build based on e901e69

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-04-08T13:07:38","documenter_version":"1.3.0"}}
+{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-06T08:48:04","documenter_version":"1.4.1"}}

dev/faq/index.html

@@ -69,4 +69,4 @@
 end
 
 upc = UprevCondition(u0[2])
-cb = DiscreteCallback(upc, upc)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../jump_solve/">« Jump solvers</a><a class="docs-footer-nextpage" href="../api/">API »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Monday 8 April 2024 13:06">Monday 8 April 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+cb = DiscreteCallback(upc, upc)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../jump_solve/">« Jump solvers</a><a class="docs-footer-nextpage" href="../api/">API »</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></select></div></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="Monday 6 May 2024 08:47">Monday 6 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/jump_types/index.html

@@ -34,4 +34,4 @@
 dprob2 = DiscreteProblem(u02, tspan2, p2)
 jprob2 = remake(jprob, prob = dprob2)
 sol2 = solve(jprob2, SSAStepper())</code></pre><p>or by directly remaking with the new parameters</p><pre><code class="language-julia hljs">jprob2 = remake(jprob, u0 = u02, p = p2, tspan = tspan2)
-sol2 = solve(jprob2, SSAStepper())</code></pre><p>To avoid ambiguities, the following will give an error</p><pre><code class="language-julia hljs">jprob2 = remake(jprob, prob = dprob2, u0 = u02)</code></pre><p>as will trying to update either <code>p</code> or <code>tspan</code> while passing a new <code>DiscreteProblem</code> using the <code>prob</code> kwarg.</p><h2 id="References"><a class="docs-heading-anchor" href="#References">References</a><a id="References-1"></a><a class="docs-heading-anchor-permalink" href="#References" title="Permalink"></a></h2><section class="footnotes is-size-7"><ul><li class="footnote" id="footnote-1"><a class="tag is-link" href="#citeref-1">1</a>V. Lemaire, M. Thieullen and N. Thomas, Exact Simulation of the Jump Times of a Class of Piecewise Deterministic Markov Processes, Journal of Scientific Computing, 75 (3), 1776-1807 (2018). doi:10.1007/s10915-017-0607-4.</li><li class="footnote" id="footnote-2"><a class="tag is-link" href="#citeref-2">2</a>D. T. Gillespie, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, Journal of Computational Physics, 22 (4), 403–434 (1976). doi:10.1016/0021-9991(76)90041-3.</li><li class="footnote" id="footnote-3"><a class="tag is-link" href="#citeref-3">3</a>A. Slepoy, A.P. Thompson and S.J. Plimpton, A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks, Journal of Chemical Physics, 128 (20), 205101 (2008). doi:10.1063/1.2919546.</li><li class="footnote" id="footnote-4"><a class="tag is-link" href="#citeref-4">4</a>J. M. McCollum, G. D. Peterson, C. D. Cox, M. L. Simpson and N. F. Samatova, The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior, Computational Biology and Chemistry, 30 (1), 39049 (2006). doi:10.1016/j.compbiolchem.2005.10.007.</li><li class="footnote" id="footnote-5"><a class="tag is-link" href="#citeref-5">5</a>V. H. Thanh, C. Priami and R. Zunino, Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays, Journal of Chemical Physics, 141 (13), 134116 (2014). doi:10.1063/1.4896985.</li><li class="footnote" id="footnote-6"><a class="tag is-link" href="#citeref-6">6</a>V. H. Thanh, R. Zunino and C. Priami, On the rejection-based algorithm for simulation and analysis of large-scale reaction networks, Journal of Chemical Physics, 142 (24), 244106 (2015). doi:10.1063/1.4922923.</li><li class="footnote" id="footnote-7"><a class="tag is-link" href="#citeref-7">7</a>V. H. Thanh, R. Zunino, and C. Priami, Efficient constant-time complexity algorithm for stochastic simulation of large reaction networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14 (3), 657-667 (2017). doi:10.1109/TCBB.2016.2530066.</li><li class="footnote" id="footnote-8"><a class="tag is-link" href="#citeref-8">8</a>M. A. Gibson and J. Bruck, Efficient exact stochastic simulation of chemical systems with many species and many channels, Journal of Physical Chemistry A, 104 (9), 1876-1889 (2000). doi:10.1021/jp993732q.</li><li class="footnote" id="footnote-9"><a class="tag is-link" href="#citeref-9">9</a>M. Farajtabar, Y. Wang, M. Gomez-Rodriguez, S. Li, H. Zha, and L. Song, COEVOLVE: a joint point process model for information diffusion and network evolution, Journal of Machine Learning Research 18(1), 1305–1353 (2017). doi: 10.5555/3122009.3122050.</li></ul></section></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../applications/advanced_point_process/">« Temporal Point Processes (TPP) with JumpProcesses and PointProcesses</a><a class="docs-footer-nextpage" href="../jump_solve/">Jump solvers »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Monday 8 April 2024 13:06">Monday 8 April 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+sol2 = solve(jprob2, SSAStepper())</code></pre><p>To avoid ambiguities, the following will give an error</p><pre><code class="language-julia hljs">jprob2 = remake(jprob, prob = dprob2, u0 = u02)</code></pre><p>as will trying to update either <code>p</code> or <code>tspan</code> while passing a new <code>DiscreteProblem</code> using the <code>prob</code> kwarg.</p><h2 id="References"><a class="docs-heading-anchor" href="#References">References</a><a id="References-1"></a><a class="docs-heading-anchor-permalink" href="#References" title="Permalink"></a></h2><section class="footnotes is-size-7"><ul><li class="footnote" id="footnote-1"><a class="tag is-link" href="#citeref-1">1</a>V. Lemaire, M. Thieullen and N. Thomas, Exact Simulation of the Jump Times of a Class of Piecewise Deterministic Markov Processes, Journal of Scientific Computing, 75 (3), 1776-1807 (2018). doi:10.1007/s10915-017-0607-4.</li><li class="footnote" id="footnote-2"><a class="tag is-link" href="#citeref-2">2</a>D. T. Gillespie, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, Journal of Computational Physics, 22 (4), 403–434 (1976). doi:10.1016/0021-9991(76)90041-3.</li><li class="footnote" id="footnote-3"><a class="tag is-link" href="#citeref-3">3</a>A. Slepoy, A.P. Thompson and S.J. Plimpton, A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks, Journal of Chemical Physics, 128 (20), 205101 (2008). doi:10.1063/1.2919546.</li><li class="footnote" id="footnote-4"><a class="tag is-link" href="#citeref-4">4</a>J. M. McCollum, G. D. Peterson, C. D. Cox, M. L. Simpson and N. F. Samatova, The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior, Computational Biology and Chemistry, 30 (1), 39049 (2006). doi:10.1016/j.compbiolchem.2005.10.007.</li><li class="footnote" id="footnote-5"><a class="tag is-link" href="#citeref-5">5</a>V. H. Thanh, C. Priami and R. Zunino, Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays, Journal of Chemical Physics, 141 (13), 134116 (2014). doi:10.1063/1.4896985.</li><li class="footnote" id="footnote-6"><a class="tag is-link" href="#citeref-6">6</a>V. H. Thanh, R. Zunino and C. Priami, On the rejection-based algorithm for simulation and analysis of large-scale reaction networks, Journal of Chemical Physics, 142 (24), 244106 (2015). doi:10.1063/1.4922923.</li><li class="footnote" id="footnote-7"><a class="tag is-link" href="#citeref-7">7</a>V. H. Thanh, R. Zunino, and C. Priami, Efficient constant-time complexity algorithm for stochastic simulation of large reaction networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14 (3), 657-667 (2017). doi:10.1109/TCBB.2016.2530066.</li><li class="footnote" id="footnote-8"><a class="tag is-link" href="#citeref-8">8</a>M. A. Gibson and J. Bruck, Efficient exact stochastic simulation of chemical systems with many species and many channels, Journal of Physical Chemistry A, 104 (9), 1876-1889 (2000). doi:10.1021/jp993732q.</li><li class="footnote" id="footnote-9"><a class="tag is-link" href="#citeref-9">9</a>M. Farajtabar, Y. Wang, M. Gomez-Rodriguez, S. Li, H. Zha, and L. Song, COEVOLVE: a joint point process model for information diffusion and network evolution, Journal of Machine Learning Research 18(1), 1305–1353 (2017). doi: 10.5555/3122009.3122050.</li></ul></section></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../applications/advanced_point_process/">« Temporal Point Processes (TPP) with JumpProcesses and PointProcesses</a><a class="docs-footer-nextpage" href="../jump_solve/">Jump solvers »</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></select></div></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="Monday 6 May 2024 08:47">Monday 6 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>