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     = 7.91 seconds
-Compute duration  = 5.49 seconds
+Wall duration     = 8.29 seconds
+Compute duration  = 5.86 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">([[1.4676402233577517, 2.0074038351557344, -1.4841937242140848], [1.4807946823073779, 2.0093123538946296, -1.5181587082519967], [1.415393196701997, 2.007056906013418, -1.4321505435894895], [1.493231958550808, 2.00341124900399, -1.5931804982180824], [1.4561374815832329, 2.011388144537265, -1.5185743201225377], [1.5218218898915163, 1.9997281004626335, -1.6081599902590913], [1.4865222773504163, 2.0060288523741434, -1.5960983644526323], [1.4645278977026965, 2.009341376402341, -1.6767083888554495], [1.512515685316033, 2.0027271841784025, -1.4073616456821285], [1.5036001911203791, 1.995789055325274, -1.5486660645040526]  …  [1.5129472987618144, 1.9931476408498332, -1.605188822644906], [1.4362468608990842, 2.01238639794947, -1.630789444029088], [1.5302979980280567, 1.995947091140596, -1.462321807636107], [1.4907390646514165, 2.0065112037496045, -1.5450615247120634], [1.490634870113431, 2.0010298354323384, -1.6301395083494823], [1.4646460455078356, 2.009722646886248, -1.552417987563257], [1.5300956489836317, 1.997405454393315, -1.6451578523810704], [1.436088289703882, 2.01085264592819, -1.591661426829158], [1.4824733020478118, 1.9996745881169993, -1.5531501748711314], [1.4809078303928631, 1.9994430010724284, -1.5688139887827495]], NamedTuple[(n_steps = 7, is_accept = true, acceptance_rate = 0.883600253830029, log_density = 7.761488891605511, hamiltonian_energy = -5.449857209110606, hamiltonian_energy_error = -0.004598836381440208, max_hamiltonian_energy_error = 0.2744620290551536, tree_depth = 3, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.9392494156413083, log_density = 7.528433449761108, hamiltonian_energy = -6.681374538522578, hamiltonian_energy_error = 0.019214956520409388, max_hamiltonian_energy_error = 0.12379508840124753, tree_depth = 2, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.7120275508653812, log_density = 4.186245521102456, hamiltonian_energy = -3.6754079091725127, hamiltonian_energy_error = 0.438488030607314, max_hamiltonian_energy_error = 0.438488030607314, tree_depth = 2, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 7, is_accept = true, acceptance_rate = 0.9605800748703299, log_density = 7.949650072506822, hamiltonian_energy = -3.1610190479831237, hamiltonian_energy_error = -0.5854110216058186, max_hamiltonian_energy_error = -0.5854110216058186, tree_depth = 3, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 7, is_accept = true, acceptance_rate = 0.96554694407735, log_density = 7.802574934285351, hamiltonian_energy = -7.459218488786334, hamiltonian_energy_error = 0.03961194141551161, max_hamiltonian_energy_error = 0.0555739612847761, tree_depth = 3, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.9505344253847955, log_density = 7.200063535130109, hamiltonian_energy = -6.840269168776417, hamiltonian_energy_error = 0.058406665731227214, max_hamiltonian_energy_error = 0.09613982298851642, tree_depth = 2, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 11, is_accept = true, acceptance_rate = 0.9969004647515886, log_density = 7.876706043725011, hamiltonian_energy = -7.016030854399295, hamiltonian_energy_error = -0.09956255341367015, max_hamiltonian_energy_error = -0.11975268992651777, tree_depth = 3, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.7818256896080591, log_density = 6.329867834048604, hamiltonian_energy = -5.638796993011745, hamiltonian_energy_error = 0.23821975937041362, max_hamiltonian_energy_error = 0.3838240200238836, tree_depth = 2, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 7, is_accept = true, acceptance_rate = 0.8885254637118603, log_density = 5.861245671846356, hamiltonian_energy = -3.8157290926649043, hamiltonian_energy_error = 0.11037000607528213, max_hamiltonian_energy_error = 0.33485362654746265, tree_depth = 2, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 11, is_accept = true, acceptance_rate = 0.9511796450153046, log_density = 6.607957774659404, hamiltonian_energy = -3.8377368477041816, hamiltonian_energy_error = -0.09436292398567758, max_hamiltonian_energy_error = -0.3038257291549553, tree_depth = 3, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false)  …  (n_steps = 7, is_accept = true, acceptance_rate = 0.8916885801927464, log_density = 5.226404588072593, hamiltonian_energy = -4.277896352320278, hamiltonian_energy_error = 0.2690165699846876, max_hamiltonian_energy_error = 0.2690165699846876, tree_depth = 3, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 11, is_accept = true, acceptance_rate = 1.0, log_density = 7.019780437862182, hamiltonian_energy = -4.819960784311828, hamiltonian_energy_error = -0.3677626374235512, max_hamiltonian_energy_error = -0.42035826865857473, tree_depth = 3, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 7, is_accept = true, acceptance_rate = 0.9132036146804784, log_density = 6.612394319079511, hamiltonian_energy = -5.386581233294251, hamiltonian_energy_error = 0.10012500899977006, max_hamiltonian_energy_error = 0.21324112747079038, tree_depth = 3, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 1.0, log_density = 7.878321485404268, hamiltonian_energy = -6.66661460787871, hamiltonian_energy_error = -0.2183710411307045, max_hamiltonian_energy_error = -0.2183710411307045, tree_depth = 2, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.7797955547387869, log_density = 7.153461855847842, hamiltonian_energy = -4.549506622611551, hamiltonian_energy_error = -0.007392300189944301, max_hamiltonian_energy_error = 0.6187067956498566, tree_depth = 2, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.9900488836858519, log_density = 8.030537772910673, hamiltonian_energy = -6.619381490352603, hamiltonian_energy_error = -0.11693593797947965, max_hamiltonian_energy_error = -0.11693593797947965, tree_depth = 2, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 7, is_accept = true, acceptance_rate = 0.7160772739874185, log_density = 6.264624132178908, hamiltonian_energy = -3.1266014248405947, hamiltonian_energy_error = 0.12538246369640227, max_hamiltonian_energy_error = 0.7535328451430714, tree_depth = 3, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 7, is_accept = true, acceptance_rate = 0.9481407681503587, log_density = 7.5173471057431875, hamiltonian_energy = -4.2587346571289055, hamiltonian_energy_error = -0.16005835781577904, max_hamiltonian_energy_error = 0.17225479155535695, tree_depth = 3, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 3, is_accept = true, acceptance_rate = 0.9513250028584923, log_density = 7.121690491698855, hamiltonian_energy = -6.636997266552586, hamiltonian_energy_error = 0.08947353718440709, max_hamiltonian_energy_error = 0.08947353718440709, tree_depth = 2, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, is_adapt = false), (n_steps = 1, is_accept = true, acceptance_rate = 0.9528697555900233, log_density = 6.8601547814818105, hamiltonian_energy = -6.703189205681179, hamiltonian_energy_error = 0.04827705246423708, max_hamiltonian_energy_error = 0.04827705246423708, tree_depth = 1, numerical_error = false, step_size = 0.7264850453013639, nom_step_size = 0.7264850453013639, 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="Sunday 6 August 2023 00:28">Sunday 6 August 2023</span>. Using Julia version 1.9.2.</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="Monday 7 August 2023 00:29">Monday 7 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>