build based on 25ff554

TuringLang · Aug 23, 2024 · afab9d8 · afab9d8
1 parent d0fb274
commit afab9d8
Show file tree

Hide file tree

Showing 7 changed files with 16 additions and 16 deletions.
diff --git a/previews/PR144/.documenter-siteinfo.json b/previews/PR144/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-23T12:54:32","documenter_version":"1.6.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-23T12:55:46","documenter_version":"1.6.0"}}
diff --git a/previews/PR144/api/index.html b/previews/PR144/api/index.html
diff --git a/previews/PR144/design/index.html b/previews/PR144/design/index.html
diff --git a/previews/PR144/gibbs/index.html b/previews/PR144/gibbs/index.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>state Interface · AbstractMCMC</title><meta name="title" content="state Interface · AbstractMCMC"/><meta property="og:title" content="state Interface · AbstractMCMC"/><meta property="twitter:title" content="state Interface · AbstractMCMC"/><meta name="description" content="Documentation for AbstractMCMC."/><meta property="og:description" content="Documentation for AbstractMCMC."/><meta property="twitter:description" content="Documentation for AbstractMCMC."/><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../search_index.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">AbstractMCMC</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><a class="tocitem" href="../api/">API</a></li><li><a class="tocitem" href="../design/">Design</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href><code>state</code> Interface</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href><code>state</code> Interface</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/TuringLang/AbstractMCMC.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/TuringLang/AbstractMCMC.jl/blob/master/docs/src/gibbs.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="state-Interface"><a class="docs-heading-anchor" href="#state-Interface"><code>state</code> Interface</a><a id="state-Interface-1"></a><a class="docs-heading-anchor-permalink" href="#state-Interface" title="Permalink"></a></h1><p>We encourage sampler packages to implement the following interface functions for the <code>state</code> type(s) they maintain:</p><pre><code class="language- hljs">get_logprob
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>state Interface Functions · AbstractMCMC</title><meta name="title" content="state Interface Functions · AbstractMCMC"/><meta property="og:title" content="state Interface Functions · AbstractMCMC"/><meta property="twitter:title" content="state Interface Functions · AbstractMCMC"/><meta name="description" content="Documentation for AbstractMCMC."/><meta property="og:description" content="Documentation for AbstractMCMC."/><meta property="twitter:description" content="Documentation for AbstractMCMC."/><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../search_index.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">AbstractMCMC</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><a class="tocitem" href="../api/">API</a></li><li><a class="tocitem" href="../design/">Design</a></li><li class="is-active"><a class="tocitem" href><code>state</code> Interface Functions</a><ul class="internal"><li><a class="tocitem" href="#Using-the-state-Interface-for-block-sampling-within-Gibbs"><span>Using the <code>state</code> Interface for block sampling within Gibbs</span></a></li><li><a class="tocitem" href="#Sampler-Packages"><span>Sampler Packages</span></a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href><code>state</code> Interface Functions</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href><code>state</code> Interface Functions</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/TuringLang/AbstractMCMC.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/TuringLang/AbstractMCMC.jl/blob/master/docs/src/gibbs.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="state-Interface-Functions"><a class="docs-heading-anchor" href="#state-Interface-Functions"><code>state</code> Interface Functions</a><a id="state-Interface-Functions-1"></a><a class="docs-heading-anchor-permalink" href="#state-Interface-Functions" title="Permalink"></a></h1><p>We encourage sampler packages to implement the following interface functions for the <code>state</code> type(s) they maintain:</p><pre><code class="language- hljs">get_logprob
 set_logprob!!
 get_params
 set_params!!</code></pre><p>These function will provide a minimum interface to interact with the <code>state</code> datatype, which a sampler package doesn&#39;t have to expose.</p><h2 id="Using-the-state-Interface-for-block-sampling-within-Gibbs"><a class="docs-heading-anchor" href="#Using-the-state-Interface-for-block-sampling-within-Gibbs">Using the <code>state</code> Interface for block sampling within Gibbs</a><a id="Using-the-state-Interface-for-block-sampling-within-Gibbs-1"></a><a class="docs-heading-anchor-permalink" href="#Using-the-state-Interface-for-block-sampling-within-Gibbs" title="Permalink"></a></h2><p>In this sections, we will demonstrate how a <code>model</code> package may use this <code>state</code> interface to support a Gibbs sampler that can support blocking sampling using different inference algorithms.</p><p>We consider a simple hierarchical model with a normal likelihood, with unknown mean and variance parameters.</p><p class="math-container">\[\begin{align}
@@ -250,4 +250,4 @@
 sampling is easy: we use random walk MH for `mu` and prior MH for `tau2`, because `tau2` has support on positive real numbers.
 </code></pre><p>julia samples = sample(     hn,     Gibbs(         OrderedDict(             (:mu,) =&gt; RWMH(1),             (:tau2,) =&gt; PriorMH(product<em>distribution([InverseGamma(1, 1)])),         ),     ),     100000;     initial</em>params=(mu=[0.0], tau2=[1.0]), )</p><pre><code class="nohighlight hljs">
 Then we can extract the samples and compute the mean of the samples.
-</code></pre><p>julia mu<em>samples = [sample.values.mu for sample in samples][20001:end] tau2</em>samples = [sample.values.tau2 for sample in samples][20001:end]</p><p>mean(mu<em>samples) mean(tau2</em>samples) ```</p></article><nav class="docs-footer"><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 1.6.0 on <span class="colophon-date" title="Friday 23 August 2024 12:54">Friday 23 August 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre><p>julia mu<em>samples = [sample.values.mu for sample in samples][20001:end] tau2</em>samples = [sample.values.tau2 for sample in samples][20001:end]</p><p>mean(mu<em>samples) mean(tau2</em>samples) ```</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../design/">« Design</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 1.6.0 on <span class="colophon-date" title="Friday 23 August 2024 12:55">Friday 23 August 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>