build based on 01e594d

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-29T00:22:47","documenter_version":"1.8.0"}}
+{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-30T00:22:49","documenter_version":"1.8.0"}}

dev/examples/quickstart/index.html

@@ -104,7 +104,7 @@
 prob_banana = BananaProblem()</code></pre><p>and then visualise it:</p><pre><code class="language-julia hljs">xrange = -3.5:0.05:3.5
 yrange = -3:0.05:7
 logp_banana(x) = LogDensityProblems.logdensity(prob_banana, x)
-contour(xrange, yrange, exp ∘ logp_banana ∘ Base.vect; xlabel=&quot;x₁&quot;, ylabel=&quot;x₂&quot;)</code></pre><img src="f9c9dfef.svg" alt="Example block output"/><p>Now we run <a href="../../lib/public/#Pathfinder.pathfinder"><code>pathfinder</code></a>.</p><pre><code class="language-julia hljs">result = pathfinder(prob_banana; init_scale=10)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Single-path Pathfinder result
+contour(xrange, yrange, exp ∘ logp_banana ∘ Base.vect; xlabel=&quot;x₁&quot;, ylabel=&quot;x₂&quot;)</code></pre><img src="c8a840dc.svg" alt="Example block output"/><p>Now we run <a href="../../lib/public/#Pathfinder.pathfinder"><code>pathfinder</code></a>.</p><pre><code class="language-julia hljs">result = pathfinder(prob_banana; init_scale=10)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Single-path Pathfinder result
   tries: 1
   draws: 5
   fit iteration: 10 (total: 17)
@@ -127,7 +127,7 @@
 
 contour(xrange, yrange, exp ∘ logp_banana ∘ Base.vect)
 scatter!(x₁_approx, x₂_approx; msw=0, ms=2, alpha=0.5, color=1)
-plot!(xlims=extrema(xrange), ylims=extrema(yrange), xlabel=&quot;x₁&quot;, ylabel=&quot;x₂&quot;, legend=false)</code></pre><img src="c51bf936.svg" alt="Example block output"/><p>While the draws do a poor job of covering the tails of the distribution, they are still useful for identifying the nonlinear correlation between these two parameters.</p><h2 id="A-100-dimensional-funnel"><a class="docs-heading-anchor" href="#A-100-dimensional-funnel">A 100-dimensional funnel</a><a id="A-100-dimensional-funnel-1"></a><a class="docs-heading-anchor-permalink" href="#A-100-dimensional-funnel" title="Permalink"></a></h2><p>As we have seen above, running multi-path Pathfinder is much more useful for target distributions that are far from normal. One particularly difficult distribution to sample is Neal&#39;s funnel:</p><p class="math-container">\[\begin{aligned}
+plot!(xlims=extrema(xrange), ylims=extrema(yrange), xlabel=&quot;x₁&quot;, ylabel=&quot;x₂&quot;, legend=false)</code></pre><img src="f187de33.svg" alt="Example block output"/><p>While the draws do a poor job of covering the tails of the distribution, they are still useful for identifying the nonlinear correlation between these two parameters.</p><h2 id="A-100-dimensional-funnel"><a class="docs-heading-anchor" href="#A-100-dimensional-funnel">A 100-dimensional funnel</a><a id="A-100-dimensional-funnel-1"></a><a class="docs-heading-anchor-permalink" href="#A-100-dimensional-funnel" title="Permalink"></a></h2><p>As we have seen above, running multi-path Pathfinder is much more useful for target distributions that are far from normal. One particularly difficult distribution to sample is Neal&#39;s funnel:</p><p class="math-container">\[\begin{aligned}
 \tau &amp;\sim \mathrm{Normal}(\mu=0, \sigma=3)\\
 \beta_i &amp;\sim \mathrm{Normal}(\mu=0, \sigma=e^{\tau/2})
 \end{aligned}\]</p><p>Such funnel geometries appear in other models (e.g. many hierarchical models) and typically frustrate MCMC sampling. Multi-path Pathfinder can&#39;t sample the funnel well, but it can quickly give us draws that can help us diagnose that we have a funnel.</p><p>In this example, we draw from a 100-dimensional funnel and visualize 2 dimensions.</p><pre><code class="language-julia hljs">using ReverseDiff, ADTypes
@@ -165,4 +165,4 @@
 
 contour(τ_range, β₁_range, exp ∘ logp_funnel ∘ Base.vect)
 scatter!(τ_approx, β₁_approx; msw=0, ms=2, alpha=0.5, color=1)
-plot!(; xlims=extrema(τ_range), ylims=extrema(β₁_range), xlabel=&quot;τ&quot;, ylabel=&quot;β₁&quot;, legend=false)</code></pre><img src="f3c74e36.svg" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../lib/internals/">« Internals</a><a class="docs-footer-nextpage" href="../initializing-hmc/">Initializing HMC »</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 29 November 2024 00:22">Friday 29 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plot!(; xlims=extrema(τ_range), ylims=extrema(β₁_range), xlabel=&quot;τ&quot;, ylabel=&quot;β₁&quot;, legend=false)</code></pre><img src="4fefe649.svg" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../lib/internals/">« Internals</a><a class="docs-footer-nextpage" href="../initializing-hmc/">Initializing HMC »</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="Saturday 30 November 2024 00:22">Saturday 30 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/examples/turing/index.html

@@ -59,8 +59,8 @@
 Iterations        = 501:1:1500
 Number of chains  = 8
 Samples per chain = 1000
-Wall duration     = 6.7 seconds
-Compute duration  = 4.93 seconds
+Wall duration     = 6.51 seconds
+Compute duration  = 4.77 seconds
 parameters        = α, β, σ
 internals         = lp, n_steps, is_accept, acceptance_rate, log_density, hamiltonian_energy, hamiltonian_energy_error, max_hamiltonian_energy_error, tree_depth, numerical_error, step_size, nom_step_size
 
@@ -102,8 +102,8 @@
 Iterations        = 51:1:1050
 Number of chains  = 8
 Samples per chain = 1000
-Wall duration     = 2.78 seconds
-Compute duration  = 2.39 seconds
+Wall duration     = 2.74 seconds
+Compute duration  = 2.36 seconds
 parameters        = α, β, σ
 internals         = lp, n_steps, is_accept, acceptance_rate, log_density, hamiltonian_energy, hamiltonian_energy_error, max_hamiltonian_energy_error, tree_depth, numerical_error, step_size, nom_step_size, is_adapt
 
@@ -123,4 +123,4 @@
            α    1.3916    1.4468    1.4750    1.5028    1.5585
            β    1.9914    2.0011    2.0061    2.0110    2.0205
            σ    0.1890    0.2057    0.2160    0.2267    0.2501
-</code></pre><p>See <a href="../initializing-hmc/#Initializing-HMC-with-Pathfinder">Initializing HMC with Pathfinder</a> for further examples.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../initializing-hmc/">« Initializing HMC</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 29 November 2024 00:22">Friday 29 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre><p>See <a href="../initializing-hmc/#Initializing-HMC-with-Pathfinder">Initializing HMC with Pathfinder</a> for further examples.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../initializing-hmc/">« Initializing HMC</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="Saturday 30 November 2024 00:22">Saturday 30 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>