Added navbar and removed insert_navbar.sh

index.html

@@ -1,2 +1,3 @@
 <!--This file is automatically generated by Documenter.jl-->
 <meta http-equiv="refresh" content="0; url=./stable/"/>
+

previews/PR431/chains/index.html

@@ -457,6 +457,7 @@
     });
 </script>
 <!-- NAVBAR END -->
+
 <div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">MCMCChains.jl</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="../">MCMCChains</a></li><li><a class="tocitem" href="../getting-started/">Getting started</a></li><li><span class="tocitem">Plotting</span><ul><li><a class="tocitem" href="../statsplots/">StatsPlots.jl</a></li><li><a class="tocitem" href="../makie/">Makie.jl</a></li><li><a class="tocitem" href="../gadfly/">Gadfly.jl</a></li></ul></li><li><span class="tocitem">API</span><ul><li class="is-active"><a class="tocitem" href>Chains</a></li><li><a class="tocitem" href="../diagnostics/">Diagnostics</a></li><li><a class="tocitem" href="../stats/">Posterior statistics</a></li><li><a class="tocitem" href="../modelstats/">Model selection</a></li><li><a class="tocitem" href="../summarize/">Summarize</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><a class="is-disabled">API</a></li><li class="is-active"><a href>Chains</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Chains</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/TuringLang/MCMCChains.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/MCMCChains.jl/blob/master/docs/src/chains.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="Chains"><a class="docs-heading-anchor" href="#Chains">Chains</a><a id="Chains-1"></a><a class="docs-heading-anchor-permalink" href="#Chains" title="Permalink"></a></h1><p>The methods listed below are defined in <code>src/chains.jl</code>.</p><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="MCMCChains.Chains-Tuple{Chains, Union{AbstractString, Symbol}}" href="#MCMCChains.Chains-Tuple{Chains, Union{AbstractString, Symbol}}"><code>MCMCChains.Chains</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">Chains(c::Chains, section::Union{Symbol,AbstractString})
 Chains(c::Chains, sections)</code></pre><p>Return a new chain with only a specific <code>section</code> or multiple <code>sections</code> pulled out.</p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; chn = Chains(rand(100, 2, 1), [:a, :b], Dict(:internals =&gt; [:a]));
 

previews/PR431/diagnostics/index.html

@@ -457,6 +457,7 @@
     });
 </script>
 <!-- NAVBAR END -->
+
 <div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">MCMCChains.jl</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="../">MCMCChains</a></li><li><a class="tocitem" href="../getting-started/">Getting started</a></li><li><span class="tocitem">Plotting</span><ul><li><a class="tocitem" href="../statsplots/">StatsPlots.jl</a></li><li><a class="tocitem" href="../makie/">Makie.jl</a></li><li><a class="tocitem" href="../gadfly/">Gadfly.jl</a></li></ul></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="../chains/">Chains</a></li><li class="is-active"><a class="tocitem" href>Diagnostics</a></li><li><a class="tocitem" href="../stats/">Posterior statistics</a></li><li><a class="tocitem" href="../modelstats/">Model selection</a></li><li><a class="tocitem" href="../summarize/">Summarize</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><a class="is-disabled">API</a></li><li class="is-active"><a href>Diagnostics</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Diagnostics</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/TuringLang/MCMCChains.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/MCMCChains.jl/blob/master/docs/src/diagnostics.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="Diagnostics"><a class="docs-heading-anchor" href="#Diagnostics">Diagnostics</a><a id="Diagnostics-1"></a><a class="docs-heading-anchor-permalink" href="#Diagnostics" title="Permalink"></a></h1><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="MCMCDiagnosticTools.discretediag-Tuple{Chains{var&quot;#s12&quot;, A} where {var&quot;#s12&quot;&lt;:Real, A&lt;:(AxisArrays.AxisArray{var&quot;#s12&quot;, 3})}}" href="#MCMCDiagnosticTools.discretediag-Tuple{Chains{var&quot;#s12&quot;, A} where {var&quot;#s12&quot;&lt;:Real, A&lt;:(AxisArrays.AxisArray{var&quot;#s12&quot;, 3})}}"><code>MCMCDiagnosticTools.discretediag</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">discretediag(chains::Chains{&lt;:Real}; sections, kwargs...)</code></pre><p>Discrete diagnostic where <code>method</code> can be <code>[:weiss, :hangartner, :DARBOOT, MCBOOT, :billinsgley, :billingsleyBOOT]</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/TuringLang/MCMCChains.jl/blob/fe645de8d1b35eb6ce892539877ce2b2eaf1e99d/src/discretediag.jl#L1-L6">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="MCMCDiagnosticTools.rstar-Tuple{Any, Chains}" href="#MCMCDiagnosticTools.rstar-Tuple{Any, Chains}"><code>MCMCDiagnosticTools.rstar</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">rstar(rng=Random.GLOBAL_RNG, classifier, chains::Chains; kwargs...)</code></pre><p>Compute the <span>$R^*$</span> convergence diagnostic of the MCMC <code>chains</code> with the <code>classifier</code>.</p><p>The keyword arguments supported here are the same as those in <code>rstar</code> for arrays of samples and chain indices.</p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; using MLJBase, MLJDecisionTreeInterface, Statistics
 
 julia&gt; chains = Chains(fill(4.0, 100, 2, 3));</code></pre><p>One can compute the distribution of the <span>$R^*$</span> statistic with the probabilistic classifier.</p><pre><code class="language-julia-repl hljs">julia&gt; distribution = rstar(DecisionTreeClassifier(), chains);

previews/PR431/gadfly/index.html

@@ -457,6 +457,7 @@
     });
 </script>
 <!-- NAVBAR END -->
+
 <div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">MCMCChains.jl</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="../">MCMCChains</a></li><li><a class="tocitem" href="../getting-started/">Getting started</a></li><li><span class="tocitem">Plotting</span><ul><li><a class="tocitem" href="../statsplots/">StatsPlots.jl</a></li><li><a class="tocitem" href="../makie/">Makie.jl</a></li><li class="is-active"><a class="tocitem" href>Gadfly.jl</a><ul class="internal"><li><a class="tocitem" href="#Multiple-parameters"><span>Multiple parameters</span></a></li><li><a class="tocitem" href="#Trace"><span>Trace</span></a></li></ul></li></ul></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="../chains/">Chains</a></li><li><a class="tocitem" href="../diagnostics/">Diagnostics</a></li><li><a class="tocitem" href="../stats/">Posterior statistics</a></li><li><a class="tocitem" href="../modelstats/">Model selection</a></li><li><a class="tocitem" href="../summarize/">Summarize</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><a class="is-disabled">Plotting</a></li><li class="is-active"><a href>Gadfly.jl</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Gadfly.jl</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/TuringLang/MCMCChains.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/MCMCChains.jl/blob/master/docs/src/gadfly.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="Gadfly.jl-plots"><a class="docs-heading-anchor" href="#Gadfly.jl-plots">Gadfly.jl plots</a><a id="Gadfly.jl-plots-1"></a><a class="docs-heading-anchor-permalink" href="#Gadfly.jl-plots" title="Permalink"></a></h1><p>To plot the Chains via <a href="https://github.com/GiovineItalia/Gadfly.jl">Gadfly.jl</a>, use the DataFrames constructor:</p><pre><code class="language-julia hljs">using DataFrames
 using CategoricalArrays
 using Gadfly

previews/PR431/getting-started/index.html

@@ -457,6 +457,7 @@
     });
 </script>
 <!-- NAVBAR END -->
+
 <div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">MCMCChains.jl</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="../">MCMCChains</a></li><li class="is-active"><a class="tocitem" href>Getting started</a><ul class="internal"><li><a class="tocitem" href="#Chains-type"><span>Chains type</span></a></li><li><a class="tocitem" href="#Indexing-and-parameter-Names"><span>Indexing and parameter Names</span></a></li><li><a class="tocitem" href="#Rename-Parameters"><span>Rename Parameters</span></a></li><li><a class="tocitem" href="#Sections"><span>Sections</span></a></li><li><a class="tocitem" href="#Groups-of-parameters"><span>Groups of parameters</span></a></li><li><a class="tocitem" href="#The-get-Function"><span>The <code>get</code> Function</span></a></li><li><a class="tocitem" href="#Saving-and-Loading-Chains"><span>Saving and Loading Chains</span></a></li><li><a class="tocitem" href="#Exporting-Chains"><span>Exporting Chains</span></a></li><li><a class="tocitem" href="#Sampling-Chains"><span>Sampling Chains</span></a></li></ul></li><li><span class="tocitem">Plotting</span><ul><li><a class="tocitem" href="../statsplots/">StatsPlots.jl</a></li><li><a class="tocitem" href="../makie/">Makie.jl</a></li><li><a class="tocitem" href="../gadfly/">Gadfly.jl</a></li></ul></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="../chains/">Chains</a></li><li><a class="tocitem" href="../diagnostics/">Diagnostics</a></li><li><a class="tocitem" href="../stats/">Posterior statistics</a></li><li><a class="tocitem" href="../modelstats/">Model selection</a></li><li><a class="tocitem" href="../summarize/">Summarize</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>Getting started</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Getting started</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/TuringLang/MCMCChains.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/MCMCChains.jl/blob/master/docs/src/getting-started.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="Getting-started"><a class="docs-heading-anchor" href="#Getting-started">Getting started</a><a id="Getting-started-1"></a><a class="docs-heading-anchor-permalink" href="#Getting-started" title="Permalink"></a></h1><h2 id="Chains-type"><a class="docs-heading-anchor" href="#Chains-type">Chains type</a><a id="Chains-type-1"></a><a class="docs-heading-anchor-permalink" href="#Chains-type" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="MCMCChains.Chains" href="#MCMCChains.Chains"><code>MCMCChains.Chains</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">Chains</code></pre><p>Parameters:</p><ul><li><code>value</code>: An <code>AxisArray</code> object with axes <code>iter</code> × <code>var</code> × <code>chains</code></li><li><code>logevidence</code> : A field containing the logevidence.</li><li><code>name_map</code> : A <code>NamedTuple</code> mapping each variable to a section.</li><li><code>info</code> : A <code>NamedTuple</code> containing miscellaneous information relevant to the chain.</li></ul><p>The <code>info</code> field can be set using <code>setinfo(c::Chains, n::NamedTuple)</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/TuringLang/MCMCChains.jl/blob/fe645de8d1b35eb6ce892539877ce2b2eaf1e99d/src/MCMCChains.jl#L54-L64">source</a></section></article><h2 id="Indexing-and-parameter-Names"><a class="docs-heading-anchor" href="#Indexing-and-parameter-Names">Indexing and parameter Names</a><a id="Indexing-and-parameter-Names-1"></a><a class="docs-heading-anchor-permalink" href="#Indexing-and-parameter-Names" title="Permalink"></a></h2><p>Chains can be constructed with parameter names. For example, to create a chains object with</p><ul><li>500 samples,</li><li>2 parameters (named <code>a</code> and <code>b</code>)</li><li>3 chains</li></ul><p>use</p><pre><code class="language-julia hljs">val = rand(500, 2, 3)
 chn = Chains(val, [:a, :b])</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Chains MCMC chain (500×2×3 Array{Float64, 3}):