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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-10-01T14:47:34","documenter_version":"1.7.0"}}
{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-07T21:56:45","documenter_version":"1.7.0"}}
62 changes: 31 additions & 31 deletions dev/api/index.html
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2 changes: 1 addition & 1 deletion dev/basics/distributed/index.html
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@everywhere using HetaSimulator

s1 = mc(scn1, df, 150, parallel_type=EnsembleDistributed())
s2 = mc([scn1, scn2, scn3], [:k2=&gt;Normal(1e-3,1e-4), :k3=&gt;Normal(1e-4,1e-5)], 150, parallel_type=EnsembleDistributed())</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../overview/">« Quick start</a><a class="docs-footer-nextpage" href="../../table-formats/scenario/">Scenarios tables »</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 1.7.0 on <span class="colophon-date" title="Tuesday 1 October 2024 14:47">Tuesday 1 October 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
s2 = mc([scn1, scn2, scn3], [:k2=&gt;Normal(1e-3,1e-4), :k3=&gt;Normal(1e-4,1e-5)], 150, parallel_type=EnsembleDistributed())</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../overview/">« Quick start</a><a class="docs-footer-nextpage" href="../../table-formats/scenario/">Scenarios tables »</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 1.7.0 on <span class="colophon-date" title="Thursday 7 November 2024 21:56">Thursday 7 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/basics/overview/index.html
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:sigma1 =&gt; 0.020347955494158528
:sigma2 =&gt; 0.31561050699802246
:sigma3 =&gt; 0.5716026958426483</code></pre><p>You can simulate and plot results with the following code.</p><pre><code class="language-julia hljs">res_optim = sim(p, parameters = optim(fit_res))
plot(res_optim, yscale=:log, ylims=(1e-3,1e2))</code></pre><p><img src="../sim5.png" alt="sim5"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« Home</a><a class="docs-footer-nextpage" href="../distributed/">Parallel simulations »</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 1.7.0 on <span class="colophon-date" title="Tuesday 1 October 2024 14:47">Tuesday 1 October 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
plot(res_optim, yscale=:log, ylims=(1e-3,1e2))</code></pre><p><img src="../sim5.png" alt="sim5"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« Home</a><a class="docs-footer-nextpage" href="../distributed/">Parallel simulations »</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 1.7.0 on <span class="colophon-date" title="Thursday 7 November 2024 21:56">Thursday 7 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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│ Float64 Float64 Float64 Symbol
─────┼─────────────────────────────────────────────
1 │ 0.0555525 11.9993 0.000666611 ode_
2 │ 0.611077 11.9927 0.00733069 ode_</code></pre><h2 id="Architecture"><a class="docs-heading-anchor" href="#Architecture">Architecture</a><a id="Architecture-1"></a><a class="docs-heading-anchor-permalink" href="#Architecture" title="Permalink"></a></h2><p>The user of HetaSimulator typically deals with the following three types:</p><ul><li><code>Model</code> - an ODE model, containing rhs, rules, initial parameters and vector of events.</li><li><code>Scenario</code> - scenario representing a specific model&#39;s setup for simulations or fitting. This setup can include initial parameters and events, output variables etc. In case of fitting <code>Scenario</code> should also include experimental data. A common usage of <code>Scenario</code> can be model&#39;s simulation with different drugs (parameters and events setup). Different <code>Scenario</code>&#39;s can be united to run multi-scenarios simulations and fitting.</li><li><code>Platform</code> - container for different <code>Model</code>s and <code>Scenario</code>s.</li></ul><p>The user can perform the following three operations with both <code>Model</code>, <code>Scenario</code> and <code>Platform</code></p><ul><li><code>sim</code> - run a single or multi-scenarios simulations. </li><li><code>fit</code> - fit a model to experimental data. </li><li><code>mc</code> - run Monte-Carlo or virtual patients simulations.</li></ul><p>See documentation for detailed overview of <strong>HetaSimulator</strong> types and functions&#39; arguments.</p><h2 id="Getting-help"><a class="docs-heading-anchor" href="#Getting-help">Getting help</a><a id="Getting-help-1"></a><a class="docs-heading-anchor-permalink" href="#Getting-help" title="Permalink"></a></h2><ul><li>Read the <a href="https://hetalang.github.io/HetaSimulator.jl/stable/">docs</a></li><li>Use <a href="https://gitter.im/hetalang/community?utm_source=readme">Gitter Chatroom</a>.</li><li>Use <a href="https://github.com/hetalang/HetaSimulator.jl/issues">Issue Tracker</a></li></ul><h2 id="License"><a class="docs-heading-anchor" href="#License">License</a><a id="License-1"></a><a class="docs-heading-anchor-permalink" href="#License" title="Permalink"></a></h2><p>This package is distributed under the terms of the <strong>MIT License</strong>.</p><p>Copyright 2020-2024, InSysBio LLC</p><h2 id="Authors-and-history"><a class="docs-heading-anchor" href="#Authors-and-history">Authors and history</a><a id="Authors-and-history-1"></a><a class="docs-heading-anchor-permalink" href="#Authors-and-history" title="Permalink"></a></h2><ul><li>Ivan Borisov</li><li>Evgeny Metelkin</li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="basics/overview/">Quick start »</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 1.7.0 on <span class="colophon-date" title="Tuesday 1 October 2024 14:47">Tuesday 1 October 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 │ 0.611077 11.9927 0.00733069 ode_</code></pre><h2 id="Architecture"><a class="docs-heading-anchor" href="#Architecture">Architecture</a><a id="Architecture-1"></a><a class="docs-heading-anchor-permalink" href="#Architecture" title="Permalink"></a></h2><p>The user of HetaSimulator typically deals with the following three types:</p><ul><li><code>Model</code> - an ODE model, containing rhs, rules, initial parameters and vector of events.</li><li><code>Scenario</code> - scenario representing a specific model&#39;s setup for simulations or fitting. This setup can include initial parameters and events, output variables etc. In case of fitting <code>Scenario</code> should also include experimental data. A common usage of <code>Scenario</code> can be model&#39;s simulation with different drugs (parameters and events setup). Different <code>Scenario</code>&#39;s can be united to run multi-scenarios simulations and fitting.</li><li><code>Platform</code> - container for different <code>Model</code>s and <code>Scenario</code>s.</li></ul><p>The user can perform the following three operations with both <code>Model</code>, <code>Scenario</code> and <code>Platform</code></p><ul><li><code>sim</code> - run a single or multi-scenarios simulations. </li><li><code>fit</code> - fit a model to experimental data. </li><li><code>mc</code> - run Monte-Carlo or virtual patients simulations.</li></ul><p>See documentation for detailed overview of <strong>HetaSimulator</strong> types and functions&#39; arguments.</p><h2 id="Getting-help"><a class="docs-heading-anchor" href="#Getting-help">Getting help</a><a id="Getting-help-1"></a><a class="docs-heading-anchor-permalink" href="#Getting-help" title="Permalink"></a></h2><ul><li>Read the <a href="https://hetalang.github.io/HetaSimulator.jl/stable/">docs</a></li><li>Use <a href="https://gitter.im/hetalang/community?utm_source=readme">Gitter Chatroom</a>.</li><li>Use <a href="https://github.com/hetalang/HetaSimulator.jl/issues">Issue Tracker</a></li></ul><h2 id="License"><a class="docs-heading-anchor" href="#License">License</a><a id="License-1"></a><a class="docs-heading-anchor-permalink" href="#License" title="Permalink"></a></h2><p>This package is distributed under the terms of the <strong>MIT License</strong>.</p><p>Copyright 2020-2024, InSysBio LLC</p><h2 id="Authors-and-history"><a class="docs-heading-anchor" href="#Authors-and-history">Authors and history</a><a id="Authors-and-history-1"></a><a class="docs-heading-anchor-permalink" href="#Authors-and-history" title="Permalink"></a></h2><ul><li>Ivan Borisov</li><li>Evgeny Metelkin</li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="basics/overview/">Quick start »</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 1.7.0 on <span class="colophon-date" title="Thursday 7 November 2024 21:56">Thursday 7 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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push!(dataone.measurements, m1)
push!(dataone.measurements, m2)
push!(dataone.measurements, m3)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../scenario/">« Scenarios tables</a><a class="docs-footer-nextpage" href="../parameters/">Parameters tables »</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 1.7.0 on <span class="colophon-date" title="Tuesday 1 October 2024 14:47">Tuesday 1 October 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
push!(dataone.measurements, m3)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../scenario/">« Scenarios tables</a><a class="docs-footer-nextpage" href="../parameters/">Parameters tables »</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 1.7.0 on <span class="colophon-date" title="Thursday 7 November 2024 21:56">Thursday 7 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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