build based on 8f220d2

dev/examples/turing/index.html

@@ -67,8 +67,8 @@
 Iterations        = 501:1:1500
 Number of chains  = 4
 Samples per chain = 1000
-Wall duration     = 9.85 seconds
-Compute duration  = 7.17 seconds
+Wall duration     = 11.56 seconds
+Compute duration  = 8.18 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
 
@@ -116,4 +116,4 @@
     progress=false,
 )</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">([[1.4426042147627391, 2.0094864584230985, -1.5097996538158076], [1.3998801943955104, 2.0201857251000255, -1.5361412109482127], [1.4051458899240876, 2.0202987017130605, -1.457309630509756], [1.4856945995579873, 1.9978364348181632, -1.422372782450631], [1.4460291970887889, 2.010382861379786, -1.4799224767217032], [1.4291875110690104, 2.0130504124589437, -1.470253900176862], [1.527268872027908, 1.9985613433085196, -1.655679525083512], [1.485022823255241, 2.0017636951026465, -1.5700450126448366], [1.4010387695566593, 2.0203389024541463, -1.5493432125802893], [1.579087552476485, 1.9885635798863892, -1.5516860356925646]  …  [1.5127023721707622, 2.003051823062902, -1.4699062231801843], [1.5126796396083544, 1.9990533669284931, -1.4175253110468966], [1.4346955418325675, 2.010892009834125, -1.7100130890108074], [1.4465467949617823, 2.005298620524573, -1.3022887516128432], [1.4727546165006193, 2.0068809214226335, -1.4989835378177188], [1.533925524540236, 1.998882122225741, -1.4953690781357463], [1.4759745894487657, 2.007929763179185, -1.587467213181056], [1.5169438878358201, 1.9998096552744524, -1.5118302842284315], [1.45650192002816, 2.0065197223553435, -1.56576920914184], [1.4750879248893007, 2.0106303352426673, -1.5443232018616122]], NamedTuple[(n_steps = 3, is_accept = true, acceptance_rate = 1.0, log_density = 7.684203337928883, hamiltonian_energy = -4.199747276702116, hamiltonian_energy_error = -0.5939044198788781, max_hamiltonian_energy_error = -0.5939044198788781, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.778975096896601, log_density = 6.314450752692314, hamiltonian_energy = -5.935015841819251, hamiltonian_energy_error = 0.30442742312767734, max_hamiltonian_energy_error = 0.30442742312767734, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 15, is_accept = true, acceptance_rate = 0.9604448951047677, log_density = 5.772673629275509, hamiltonian_energy = -4.914929071630293, hamiltonian_energy_error = 0.06343006617318014, max_hamiltonian_energy_error = -0.30294479871613333, tree_depth = 4, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 7, is_accept = true, acceptance_rate = 0.8880909364139795, log_density = 5.327309910543318, hamiltonian_energy = -4.040199973766979, hamiltonian_energy_error = 0.13572020911629323, max_hamiltonian_energy_error = 0.4287639050728651, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.9511254440273101, log_density = 7.507613996453539, hamiltonian_energy = -4.732347339027851, hamiltonian_energy_error = -0.4308394681312011, max_hamiltonian_energy_error = -0.4308394681312011, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.7623678233077849, log_density = 7.064609836790011, hamiltonian_energy = -4.582233792253414, hamiltonian_energy_error = 0.07249563677501136, max_hamiltonian_energy_error = 0.4097372021717405, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.9370419201960098, log_density = 6.128176970824219, hamiltonian_energy = -5.6457048820558295, hamiltonian_energy_error = 0.10692338661544731, max_hamiltonian_energy_error = -0.1784358796176253, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.947963647387175, log_density = 7.8348001294198735, hamiltonian_energy = -5.504518177864945, hamiltonian_energy_error = -0.24978076169693075, max_hamiltonian_energy_error = -0.24978076169693075, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.8344836836075172, log_density = 6.262682678277982, hamiltonian_energy = -5.970467983901393, hamiltonian_energy_error = 0.37052358239180805, max_hamiltonian_energy_error = 0.37052358239180805, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 7, is_accept = true, acceptance_rate = 0.9041123906525679, log_density = 5.004838509212749, hamiltonian_energy = -4.191941588271407, hamiltonian_energy_error = 0.24053874065999992, max_hamiltonian_energy_error = 0.29145831549519574, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false)  …  (n_steps = 63, is_accept = true, acceptance_rate = 0.9835631111087395, log_density = 7.0315323875482, hamiltonian_energy = -5.77659677382491, hamiltonian_energy_error = -0.07822188039970257, max_hamiltonian_energy_error = -0.2571471826020124, tree_depth = 5, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.9029265124072229, log_density = 6.176505119575974, hamiltonian_energy = -5.5278705249551185, hamiltonian_energy_error = 0.1735084234032236, max_hamiltonian_energy_error = 0.1735084234032236, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.8833314201251646, log_density = 4.643642412265735, hamiltonian_energy = -3.0415758939301765, hamiltonian_energy_error = 0.022131566587327622, max_hamiltonian_energy_error = -0.4654939629228574, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 15, is_accept = true, acceptance_rate = 0.7183012209717858, log_density = 2.125536061715974, hamiltonian_energy = 0.8002028846063025, hamiltonian_energy_error = 0.5110369324654185, max_hamiltonian_energy_error = 0.7205762061592034, tree_depth = 3, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 1.0, log_density = 7.9398939062048, hamiltonian_energy = -2.796630947823016, hamiltonian_energy_error = -0.7795285752002163, max_hamiltonian_energy_error = -0.7795285752002163, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.8971893464299524, log_density = 6.956243956522768, hamiltonian_energy = -6.740456103395156, hamiltonian_energy_error = 0.15638766340715105, max_hamiltonian_energy_error = 0.15638766340715105, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.8009452909366125, log_density = 7.9398838489398145, hamiltonian_energy = -4.520313626376483, hamiltonian_energy_error = -0.20572759349833447, max_hamiltonian_energy_error = 0.437393378055142, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.758449776862797, log_density = 7.608920626665104, hamiltonian_energy = -5.635998941369806, hamiltonian_energy_error = 0.11261034283846261, max_hamiltonian_energy_error = 0.4972558146558246, tree_depth = 2, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 19, is_accept = true, acceptance_rate = 0.9949662919820594, log_density = 7.8705920752571705, hamiltonian_energy = -7.297503627254557, hamiltonian_energy_error = -0.06226479993551948, max_hamiltonian_energy_error = -0.09578892650285908, tree_depth = 4, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false), (n_steps = 11, is_accept = true, acceptance_rate = 0.954410598110778, log_density = 7.464713369734034, hamiltonian_energy = -7.375261478962942, hamiltonian_energy_error = 0.09882393074116447, max_hamiltonian_energy_error = 0.09882393074116447, tree_depth = 3, numerical_error = false, step_size = 0.7965357614972391, nom_step_size = 0.7965357614972391, is_adapt = false)])</code></pre><p>Now we pack the samples into an <code>MCMCChains.Chains</code>:</p><pre><code class="language- hljs">samples_transformed = reduce(vcat, fun.transform.(samples)&#39;)
 varnames = Pathfinder.flattened_varnames_list(model)
-chns = MCMCChains.Chains(samples_transformed, varnames)</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 28 August 2023 00:30">Monday 28 August 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+chns = MCMCChains.Chains(samples_transformed, varnames)</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Tuesday 29 August 2023 01:32">Tuesday 29 August 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>