build based on 12a21c6

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-12-12T13:02:21","documenter_version":"1.8.0"}}
+{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2024-12-13T12:48:30","documenter_version":"1.8.0"}}

dev/developer/checklist/index.html

@@ -20,4 +20,4 @@
 
    Either of those should automatically publish a new version to the Julia registry.
  - Once registered, the `TagBot.yml` workflow should create a tag, and rebuild the documentation for this tag.
- - These steps can take quite a bit of time (1 hour or more), so don&#39;t be surprised if the new documentation takes a while to appear.</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../contributing/">« Contributing</a><a class="docs-footer-nextpage" href="../../release-notes/">Release notes »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Thursday 12 December 2024 13:02">Thursday 12 December 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ - These steps can take quite a bit of time (1 hour or more), so don&#39;t be surprised if the new documentation takes a while to appear.</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../contributing/">« Contributing</a><a class="docs-footer-nextpage" href="../../release-notes/">Release notes »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 13 December 2024 12:48">Friday 13 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/developer/contributing/index.html

@@ -7,4 +7,4 @@
 using Pkg: Pkg
 Pkg.activate(docs_dir)
 Pkg.develop(; path = pkg_dir)
-Pkg.instantiate()</code></pre><h4 id="Adding-a-new-Pluto-notebook"><a class="docs-heading-anchor" href="#Adding-a-new-Pluto-notebook">Adding a new Pluto notebook</a><a id="Adding-a-new-Pluto-notebook-1"></a><a class="docs-heading-anchor-permalink" href="#Adding-a-new-Pluto-notebook" title="Permalink"></a></h4><p>Adding a new <code>Pluto.jl</code> notebook to the <code>EpiAware</code> documentation is the same as adding any other file to the repository. However, in addition to following the guidelines for modifying an <a href="#modifying-an-existing-pluto-notebook">existing notebook</a>, please note that the new notebook is added to the set of notebook builds using <code>build</code> in the <code>EpiAware/docs/make.jl</code> file. This will generate an <code>.md</code> of the same name as the notebook which can be rendered when <code>makedocs</code> is run. For this document to be added to the overall documentation the path to the <code>.md</code> file must be added to the <code>Pages</code> array defined in <code>EpiAware/docs/pages.jl</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Overview</a><a class="docs-footer-nextpage" href="../checklist/">Release checklist »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Thursday 12 December 2024 13:02">Thursday 12 December 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+Pkg.instantiate()</code></pre><h4 id="Adding-a-new-Pluto-notebook"><a class="docs-heading-anchor" href="#Adding-a-new-Pluto-notebook">Adding a new Pluto notebook</a><a id="Adding-a-new-Pluto-notebook-1"></a><a class="docs-heading-anchor-permalink" href="#Adding-a-new-Pluto-notebook" title="Permalink"></a></h4><p>Adding a new <code>Pluto.jl</code> notebook to the <code>EpiAware</code> documentation is the same as adding any other file to the repository. However, in addition to following the guidelines for modifying an <a href="#modifying-an-existing-pluto-notebook">existing notebook</a>, please note that the new notebook is added to the set of notebook builds using <code>build</code> in the <code>EpiAware/docs/make.jl</code> file. This will generate an <code>.md</code> of the same name as the notebook which can be rendered when <code>makedocs</code> is run. For this document to be added to the overall documentation the path to the <code>.md</code> file must be added to the <code>Pages</code> array defined in <code>EpiAware/docs/pages.jl</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Overview</a><a class="docs-footer-nextpage" href="../checklist/">Release checklist »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 13 December 2024 12:48">Friday 13 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/getting-started/explainers/intro/index.html

@@ -60,4 +60,4 @@
 
 E-->|sample...NUTS...| G
 G-->H
-H--&gt;I</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../julia/">« Working with Julia</a><a class="docs-footer-nextpage" href="../modelling-infections/">Modelling infections »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Thursday 12 December 2024 13:02">Thursday 12 December 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+H--&gt;I</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../julia/">« Working with Julia</a><a class="docs-footer-nextpage" href="../modelling-infections/">Modelling infections »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 13 December 2024 12:48">Friday 13 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/getting-started/explainers/julia/index.html

@@ -36,4 +36,4 @@
     },
     "julia.liveTestFile": "path/to/runtests.jl",
     "julia.environmentPath": "path/to/project/directory",
-}</code></pre><p>These settings set basic code formatting and whitespace settings for Julia files, as well as setting the path to the test file for the project and the path to the project directory for the environment.</p><p>The <code>VS-Code</code> command <code>Julia: Start REPL</code> will start a REPL in <code>TERMINAL</code> tab in the editor with the environment set to the project directory and the <code>Testing</code> tab will detect the defined tests for the project.</p><h2 id="Literate-programming-with-Julia-in-EpiAware"><a class="docs-heading-anchor" href="#Literate-programming-with-Julia-in-EpiAware">Literate programming with Julia in EpiAware</a><a id="Literate-programming-with-Julia-in-EpiAware-1"></a><a class="docs-heading-anchor-permalink" href="#Literate-programming-with-Julia-in-EpiAware" title="Permalink"></a></h2><p>Its common to develop technical computing projects using a literate programming style, where code and documentation are interwoven. Julia supports this style of programming through a number of packages. In <code>EpiAware</code> we recommend the following:</p><ul><li><code>Pluto</code>: A native Julia notebook for interactive development. <code>Pluto</code> notebooks are reactive, meaning that the output of all cells are updated as input changes. Installation instructions are available <a href="https://github.com/fonsp/Pluto.jl">here</a>. Pluto notebook files have the extension <code>.jl</code> and can be run as scripts.</li><li><code>Quarto</code>: A literate programming tool that allows you to write documents in markdown with embedded Julia code. Installation instructions are available <a href="https://quarto.org/">here</a>. Quarto files have the extension <code>.qmd</code>.</li></ul><p>We use <code>Pluto</code> for interactive development and <code>Quarto</code> for generating reports and academic articles. Both tools are useful for developing reproducible workflows.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Overview</a><a class="docs-footer-nextpage" href="../intro/">Introduction to EpiAware »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Thursday 12 December 2024 13:02">Thursday 12 December 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+}</code></pre><p>These settings set basic code formatting and whitespace settings for Julia files, as well as setting the path to the test file for the project and the path to the project directory for the environment.</p><p>The <code>VS-Code</code> command <code>Julia: Start REPL</code> will start a REPL in <code>TERMINAL</code> tab in the editor with the environment set to the project directory and the <code>Testing</code> tab will detect the defined tests for the project.</p><h2 id="Literate-programming-with-Julia-in-EpiAware"><a class="docs-heading-anchor" href="#Literate-programming-with-Julia-in-EpiAware">Literate programming with Julia in EpiAware</a><a id="Literate-programming-with-Julia-in-EpiAware-1"></a><a class="docs-heading-anchor-permalink" href="#Literate-programming-with-Julia-in-EpiAware" title="Permalink"></a></h2><p>Its common to develop technical computing projects using a literate programming style, where code and documentation are interwoven. Julia supports this style of programming through a number of packages. In <code>EpiAware</code> we recommend the following:</p><ul><li><code>Pluto</code>: A native Julia notebook for interactive development. <code>Pluto</code> notebooks are reactive, meaning that the output of all cells are updated as input changes. Installation instructions are available <a href="https://github.com/fonsp/Pluto.jl">here</a>. Pluto notebook files have the extension <code>.jl</code> and can be run as scripts.</li><li><code>Quarto</code>: A literate programming tool that allows you to write documents in markdown with embedded Julia code. Installation instructions are available <a href="https://quarto.org/">here</a>. Quarto files have the extension <code>.qmd</code>.</li></ul><p>We use <code>Pluto</code> for interactive development and <code>Quarto</code> for generating reports and academic articles. Both tools are useful for developing reproducible workflows.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Overview</a><a class="docs-footer-nextpage" href="../intro/">Introduction to EpiAware »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 13 December 2024 12:48">Friday 13 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/getting-started/tutorials/censored-obs/index.html

@@ -26,7 +26,7 @@
     # This information is used for caching.
     [PlutoStaticHTML.State]
     input_sha = "d10cfdddd31856f03e3d18c39a1057f65a57ee55f2f1c35433996fc0734aca66"
-    julia_version = "1.11.1"
+    julia_version = "1.11.2"
 -->
 
 <div class="markdown"><h1>Fitting distributions using <code>EpiAware</code> and Turing PPL</h1><h2>Introduction</h2><h3>What are we going to do in this Vignette</h3><p>In this vignette, we'll demonstrate how to use the CDF function for censored delay distributions <code>EpiAwareUtils.∫F</code>, which underlies <code>EpiAwareUtils.censored_pmf</code> in conjunction with the Turing PPL for Bayesian inference of epidemiological delay distributions. We'll cover the following key points:</p><ol><li><p>Simulating censored delay distribution data</p></li><li><p>Fitting a naive model using Turing</p></li><li><p>Evaluating the naive model's performance</p></li><li><p>Fitting an improved model using censored delay functionality from <code>EpiAware</code>.</p></li><li><p>Comparing the censored delay model's performance to the naive model</p></li></ol><h3>What might I need to know before starting</h3><p>This note builds on the concepts introduced in the R/stan package <a href="https://github.com/epinowcast/primarycensoreddist"><code>primarycensoreddist</code></a>, especially the <a href="https://primarycensoreddist.epinowcast.org/articles/fitting-dists-with-stan.html">Fitting distributions using primarycensorseddist and cmdstan</a> vignette and assumes familiarity with using Turing tools as covered in the <a href="https://turinglang.org/">Turing documentation</a>.</p><p>This note is generated using the <code>EpiAware</code> package locally via <code>Pkg.develop</code>, in the <code>EpiAware/docs</code> environment. It is also possible to install <code>EpiAware</code> using</p><pre><code class="language-julia">Pkg.add(url="https://github.com/CDCgov/Rt-without-renewal", subdir="EpiAware")</code></pre><h3>Packages used in this vignette</h3><p>As well as <code>EpiAware</code> and <code>Turing</code> we will use <code>Makie</code> ecosystem packages for plotting and <code>DataFramesMeta</code> for data manipulation.</p></div>
@@ -274,7 +274,7 @@ <h2 id="Fitting-a-naive-model-using-Turing"><a class="docs-heading-anchor" href=
 <table><tbody><tr><th></th><th>iteration</th><th>chain</th><th>mu</th><th>sigma</th><th>lp</th><th>n_steps</th><th>is_accept</th><th>acceptance_rate</th><th>...</th></tr><tr><td>1</td><td>251</td><td>1</td><td>0.569828</td><td>3.16687</td><td>-6326.42</td><td>3.0</td><td>1.0</td><td>0.889234</td><td></td></tr><tr><td>2</td><td>252</td><td>1</td><td>0.51554</td><td>3.21602</td><td>-6327.17</td><td>3.0</td><td>1.0</td><td>0.748919</td><td></td></tr><tr><td>3</td><td>253</td><td>1</td><td>0.699124</td><td>3.15787</td><td>-6327.72</td><td>7.0</td><td>1.0</td><td>0.895135</td><td></td></tr><tr><td>4</td><td>254</td><td>1</td><td>0.523035</td><td>3.16482</td><td>-6326.8</td><td>3.0</td><td>1.0</td><td>0.728358</td><td></td></tr><tr><td>5</td><td>255</td><td>1</td><td>0.497583</td><td>3.17839</td><td>-6327.16</td><td>3.0</td><td>1.0</td><td>0.840027</td><td></td></tr><tr><td>6</td><td>256</td><td>1</td><td>0.548956</td><td>3.15474</td><td>-6326.61</td><td>3.0</td><td>1.0</td><td>0.792753</td><td></td></tr><tr><td>7</td><td>257</td><td>1</td><td>0.569335</td><td>3.16453</td><td>-6326.43</td><td>3.0</td><td>1.0</td><td>1.0</td><td></td></tr><tr><td>8</td><td>258</td><td>1</td><td>0.606234</td><td>3.2018</td><td>-6326.53</td><td>3.0</td><td>1.0</td><td>0.977859</td><td></td></tr><tr><td>9</td><td>259</td><td>1</td><td>0.530658</td><td>3.17006</td><td>-6326.69</td><td>3.0</td><td>1.0</td><td>0.900204</td><td></td></tr><tr><td>10</td><td>260</td><td>1</td><td>0.627117</td><td>3.11173</td><td>-6327.41</td><td>7.0</td><td>1.0</td><td>0.761508</td><td></td></tr><tr><td>...</td></tr></tbody></table>
 
 <pre class='language-julia'><code class='language-julia'>summarize(naive_fit)</code></pre>
-<table><tbody><tr><th></th><th>parameters</th><th>mean</th><th>std</th><th>mcse</th><th>ess_bulk</th><th>ess_tail</th><th>rhat</th><th>ess_per_sec</th></tr><tr><td>1</td><td>:mu</td><td>0.584129</td><td>0.0704067</td><td>0.00151449</td><td>2153.02</td><td>1487.54</td><td>1.00003</td><td>332.873</td></tr><tr><td>2</td><td>:sigma</td><td>3.17766</td><td>0.0495775</td><td>0.00113542</td><td>1905.04</td><td>1306.94</td><td>1.00127</td><td>294.533</td></tr></tbody></table>
+<table><tbody><tr><th></th><th>parameters</th><th>mean</th><th>std</th><th>mcse</th><th>ess_bulk</th><th>ess_tail</th><th>rhat</th><th>ess_per_sec</th></tr><tr><td>1</td><td>:mu</td><td>0.584129</td><td>0.0704067</td><td>0.00151449</td><td>2153.02</td><td>1487.54</td><td>1.00003</td><td>330.98</td></tr><tr><td>2</td><td>:sigma</td><td>3.17766</td><td>0.0495775</td><td>0.00113542</td><td>1905.04</td><td>1306.94</td><td>1.00127</td><td>292.858</td></tr></tbody></table>
 
 <pre class='language-julia'><code class='language-julia'>let
     f = pairplot(naive_fit)
@@ -335,7 +335,7 @@ <h2 id="Fitting-an-improved-model-using-censoring-utilities"><a class="docs-head
 <table><tbody><tr><th></th><th>iteration</th><th>chain</th><th>mu</th><th>sigma</th><th>lp</th><th>n_steps</th><th>is_accept</th><th>acceptance_rate</th><th>...</th></tr><tr><td>1</td><td>501</td><td>1</td><td>1.46819</td><td>0.771804</td><td>-3376.41</td><td>3.0</td><td>1.0</td><td>1.0</td><td></td></tr><tr><td>2</td><td>502</td><td>1</td><td>1.46877</td><td>0.738944</td><td>-3375.1</td><td>3.0</td><td>1.0</td><td>0.999202</td><td></td></tr><tr><td>3</td><td>503</td><td>1</td><td>1.49735</td><td>0.740651</td><td>-3376.39</td><td>3.0</td><td>1.0</td><td>0.741842</td><td></td></tr><tr><td>4</td><td>504</td><td>1</td><td>1.47618</td><td>0.762895</td><td>-3375.61</td><td>3.0</td><td>1.0</td><td>0.983406</td><td></td></tr><tr><td>5</td><td>505</td><td>1</td><td>1.48132</td><td>0.74067</td><td>-3375.47</td><td>3.0</td><td>1.0</td><td>0.852127</td><td></td></tr><tr><td>6</td><td>506</td><td>1</td><td>1.40746</td><td>0.711968</td><td>-3375.63</td><td>7.0</td><td>1.0</td><td>0.914995</td><td></td></tr><tr><td>7</td><td>507</td><td>1</td><td>1.44329</td><td>0.747661</td><td>-3375.55</td><td>7.0</td><td>1.0</td><td>0.89498</td><td></td></tr><tr><td>8</td><td>508</td><td>1</td><td>1.43568</td><td>0.734698</td><td>-3375.17</td><td>3.0</td><td>1.0</td><td>0.977821</td><td></td></tr><tr><td>9</td><td>509</td><td>1</td><td>1.42456</td><td>0.696408</td><td>-3375.79</td><td>3.0</td><td>1.0</td><td>0.941795</td><td></td></tr><tr><td>10</td><td>510</td><td>1</td><td>1.46966</td><td>0.758485</td><td>-3375.46</td><td>5.0</td><td>1.0</td><td>1.0</td><td></td></tr><tr><td>...</td></tr></tbody></table>
 
 <pre class='language-julia'><code class='language-julia'>summarize(primarycensoreddist_fit)</code></pre>
-<table><tbody><tr><th></th><th>parameters</th><th>mean</th><th>std</th><th>mcse</th><th>ess_bulk</th><th>ess_tail</th><th>rhat</th><th>ess_per_sec</th></tr><tr><td>1</td><td>:mu</td><td>1.45168</td><td>0.0355514</td><td>0.00108636</td><td>1087.88</td><td>1420.31</td><td>1.00169</td><td>61.2306</td></tr><tr><td>2</td><td>:sigma</td><td>0.733008</td><td>0.0274925</td><td>0.00082729</td><td>1110.27</td><td>1643.86</td><td>1.00173</td><td>62.4903</td></tr></tbody></table>
+<table><tbody><tr><th></th><th>parameters</th><th>mean</th><th>std</th><th>mcse</th><th>ess_bulk</th><th>ess_tail</th><th>rhat</th><th>ess_per_sec</th></tr><tr><td>1</td><td>:mu</td><td>1.45168</td><td>0.0355514</td><td>0.00108636</td><td>1087.88</td><td>1420.31</td><td>1.00169</td><td>61.3964</td></tr><tr><td>2</td><td>:sigma</td><td>0.733008</td><td>0.0274925</td><td>0.00082729</td><td>1110.27</td><td>1643.86</td><td>1.00173</td><td>62.6596</td></tr></tbody></table>
 
 <pre class='language-julia'><code class='language-julia'>let
     f = pairplot(primarycensoreddist_fit)
@@ -348,4 +348,4 @@ <h2 id="Fitting-an-improved-model-using-censoring-utilities"><a class="docs-head
 
 <div class="markdown"><p>We see that the model has converged and the diagnostics look good. We also see that the posterior means are very near the true parameters and the 90% credible intervals include the true parameters.</p></div>
 
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