+</h2>
+<p>This document provides a summary of a hierarchical statistical model
+of antibody kinetics, implemented in Stan. The model is designed to
+analyse longitudinal titre data, accounting for boosting and waning
+effects over time. It incorporates individual-level random effects and
+covariate influences on key model parameters. A full description of the
+model can be found in the supplementary material in the published paper
+using the methods described here: <a href="https://doi.org/10.1016/s1473-3099(24)00484-5" class="external-link">Russell TW et
+al. Real-time estimation of immunological responses against emerging
+SARS-CoV-2 variants in the UK: a mathematical modelling study. Lancet
+Infect Dis. 2024 Sep 11:S1473-3099(24)00484-5</a>.</p>
+</div>
+<div class="section level2">
+<h2 id="usage-notes">Usage Notes<a class="anchor" aria-label="anchor" href="#usage-notes"></a>
+</h2>
+<p>This model is suitable for analysing longitudinal titre data with
+either lower, upper, both (or no) censoring and incorporates both
+individual-level variability and arbitrary regression structure to
+adjust for covariates. Users can adapt the model by specifying
+appropriate covariates via a R style linear model formula, priors, and
+data inputs relevant to their study.</p>
+</div>
+<div class="section level2">
+<h2 id="model-specification">Model Specification<a class="anchor" aria-label="anchor" href="#model-specification"></a>
+</h2>
+<div class="section level3">
+<h3 id="overview">Overview<a class="anchor" aria-label="anchor" href="#overview"></a>
+</h3>
+<p>The model describes the expected log-transformed titre value
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>μ</mi><mi>n</mi></msub><annotation encoding="application/x-tex">\mu_{n}</annotation></semantics></math>
+for individual
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>n</mi><annotation encoding="application/x-tex">n</annotation></semantics></math>
+at time
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>t</mi><mi>n</mi></msub><annotation encoding="application/x-tex">t_n</annotation></semantics></math>
+and titre type
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>k</mi><annotation encoding="application/x-tex">k</annotation></semantics></math>,
+using a piecewise linear function to capture boosting and waning
+phases:</p>
+<ul>
+<li>
+<strong>Boosting Phase</strong>: For
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>t</mi><mi>n</mi></msub><mo>&lt;</mo><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub></mrow><annotation encoding="application/x-tex">t_n &lt; t_{p,n}</annotation></semantics></math>,
+the titre increases at rate
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>m</mi><mrow><mn>1</mn><mo>,</mo><mi>n</mi></mrow></msub><annotation encoding="application/x-tex">m_{1,n}</annotation></semantics></math>.</li>
+<li>
+<strong>Plateau Phase</strong>: For
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub><mo>≤</mo><msub><mi>t</mi><mi>n</mi></msub><mo>≤</mo><msub><mi>t</mi><mrow><mi>s</mi><mo>,</mo><mi>n</mi></mrow></msub></mrow><annotation encoding="application/x-tex">t_{p,n} \leq t_n \leq t_{s,n}</annotation></semantics></math>,
+the titre remains elevated.</li>
+<li>
+<strong>Waning Phase</strong>: For
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>t</mi><mi>n</mi></msub><mo>&gt;</mo><msub><mi>t</mi><mrow><mi>s</mi><mo>,</mo><mi>n</mi></mrow></msub></mrow><annotation encoding="application/x-tex">t_n &gt; t_{s,n}</annotation></semantics></math>,
+the titre decreases at rate
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>m</mi><mrow><mn>3</mn><mo>,</mo><mi>n</mi></mrow></msub><annotation encoding="application/x-tex">m_{3,n}</annotation></semantics></math>.</li>
+</ul>
+</div>
+<div class="section level3">
+<h3 id="mathematical-formulation">Mathematical Formulation<a class="anchor" aria-label="anchor" href="#mathematical-formulation"></a>
+</h3>
+<div class="section level4">
+<h4 id="expected-titre-value">Expected Titre Value<a class="anchor" aria-label="anchor" href="#expected-titre-value"></a>
+</h4>
+<p>The expected log-transformed titre value
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>μ</mi><mi>n</mi></msub><annotation encoding="application/x-tex">\mu_{n}</annotation></semantics></math>
+is given by:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>μ</mi><mi>n</mi></msub><mo>=</mo><msub><mi>t</mi><mrow><mn>0</mn><mo>,</mo><mi>n</mi></mrow></msub><mo>+</mo><mrow><mo stretchy="true" form="prefix">{</mo><mtable><mtr><mtd columnalign="left" style="text-align: left"><msub><mi>m</mi><mrow><mn>1</mn><mo>,</mo><mi>n</mi></mrow></msub><mo>⋅</mo><msub><mi>t</mi><mi>n</mi></msub><mo>,</mo></mtd><mtd columnalign="left" style="text-align: left"><mrow><mtext mathvariant="normal">if </mtext><mspace width="0.333em"></mspace></mrow><msub><mi>t</mi><mi>n</mi></msub><mo>&lt;</mo><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub></mtd></mtr><mtr><mtd columnalign="left" style="text-align: left"><msub><mi>m</mi><mrow><mn>1</mn><mo>,</mo><mi>n</mi></mrow></msub><mo>⋅</mo><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub><mo>+</mo><msub><mi>m</mi><mrow><mn>2</mn><mo>,</mo><mi>n</mi></mrow></msub><mo>⋅</mo><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>t</mi><mi>n</mi></msub><mo>−</mo><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>,</mo></mtd><mtd columnalign="left" style="text-align: left"><mrow><mtext mathvariant="normal">if </mtext><mspace width="0.333em"></mspace></mrow><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub><mo>≤</mo><msub><mi>t</mi><mi>n</mi></msub><mo>≤</mo><msub><mi>t</mi><mrow><mi>s</mi><mo>,</mo><mi>n</mi></mrow></msub></mtd></mtr><mtr><mtd columnalign="left" style="text-align: left"><msub><mi>m</mi><mrow><mn>1</mn><mo>,</mo><mi>n</mi></mrow></msub><mo>⋅</mo><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub><mo>+</mo><msub><mi>m</mi><mrow><mn>2</mn><mo>,</mo><mi>n</mi></mrow></msub><mo>⋅</mo><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>t</mi><mrow><mi>s</mi><mo>,</mo><mi>n</mi></mrow></msub><mo>−</mo><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>+</mo><msub><mi>m</mi><mrow><mn>3</mn><mo>,</mo><mi>n</mi></mrow></msub><mo>⋅</mo><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>t</mi><mi>n</mi></msub><mo>−</mo><msub><mi>t</mi><mrow><mi>s</mi><mo>,</mo><mi>n</mi></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>,</mo></mtd><mtd columnalign="left" style="text-align: left"><mrow><mtext mathvariant="normal">if </mtext><mspace width="0.333em"></mspace></mrow><msub><mi>t</mi><mi>n</mi></msub><mo>&gt;</mo><msub><mi>t</mi><mrow><mi>s</mi><mo>,</mo><mi>n</mi></mrow></msub></mtd></mtr></mtable></mrow></mrow><annotation encoding="application/x-tex">
+\mu_{n} = t_{0,n} + \begin{cases}
+m_{1,n} \cdot t_n, &amp; \text{if } t_n &lt; t_{p,n} \\
+m_{1,n} \cdot t_{p,n} + m_{2,n} \cdot (t_n - t_{p,n}), &amp; \text{if } t_{p,n} \leq t_n \leq t_{s,n} \\
+m_{1,n} \cdot t_{p,n} + m_{2,n} \cdot (t_{s,n} - t_{p,n}) + m_{3,n} \cdot (t_n - t_{s,n}), &amp; \text{if } t_n &gt; t_{s,n}
+\end{cases}
+</annotation></semantics></math></p>
+<p>where:</p>
+<ul>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>t</mi><mrow><mn>0</mn><mo>,</mo><mi>n</mi></mrow></msub><annotation encoding="application/x-tex">t_{0,n}</annotation></semantics></math>:
+Baseline titre level for individual
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>n</mi><annotation encoding="application/x-tex">n</annotation></semantics></math>
+and titre type
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>k</mi><annotation encoding="application/x-tex">k</annotation></semantics></math>.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub><annotation encoding="application/x-tex">t_{p,n}</annotation></semantics></math>:
+Time to peak titre for individual
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>n</mi><annotation encoding="application/x-tex">n</annotation></semantics></math>
+and titre type
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>k</mi><annotation encoding="application/x-tex">k</annotation></semantics></math>.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>t</mi><mrow><mi>s</mi><mo>,</mo><mi>n</mi></mrow></msub><annotation encoding="application/x-tex">t_{s,n}</annotation></semantics></math>:
+Time to start of waning for individual
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>n</mi><annotation encoding="application/x-tex">n</annotation></semantics></math>
+and titre type
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>k</mi><annotation encoding="application/x-tex">k</annotation></semantics></math>.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>m</mi><mrow><mn>1</mn><mo>,</mo><mi>n</mi></mrow></msub><annotation encoding="application/x-tex">m_{1,n}</annotation></semantics></math>:
+Boosting rate for individual
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>n</mi><annotation encoding="application/x-tex">n</annotation></semantics></math>
+and titre type
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>k</mi><annotation encoding="application/x-tex">k</annotation></semantics></math>.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>m</mi><mrow><mn>2</mn><mo>,</mo><mi>n</mi></mrow></msub><annotation encoding="application/x-tex">m_{2,n}</annotation></semantics></math>:
+Plateau rate (assumed to be zero in this model).</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>m</mi><mrow><mn>3</mn><mo>,</mo><mi>n</mi></mrow></msub><annotation encoding="application/x-tex">m_{3,n}</annotation></semantics></math>:
+Waning rate for individual
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>n</mi><annotation encoding="application/x-tex">n</annotation></semantics></math>
+and titre type
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>k</mi><annotation encoding="application/x-tex">k</annotation></semantics></math>.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>t</mi><mi>n</mi></msub><annotation encoding="application/x-tex">t_n</annotation></semantics></math>:
+Observation time for individual
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>n</mi><annotation encoding="application/x-tex">n</annotation></semantics></math>.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>μ</mi><mi>n</mi></msub><mo>≥</mo><mn>0</mn></mrow><annotation encoding="application/x-tex">\mu_{n} \geq 0</annotation></semantics></math>:
+Ensured by taking the maximum with zero.</li>
+</ul>
+</div>
+<div class="section level4">
+<h4 id="observation-model">Observation Model<a class="anchor" aria-label="anchor" href="#observation-model"></a>
+</h4>
+<p>The observed log-transformed titre values
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>y</mi><mi>n</mi></msub><annotation encoding="application/x-tex">y_n</annotation></semantics></math>
+are modeled as:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>y</mi><mi>n</mi></msub><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>μ</mi><mi>n</mi></msub><mo>,</mo><mi>σ</mi><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">
+y_n \sim \text{Normal}(\mu_{n}, \sigma)
+</annotation></semantics></math></p>
+<p>where
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>σ</mi><annotation encoding="application/x-tex">\sigma</annotation></semantics></math>
+is the measurement error standard deviation.</p>
+</div>
+<div class="section level4">
+<h4 id="censoring">Censoring<a class="anchor" aria-label="anchor" href="#censoring"></a>
+</h4>
+<p>The model accounts for left-censoring and right-censoring:</p>
+<ul>
+<li>
+<p><strong>Left-Censoring</strong>: For observations below detection
+limit
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>L</mi><annotation encoding="application/x-tex">L</annotation></semantics></math>,
+the likelihood contribution is:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>y</mi><mi>n</mi></msub><mo>≤</mo><mi>L</mi><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mi>Φ</mi><mrow><mo stretchy="true" form="prefix">(</mo><mfrac displaystyle="true"><mrow><mi>L</mi><mo>−</mo><msub><mi>μ</mi><mi>n</mi></msub></mrow><mi>σ</mi></mfrac><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">
+P(y_n \leq L) = \Phi\left(\dfrac{L - \mu_{n}}{\sigma}\right)
+</annotation></semantics></math></p>
+</li>
+<li>
+<p><strong>Right-Censoring</strong>: For observations above
+detection limit
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>U</mi><annotation encoding="application/x-tex">U</annotation></semantics></math>,
+the likelihood contribution is:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>y</mi><mi>n</mi></msub><mo>≥</mo><mi>U</mi><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mn>1</mn><mo>−</mo><mi>Φ</mi><mrow><mo stretchy="true" form="prefix">(</mo><mfrac displaystyle="true"><mrow><mi>U</mi><mo>−</mo><msub><mi>μ</mi><mi>n</mi></msub></mrow><mi>σ</mi></mfrac><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">
+P(y_n \geq U) = 1 - \Phi\left(\dfrac{U - \mu_{n}}{\sigma}\right)
+</annotation></semantics></math></p>
+</li>
+</ul>
+<p>where
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>Φ</mi><mrow><mo stretchy="true" form="prefix">(</mo><mo>⋅</mo><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\Phi(\cdot)</annotation></semantics></math>
+is the cumulative distribution function of the standard normal
+distribution.</p>
+</div>
+</div>
+<div class="section level3">
+<h3 id="hierarchical-structure">Hierarchical Structure<a class="anchor" aria-label="anchor" href="#hierarchical-structure"></a>
+</h3>
+<div class="section level4">
+<h4 id="individual-level-parameters">Individual-Level Parameters<a class="anchor" aria-label="anchor" href="#individual-level-parameters"></a>
+</h4>
+<p>For each individual
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>n</mi><annotation encoding="application/x-tex">n</annotation></semantics></math>
+and titre type
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>k</mi><annotation encoding="application/x-tex">k</annotation></semantics></math>,
+the parameters are modeled as:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right" style="text-align: right"><msub><mi>t</mi><mrow><mn>0</mn><mo>,</mo><mi>n</mi></mrow></msub></mtd><mtd columnalign="left" style="text-align: left"><mo>=</mo><msub><mi>t</mi><mrow><mn>0</mn><mo>,</mo><mi>k</mi></mrow></msub><mo>+</mo><msubsup><mi>𝐱</mi><mi>n</mi><mi>⊤</mi></msubsup><msub><mi>𝛃</mi><msub><mi>t</mi><mn>0</mn></msub></msub><mo>+</mo><msub><mi>σ</mi><mrow><msub><mi>t</mi><mn>0</mn></msub><mo>,</mo><mi>k</mi></mrow></msub><mo>⋅</mo><msub><mi>z</mi><mrow><msub><mi>t</mi><mn>0</mn></msub><mo>,</mo><mi>n</mi></mrow></msub></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub></mtd><mtd columnalign="left" style="text-align: left"><mo>=</mo><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>k</mi></mrow></msub><mo>+</mo><msubsup><mi>𝐱</mi><mi>n</mi><mi>⊤</mi></msubsup><msub><mi>𝛃</mi><msub><mi>t</mi><mi>p</mi></msub></msub><mo>+</mo><msub><mi>σ</mi><mrow><msub><mi>t</mi><mi>p</mi></msub><mo>,</mo><mi>k</mi></mrow></msub><mo>⋅</mo><msub><mi>z</mi><mrow><msub><mi>t</mi><mi>p</mi></msub><mo>,</mo><mi>n</mi></mrow></msub></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"><msub><mi>t</mi><mrow><mi>s</mi><mo>,</mo><mi>n</mi></mrow></msub></mtd><mtd columnalign="left" style="text-align: left"><mo>=</mo><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>n</mi></mrow></msub><mo>+</mo><mi>Δ</mi><msub><mi>t</mi><mrow><mi>s</mi><mo>,</mo><mi>k</mi></mrow></msub><mo>+</mo><msubsup><mi>𝐱</mi><mi>n</mi><mi>⊤</mi></msubsup><msub><mi>𝛃</mi><msub><mi>t</mi><mi>s</mi></msub></msub><mo>+</mo><msub><mi>σ</mi><mrow><msub><mi>t</mi><mi>s</mi></msub><mo>,</mo><mi>k</mi></mrow></msub><mo>⋅</mo><msub><mi>z</mi><mrow><msub><mi>t</mi><mi>s</mi></msub><mo>,</mo><mi>n</mi></mrow></msub></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"><msub><mi>m</mi><mrow><mn>1</mn><mo>,</mo><mi>n</mi></mrow></msub></mtd><mtd columnalign="left" style="text-align: left"><mo>=</mo><msub><mi>m</mi><mrow><mn>1</mn><mo>,</mo><mi>k</mi></mrow></msub><mo>+</mo><msubsup><mi>𝐱</mi><mi>n</mi><mi>⊤</mi></msubsup><msub><mi>𝛃</mi><msub><mi>m</mi><mn>1</mn></msub></msub><mo>+</mo><msub><mi>σ</mi><mrow><msub><mi>m</mi><mn>1</mn></msub><mo>,</mo><mi>k</mi></mrow></msub><mo>⋅</mo><msub><mi>z</mi><mrow><msub><mi>m</mi><mn>1</mn></msub><mo>,</mo><mi>n</mi></mrow></msub></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"><msub><mi>m</mi><mrow><mn>2</mn><mo>,</mo><mi>n</mi></mrow></msub></mtd><mtd columnalign="left" style="text-align: left"><mo>=</mo><msub><mi>m</mi><mrow><mn>2</mn><mo>,</mo><mi>k</mi></mrow></msub><mo>+</mo><msubsup><mi>𝐱</mi><mi>n</mi><mi>⊤</mi></msubsup><msub><mi>𝛃</mi><msub><mi>m</mi><mn>2</mn></msub></msub><mo>+</mo><msub><mi>σ</mi><mrow><msub><mi>m</mi><mn>2</mn></msub><mo>,</mo><mi>k</mi></mrow></msub><mo>⋅</mo><msub><mi>z</mi><mrow><msub><mi>m</mi><mn>2</mn></msub><mo>,</mo><mi>n</mi></mrow></msub></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"><msub><mi>m</mi><mrow><mn>3</mn><mo>,</mo><mi>n</mi></mrow></msub></mtd><mtd columnalign="left" style="text-align: left"><mo>=</mo><msub><mi>m</mi><mrow><mn>3</mn><mo>,</mo><mi>k</mi></mrow></msub><mo>+</mo><msubsup><mi>𝐱</mi><mi>n</mi><mi>⊤</mi></msubsup><msub><mi>𝛃</mi><msub><mi>m</mi><mn>3</mn></msub></msub><mo>+</mo><msub><mi>σ</mi><mrow><msub><mi>m</mi><mn>3</mn></msub><mo>,</mo><mi>k</mi></mrow></msub><mo>⋅</mo><msub><mi>z</mi><mrow><msub><mi>m</mi><mn>3</mn></msub><mo>,</mo><mi>n</mi></mrow></msub></mtd></mtr></mtable><annotation encoding="application/x-tex">
+\begin{aligned}
+t_{0,n} &amp;= t_{0,k} + \mathbf{x}_n^\top \boldsymbol{\beta}_{t_0} + \sigma_{t_0,k} \cdot z_{t_0,n} \\
+t_{p,n} &amp;= t_{p,k} + \mathbf{x}_n^\top \boldsymbol{\beta}_{t_p} + \sigma_{t_p,k} \cdot z_{t_p,n} \\
+t_{s,n} &amp;= t_{p,n} + \Delta t_{s,k} + \mathbf{x}_n^\top \boldsymbol{\beta}_{t_s} + \sigma_{t_s,k} \cdot z_{t_s,n} \\
+m_{1,n} &amp;= m_{1,k} + \mathbf{x}_n^\top \boldsymbol{\beta}_{m_1} + \sigma_{m_1,k} \cdot z_{m_1,n} \\
+m_{2,n} &amp;= m_{2,k} + \mathbf{x}_n^\top \boldsymbol{\beta}_{m_2} + \sigma_{m_2,k} \cdot z_{m_2,n} \\
+m_{3,n} &amp;= m_{3,k} + \mathbf{x}_n^\top \boldsymbol{\beta}_{m_3} + \sigma_{m_3,k} \cdot z_{m_3,n}
+\end{aligned}
+</annotation></semantics></math></p>
+<p>where:</p>
+<ul>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>𝐱</mi><mi>n</mi></msub><annotation encoding="application/x-tex">\mathbf{x}_n</annotation></semantics></math>:
+Covariate vector for individual
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>n</mi><annotation encoding="application/x-tex">n</annotation></semantics></math>.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>𝛃</mi><mo>⋅</mo></msub><annotation encoding="application/x-tex">\boldsymbol{\beta}_{\cdot}</annotation></semantics></math>:
+Regression coefficients for the corresponding parameter.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>σ</mi><mrow><mo>⋅</mo><mo>,</mo><mi>k</mi></mrow></msub><annotation encoding="application/x-tex">\sigma_{\cdot,k}</annotation></semantics></math>:
+Standard deviation of individual-level random effects for titre type
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>k</mi><annotation encoding="application/x-tex">k</annotation></semantics></math>.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>z</mi><mrow><mo>⋅</mo><mo>,</mo><mi>n</mi></mrow></msub><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><mn>0</mn><mo>,</mo><mn>1</mn><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">z_{\cdot,n} \sim \text{Normal}(0, 1)</annotation></semantics></math>:
+Standard normal random variables.</li>
+</ul>
+</div>
+<div class="section level4">
+<h4 id="population-level-parameters">Population-Level Parameters<a class="anchor" aria-label="anchor" href="#population-level-parameters"></a>
+</h4>
+<p>The population-level parameters for each titre type
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>k</mi><annotation encoding="application/x-tex">k</annotation></semantics></math>
+have the following priors:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right" style="text-align: right"><msubsup><mi>T</mi><mn>0</mn><mrow><mi>p</mi><mo>,</mo><mi>k</mi></mrow></msubsup></mtd><mtd columnalign="left" style="text-align: left"><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>μ</mi><msub><mi>t</mi><mn>0</mn></msub></msub><mo>,</mo><msub><mi>σ</mi><msub><mi>t</mi><mn>0</mn></msub></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"><msubsup><mi>t</mi><mi>p</mi><mrow><mi>p</mi><mo>,</mo><mi>k</mi></mrow></msubsup></mtd><mtd columnalign="left" style="text-align: left"><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>μ</mi><msub><mi>t</mi><mi>p</mi></msub></msub><mo>,</mo><msub><mi>σ</mi><msub><mi>t</mi><mi>p</mi></msub></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"><mi>Δ</mi><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>k</mi></mrow></msub></mtd><mtd columnalign="left" style="text-align: left"><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>μ</mi><msub><mi>t</mi><mi>s</mi></msub></msub><mo>−</mo><msub><mi>μ</mi><msub><mi>t</mi><mi>p</mi></msub></msub><mo>,</mo><msub><mi>σ</mi><msub><mi>t</mi><mi>s</mi></msub></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"><msubsup><mi>m</mi><mn>1</mn><mrow><mi>p</mi><mo>,</mo><mi>k</mi></mrow></msubsup></mtd><mtd columnalign="left" style="text-align: left"><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>μ</mi><msub><mi>m</mi><mn>1</mn></msub></msub><mo>,</mo><msub><mi>σ</mi><msub><mi>m</mi><mn>1</mn></msub></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"><msubsup><mi>m</mi><mn>2</mn><mrow><mi>p</mi><mo>,</mo><mi>k</mi></mrow></msubsup></mtd><mtd columnalign="left" style="text-align: left"><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>μ</mi><msub><mi>m</mi><mn>2</mn></msub></msub><mo>,</mo><msub><mi>σ</mi><msub><mi>m</mi><mn>2</mn></msub></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"><msubsup><mi>m</mi><mn>3</mn><mrow><mi>p</mi><mo>,</mo><mi>k</mi></mrow></msubsup></mtd><mtd columnalign="left" style="text-align: left"><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>μ</mi><msub><mi>m</mi><mn>3</mn></msub></msub><mo>,</mo><msub><mi>σ</mi><msub><mi>m</mi><mn>3</mn></msub></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr></mtable><annotation encoding="application/x-tex">
+\begin{aligned}
+T_0^{p,k} &amp;\sim \text{Normal}(\mu_{t_0}, \sigma_{t_0}) \\
+t_p^{p,k} &amp;\sim \text{Normal}(\mu_{t_p}, \sigma_{t_p}) \\
+\Delta t_{p,k} &amp;\sim \text{Normal}(\mu_{t_s} - \mu_{t_p}, \sigma_{t_s}) \\
+m_1^{p,k} &amp;\sim \text{Normal}(\mu_{m_1}, \sigma_{m_1}) \\
+m_2^{p,k} &amp;\sim \text{Normal}(\mu_{m_2}, \sigma_{m_2}) \\
+m_3^{p,k} &amp;\sim \text{Normal}(\mu_{m_3}, \sigma_{m_3})
+\end{aligned}
+</annotation></semantics></math></p>
+<p>The standard deviations of the individual-level random effects have
+priors:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>σ</mi><mi>k</mi></msub><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><mn>0</mn><mo>,</mo><msub><mi>σ</mi><mi>p</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">
+\sigma_{k} \sim \text{Normal}(0, \sigma_{p})
+</annotation></semantics></math></p>
+</div>
+<div class="section level4">
+<h4 id="regression-coefficients">Regression Coefficients<a class="anchor" aria-label="anchor" href="#regression-coefficients"></a>
+</h4>
+<p>The regression coefficients have the following priors:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>𝛃</mi><mo>⋅</mo></msub><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><mn>𝟎</mn><mo>,</mo><msub><mi>σ</mi><msub><mi>β</mi><mo>⋅</mo></msub></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">
+\boldsymbol{\beta}_{\cdot} \sim \text{Normal}(\mathbf{0}, \sigma_{\beta_{\cdot}})
+</annotation></semantics></math></p>
+<p>with appropriate constraints for parameters that must be positive or
+negative.</p>
+</div>
+</div>
+</div>
+<div class="section level2">
+<h2 id="data-and-parameters">Data and Parameters<a class="anchor" aria-label="anchor" href="#data-and-parameters"></a>
+</h2>
+<div class="section level3">
+<h3 id="data-inputs">Data Inputs<a class="anchor" aria-label="anchor" href="#data-inputs"></a>
+</h3>
+<ul>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>N</mi><annotation encoding="application/x-tex">N</annotation></semantics></math>:
+Total number of observations.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>K</mi><annotation encoding="application/x-tex">K</annotation></semantics></math>:
+Number of titre types.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>t</mi><mi>n</mi></msub><annotation encoding="application/x-tex">t_n</annotation></semantics></math>:
+Observation times.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>y</mi><mi>n</mi></msub><annotation encoding="application/x-tex">y_n</annotation></semantics></math>:
+Observed log-transformed titre values.</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>𝐱</mi><mi>n</mi></msub><annotation encoding="application/x-tex">\mathbf{x}_n</annotation></semantics></math>:
+Covariate vector for each individual.</li>
+<li>Censoring indicators for left and right censoring.</li>
+</ul>
+</div>
+<div class="section level3">
+<h3 id="parameters-to-estimate">Parameters to Estimate<a class="anchor" aria-label="anchor" href="#parameters-to-estimate"></a>
+</h3>
+<ul>
+<li>Population-level parameters:
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>t</mi><mrow><mn>0</mn><mo>,</mo><mi>k</mi></mrow></msub><annotation encoding="application/x-tex">t_{0,k}</annotation></semantics></math>,
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>t</mi><mrow><mi>p</mi><mo>,</mo><mi>k</mi></mrow></msub><annotation encoding="application/x-tex">t_{p,k}</annotation></semantics></math>,
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>Δ</mi><msub><mi>t</mi><mrow><mi>s</mi><mo>,</mo><mi>k</mi></mrow></msub></mrow><annotation encoding="application/x-tex">\Delta t_{s,k}</annotation></semantics></math>,
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>m</mi><mrow><mn>1</mn><mo>,</mo><mi>k</mi></mrow></msub><annotation encoding="application/x-tex">m_{1,k}</annotation></semantics></math>,
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>m</mi><mrow><mn>2</mn><mo>,</mo><mi>k</mi></mrow></msub><annotation encoding="application/x-tex">m_{2,k}</annotation></semantics></math>,
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>m</mi><mrow><mn>3</mn><mo>,</mo><mi>k</mi></mrow></msub><annotation encoding="application/x-tex">m_{3,k}</annotation></semantics></math>.</li>
+<li>Individual-level random effects:
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>z</mi><mrow><mo>⋅</mo><mo>,</mo><mi>n</mi></mrow></msub><annotation encoding="application/x-tex">z_{\cdot,n}</annotation></semantics></math>.</li>
+<li>Regression coefficients:
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>𝛃</mi><mo>⋅</mo></msub><annotation encoding="application/x-tex">\boldsymbol{\beta}_{\cdot}</annotation></semantics></math>.</li>
+<li>Measurement error standard deviation:
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>σ</mi><annotation encoding="application/x-tex">\sigma</annotation></semantics></math>.</li>
+</ul>
+</div>
+</div>
+<div class="section level2">
+<h2 id="priors">Priors<a class="anchor" aria-label="anchor" href="#priors"></a>
+</h2>
+<p>The prior distributions are specified based on previous studies and
+domain knowledge:</p>
+<ul>
+<li>
+<strong>Population Means</strong>: Specified using normal
+distributions with means
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>μ</mi><mo>⋅</mo></msub><annotation encoding="application/x-tex">\mu_{\cdot}</annotation></semantics></math>
+and standard deviations
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>σ</mi><mo>⋅</mo></msub><annotation encoding="application/x-tex">\sigma_{\cdot}</annotation></semantics></math>.</li>
+<li>
+<strong>Random Effect Standard Deviations</strong>: Weakly
+informative normal priors centered at zero.</li>
+<li>
+<strong>Regression Coefficients</strong>: Weakly informative normal
+priors centered at zero.</li>
+<li>
+<strong>Measurement Error</strong>:
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>σ</mi><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><mn>0</mn><mo>,</mo><mn>2</mn><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\sigma \sim \text{Normal}(0, 2)</annotation></semantics></math>,
+constrained to be positive.</li>
+</ul>
+</div>
+<div class="section level2">
+<h2 id="likelihood">Likelihood<a class="anchor" aria-label="anchor" href="#likelihood"></a>
+</h2>
+<p>The likelihood function combines the observation model with the
+censoring mechanisms:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right" style="text-align: right"></mtd><mtd columnalign="left" style="text-align: left"><mtext mathvariant="normal">For uncensored observations:</mtext><mspace width="1.0em"></mspace><msub><mi>y</mi><mi>n</mi></msub><mo>∼</mo><mtext mathvariant="normal">Normal</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>μ</mi><mi>n</mi></msub><mo>,</mo><mi>σ</mi><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"></mtd><mtd columnalign="left" style="text-align: left"><mtext mathvariant="normal">For left-censored observations:</mtext><mspace width="1.0em"></mspace><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>y</mi><mi>n</mi></msub><mo>≤</mo><mi>L</mi><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mi>Φ</mi><mrow><mo stretchy="true" form="prefix">(</mo><mfrac displaystyle="true"><mrow><mi>L</mi><mo>−</mo><msub><mi>μ</mi><mi>n</mi></msub></mrow><mi>σ</mi></mfrac><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr><mtr><mtd columnalign="right" style="text-align: right"></mtd><mtd columnalign="left" style="text-align: left"><mtext mathvariant="normal">For right-censored observations:</mtext><mspace width="1.0em"></mspace><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>y</mi><mi>n</mi></msub><mo>≥</mo><mi>U</mi><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mn>1</mn><mo>−</mo><mi>Φ</mi><mrow><mo stretchy="true" form="prefix">(</mo><mfrac displaystyle="true"><mrow><mi>U</mi><mo>−</mo><msub><mi>μ</mi><mi>n</mi></msub></mrow><mi>σ</mi></mfrac><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr></mtable><annotation encoding="application/x-tex">
+\begin{aligned}
+&amp;\text{For uncensored observations:} \quad y_n \sim \text{Normal}(\mu_{n}, \sigma) \\
+&amp;\text{For left-censored observations:} \quad P(y_n \leq L) = \Phi\left(\dfrac{L - \mu_{n}}{\sigma}\right) \\
+&amp;\text{For right-censored observations:} \quad P(y_n \geq U) = 1 - \Phi\left(\dfrac{U - \mu_{n}}{\sigma}\right)
+\end{aligned}
+</annotation></semantics></math></p>
+</div>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/authors.html b/authors.html
index a19c9bb..3e3a222 100644
--- a/authors.html
+++ b/authors.html
@@ -38,7 +38,7 @@
       <a href="articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="articles/model.html">Model</a>
+      <a href="articles/model.html">Summary of the Stan Model</a>
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   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
diff --git a/index.html b/index.html
index bc1ea8d..a3f5342 100644
--- a/index.html
+++ b/index.html
@@ -56,7 +56,7 @@
       <a href="articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="articles/model.html">Model</a>
+      <a href="articles/model.html">Summary of the Stan Model</a>
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 </li>
diff --git a/pkgdown.yml b/pkgdown.yml
index d6d689b..727c43d 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,4 +5,4 @@ articles:
   biokinetics: biokinetics.html
   data: data.html
   model: model.html
-last_built: 2024-10-23T12:35Z
+last_built: 2024-10-24T14:34Z
diff --git a/reference/add_exposure_data.html b/reference/add_exposure_data.html
index 56afd23..0b915c7 100644
--- a/reference/add_exposure_data.html
+++ b/reference/add_exposure_data.html
@@ -40,7 +40,7 @@
       <a href="../articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="../articles/model.html">Model</a>
+      <a href="../articles/model.html">Summary of the Stan Model</a>
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diff --git a/reference/biokinetics.html b/reference/biokinetics.html
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@@ -39,7 +39,7 @@
       <a href="../articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="../articles/model.html">Model</a>
+      <a href="../articles/model.html">Summary of the Stan Model</a>
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diff --git a/reference/biokinetics_priors.html b/reference/biokinetics_priors.html
index f36b70e..9c08e18 100644
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+++ b/reference/biokinetics_priors.html
@@ -41,7 +41,7 @@
       <a href="../articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="../articles/model.html">Model</a>
+      <a href="../articles/model.html">Summary of the Stan Model</a>
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diff --git a/reference/convert_log2_scale_inverse.html b/reference/convert_log2_scale_inverse.html
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       <a href="../articles/data.html">A guide to model input and output data</a>
     </li>
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-      <a href="../articles/model.html">Model</a>
+      <a href="../articles/model.html">Summary of the Stan Model</a>
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diff --git a/reference/epikinetics-package.html b/reference/epikinetics-package.html
index c5b7a3b..b0915c9 100644
--- a/reference/epikinetics-package.html
+++ b/reference/epikinetics-package.html
@@ -38,7 +38,7 @@
       <a href="../articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="../articles/model.html">Model</a>
+      <a href="../articles/model.html">Summary of the Stan Model</a>
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diff --git a/reference/index.html b/reference/index.html
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+++ b/reference/index.html
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       <a href="../articles/data.html">A guide to model input and output data</a>
     </li>
     <li>
-      <a href="../articles/model.html">Model</a>
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