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@@ -14,23 +14,23 @@
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   "evaluation" => 2-element BenchmarkTools.BenchmarkGroup:
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-	  "linked" => Trial(360.000 ns)
-	  "standard" => Trial(310.000 ns)
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   "gradient" => 4-element BenchmarkTools.BenchmarkGroup:
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 	  "ADTypes.AutoForwardDiff{0, Nothing}(nothing)" => 2-element BenchmarkTools.BenchmarkGroup:
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-		  "linked" => Trial(551.000 ns)
-		  "standard" => Trial(510.000 ns)
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 	  "ADTypes.AutoReverseDiff(true)" => 2-element BenchmarkTools.BenchmarkGroup:
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 		  "linked" => Trial(1.482 μs)
 		  "standard" => Trial(1.462 μs)
 	  "ADTypes.AutoReverseDiff(false)" => 2-element BenchmarkTools.BenchmarkGroup:
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-		  "linked" => Trial(8.616 μs)
-		  "standard" => Trial(8.335 μs)
+		  "linked" => Trial(8.696 μs)
+		  "standard" => Trial(8.516 μs)
 	  "ADTypes.AutoZygote()" => 2-element BenchmarkTools.BenchmarkGroup:
 		  tags: ["Zygote"]
-		  "linked" => Trial(501.679 μs)
-		  "standard" =&gt; Trial(478.295 μs)</code></pre><h2 id="API"><a class="docs-heading-anchor" href="#API">API</a><a id="API-1"></a><a class="docs-heading-anchor-permalink" href="#API" title="Permalink"></a></h2><ul><li><a href="#TuringBenchmarking.benchmark_model-Tuple{DynamicPPL.Model}"><code>TuringBenchmarking.benchmark_model</code></a></li><li><a href="#TuringBenchmarking.extract_stan_data"><code>TuringBenchmarking.extract_stan_data</code></a></li><li><a href="#TuringBenchmarking.make_stan_suite"><code>TuringBenchmarking.make_stan_suite</code></a></li><li><a href="#TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}"><code>TuringBenchmarking.make_turing_suite</code></a></li><li><a href="#TuringBenchmarking.stan_model_string"><code>TuringBenchmarking.stan_model_string</code></a></li></ul><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" href="#TuringBenchmarking.benchmark_model-Tuple{DynamicPPL.Model}" id="TuringBenchmarking.benchmark_model-Tuple{DynamicPPL.Model}"><code>TuringBenchmarking.benchmark_model</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">benchmark_model(model::Turing.Model; suite_kwargs..., kwargs...)</code></pre><p>Create and run a benchmark suite for <code>model</code>.</p><p>The benchmarking suite will be created using <a href="#TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}"><code>make_turing_suite</code></a>. See <a href="#TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}"><code>make_turing_suite</code></a> for the available keyword arguments and more information.</p><p><strong>Keyword arguments</strong></p><ul><li><code>suite_kwargs</code>: Keyword arguments passed to <a href="#TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}"><code>make_turing_suite</code></a>.</li><li><code>kwargs</code>: Keyword arguments passed to <code>BenchmarkTools.run</code>.</li></ul></div><a class="docs-sourcelink" href="https://github.com/TuringLang/TuringBenchmarking.jl/blob/c9d62d39926910fed351e87d562bd9e71ee8c7bd/src/TuringBenchmarking.jl#L64-L75" target="_blank">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" href="#TuringBenchmarking.extract_stan_data" id="TuringBenchmarking.extract_stan_data"><code>TuringBenchmarking.extract_stan_data</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">extract_stan_data(model::DynamicPPL.Model)</code></pre><p>Return the data in <code>model</code> in a format consumable by the corresponding Stan model.</p><p>The Stan model requires the return data to be either</p><ol><li>A JSON string representing a dictionary with the data.</li><li>A path to a data file ending in <code>.json</code>.</li></ol></div><a class="docs-sourcelink" href="https://github.com/TuringLang/TuringBenchmarking.jl/blob/c9d62d39926910fed351e87d562bd9e71ee8c7bd/src/TuringBenchmarking.jl#L315-L323" target="_blank">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" href="#TuringBenchmarking.make_stan_suite" id="TuringBenchmarking.make_stan_suite"><code>TuringBenchmarking.make_stan_suite</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">make_stan_suite(model::Turing.Model; kwargs...)</code></pre><p>Create default benchmark suite for the Stan model corresponding to <code>model</code>.</p></div><a class="docs-sourcelink" href="https://github.com/TuringLang/TuringBenchmarking.jl/blob/c9d62d39926910fed351e87d562bd9e71ee8c7bd/src/TuringBenchmarking.jl#L333-L337" target="_blank">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" href="#TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}" id="TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}"><code>TuringBenchmarking.make_turing_suite</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">make_turing_suite(model::Turing.Model; kwargs...)</code></pre><p>Create default benchmark suite for <code>model</code>.</p><p><strong>Keyword arguments</strong></p><ul><li><code>adbackends</code>: a collection of adbackends to use, specified either as a type from</li></ul><p>ADTypes.jl or using a <code>Symbol</code>. Defaults to <code>ADTypes.AbstractADType[ADTypes.AutoForwardDiff{0, Nothing}(nothing), ADTypes.AutoReverseDiff(false), ADTypes.AutoReverseDiff(true), ADTypes.AutoZygote()]</code>.</p><ul><li><code>run_once=true</code>: if <code>true</code>, the body of each benchmark will be run once to avoid compilation to be included in the timings (this may occur if compilation runs longer than the allowed time limit).</li><li><code>check=false</code>: if <code>true</code>, the log-density evaluations and the gradients will be compared against each other to ensure that they are consistent. Note that this will force <code>run_once=true</code>.</li><li><code>error_on_failed_check=false</code>: if <code>true</code>, an error will be thrown if the check fails rather than just printing a warning, as is done by default.</li><li><code>error_on_failed_backend=false</code>: if <code>true</code>, an error will be thrown if the evaluation of the log-density or the gradient fails for any of the backends rather than just printing a warning, as is done by default.</li><li><code>varinfo</code>: the <code>VarInfo</code> to use. Defaults to <code>DynamicPPL.VarInfo(model)</code>.</li><li><code>sampler</code>: the <code>Sampler</code> to use. Defaults to <code>nothing</code> (i.e. no sampler).</li><li><code>context</code>: the <code>Context</code> to use. Defaults to <code>DynamicPPL.DefaultContext()</code>.</li><li><code>θ</code>: the parameters to use. Defaults to <code>rand(Vector, model)</code>.</li><li><code>θ_linked</code>: the linked parameters to use. Defaults to <code>randn(d)</code> where <code>d</code>  is the length of the linked parameters..</li><li><code>atol</code>: the absolute tolerance to use for comparisons.</li><li><code>rtol</code>: the relative tolerance to use for comparisons.</li></ul><p><strong>Notes</strong></p><ul><li>A separate "parameter" instance (<code>DynamicPPL.VarInfo</code>) will be created for <em>each test</em>. Hence if you have a particularly large model, you might want to only pass one <code>adbackend</code> at the time.</li></ul></div><a class="docs-sourcelink" href="https://github.com/TuringLang/TuringBenchmarking.jl/blob/c9d62d39926910fed351e87d562bd9e71ee8c7bd/src/TuringBenchmarking.jl#L110-L142" target="_blank">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" href="#TuringBenchmarking.stan_model_string" id="TuringBenchmarking.stan_model_string"><code>TuringBenchmarking.stan_model_string</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">stan_model_string(model::DynamicPPL.Model)</code></pre><p>Return a string defining the Stan model corresponding to <code>model</code>.</p></div><a class="docs-sourcelink" href="https://github.com/TuringLang/TuringBenchmarking.jl/blob/c9d62d39926910fed351e87d562bd9e71ee8c7bd/src/TuringBenchmarking.jl#L326-L330" target="_blank">source</a></section></article></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></p><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></select></div><p></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.0 on <span class="colophon-date" title="Wednesday 24 April 2024 14:24">Wednesday 24 April 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></HTML>
+		  "linked" =&gt; Trial(554.251 μs)
+		  "standard" =&gt; Trial(531.370 μs)</code></pre><h2 id="API"><a class="docs-heading-anchor" href="#API">API</a><a id="API-1"></a><a class="docs-heading-anchor-permalink" href="#API" title="Permalink"></a></h2><ul><li><a href="#TuringBenchmarking.benchmark_model-Tuple{DynamicPPL.Model}"><code>TuringBenchmarking.benchmark_model</code></a></li><li><a href="#TuringBenchmarking.extract_stan_data"><code>TuringBenchmarking.extract_stan_data</code></a></li><li><a href="#TuringBenchmarking.make_stan_suite"><code>TuringBenchmarking.make_stan_suite</code></a></li><li><a href="#TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}"><code>TuringBenchmarking.make_turing_suite</code></a></li><li><a href="#TuringBenchmarking.stan_model_string"><code>TuringBenchmarking.stan_model_string</code></a></li></ul><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" href="#TuringBenchmarking.benchmark_model-Tuple{DynamicPPL.Model}" id="TuringBenchmarking.benchmark_model-Tuple{DynamicPPL.Model}"><code>TuringBenchmarking.benchmark_model</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">benchmark_model(model::Turing.Model; suite_kwargs..., kwargs...)</code></pre><p>Create and run a benchmark suite for <code>model</code>.</p><p>The benchmarking suite will be created using <a href="#TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}"><code>make_turing_suite</code></a>. See <a href="#TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}"><code>make_turing_suite</code></a> for the available keyword arguments and more information.</p><p><strong>Keyword arguments</strong></p><ul><li><code>suite_kwargs</code>: Keyword arguments passed to <a href="#TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}"><code>make_turing_suite</code></a>.</li><li><code>kwargs</code>: Keyword arguments passed to <code>BenchmarkTools.run</code>.</li></ul></div><a class="docs-sourcelink" href="https://github.com/TuringLang/TuringBenchmarking.jl/blob/daa41c8e43fdcf5a41d71c234ea8fb6980649799/src/TuringBenchmarking.jl#L64-L75" target="_blank">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" href="#TuringBenchmarking.extract_stan_data" id="TuringBenchmarking.extract_stan_data"><code>TuringBenchmarking.extract_stan_data</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">extract_stan_data(model::DynamicPPL.Model)</code></pre><p>Return the data in <code>model</code> in a format consumable by the corresponding Stan model.</p><p>The Stan model requires the return data to be either</p><ol><li>A JSON string representing a dictionary with the data.</li><li>A path to a data file ending in <code>.json</code>.</li></ol></div><a class="docs-sourcelink" href="https://github.com/TuringLang/TuringBenchmarking.jl/blob/daa41c8e43fdcf5a41d71c234ea8fb6980649799/src/TuringBenchmarking.jl#L315-L323" target="_blank">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" href="#TuringBenchmarking.make_stan_suite" id="TuringBenchmarking.make_stan_suite"><code>TuringBenchmarking.make_stan_suite</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">make_stan_suite(model::Turing.Model; kwargs...)</code></pre><p>Create default benchmark suite for the Stan model corresponding to <code>model</code>.</p></div><a class="docs-sourcelink" href="https://github.com/TuringLang/TuringBenchmarking.jl/blob/daa41c8e43fdcf5a41d71c234ea8fb6980649799/src/TuringBenchmarking.jl#L333-L337" target="_blank">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" href="#TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}" id="TuringBenchmarking.make_turing_suite-Tuple{DynamicPPL.Model}"><code>TuringBenchmarking.make_turing_suite</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">make_turing_suite(model::Turing.Model; kwargs...)</code></pre><p>Create default benchmark suite for <code>model</code>.</p><p><strong>Keyword arguments</strong></p><ul><li><code>adbackends</code>: a collection of adbackends to use, specified either as a type from</li></ul><p>ADTypes.jl or using a <code>Symbol</code>. Defaults to <code>ADTypes.AbstractADType[ADTypes.AutoForwardDiff{0, Nothing}(nothing), ADTypes.AutoReverseDiff(false), ADTypes.AutoReverseDiff(true), ADTypes.AutoZygote()]</code>.</p><ul><li><code>run_once=true</code>: if <code>true</code>, the body of each benchmark will be run once to avoid compilation to be included in the timings (this may occur if compilation runs longer than the allowed time limit).</li><li><code>check=false</code>: if <code>true</code>, the log-density evaluations and the gradients will be compared against each other to ensure that they are consistent. Note that this will force <code>run_once=true</code>.</li><li><code>error_on_failed_check=false</code>: if <code>true</code>, an error will be thrown if the check fails rather than just printing a warning, as is done by default.</li><li><code>error_on_failed_backend=false</code>: if <code>true</code>, an error will be thrown if the evaluation of the log-density or the gradient fails for any of the backends rather than just printing a warning, as is done by default.</li><li><code>varinfo</code>: the <code>VarInfo</code> to use. Defaults to <code>DynamicPPL.VarInfo(model)</code>.</li><li><code>sampler</code>: the <code>Sampler</code> to use. Defaults to <code>nothing</code> (i.e. no sampler).</li><li><code>context</code>: the <code>Context</code> to use. Defaults to <code>DynamicPPL.DefaultContext()</code>.</li><li><code>θ</code>: the parameters to use. Defaults to <code>rand(Vector, model)</code>.</li><li><code>θ_linked</code>: the linked parameters to use. Defaults to <code>randn(d)</code> where <code>d</code>  is the length of the linked parameters..</li><li><code>atol</code>: the absolute tolerance to use for comparisons.</li><li><code>rtol</code>: the relative tolerance to use for comparisons.</li></ul><p><strong>Notes</strong></p><ul><li>A separate "parameter" instance (<code>DynamicPPL.VarInfo</code>) will be created for <em>each test</em>. Hence if you have a particularly large model, you might want to only pass one <code>adbackend</code> at the time.</li></ul></div><a class="docs-sourcelink" href="https://github.com/TuringLang/TuringBenchmarking.jl/blob/daa41c8e43fdcf5a41d71c234ea8fb6980649799/src/TuringBenchmarking.jl#L110-L142" target="_blank">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" href="#TuringBenchmarking.stan_model_string" id="TuringBenchmarking.stan_model_string"><code>TuringBenchmarking.stan_model_string</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">stan_model_string(model::DynamicPPL.Model)</code></pre><p>Return a string defining the Stan model corresponding to <code>model</code>.</p></div><a class="docs-sourcelink" href="https://github.com/TuringLang/TuringBenchmarking.jl/blob/daa41c8e43fdcf5a41d71c234ea8fb6980649799/src/TuringBenchmarking.jl#L326-L330" target="_blank">source</a></section></article></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></p><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></select></div><p></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Sunday 5 May 2024 15:49">Sunday 5 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></HTML>