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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-10-28T04:46:10","documenter_version":"1.7.0"}}
{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-10-28T05:16:25","documenter_version":"1.7.0"}}
2 changes: 1 addition & 1 deletion dev/examples/binomial_normal_approximation/index.html
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using Plots; gr()

plots = plot_bivariate_profiles(model, 0.2, 0.2; include_internal_points=true, markeralpha=0.9, format...)
display(plots[1])</code></pre><p><img src="../../assets/figures/binomial/binomial_bivariate_plot.png" alt/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../two-species_logistic/">« Two-Species Logistic Model</a><a class="docs-footer-nextpage" href="../logistic_timing_estimates/">Function Evaluation Timing - Logistic Model »</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="Monday 28 October 2024 04:46">Monday 28 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
display(plots[1])</code></pre><p><img src="../../assets/figures/binomial/binomial_bivariate_plot.png" alt/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../two-species_logistic/">« Two-Species Logistic Model</a><a class="docs-footer-nextpage" href="../logistic_timing_estimates/">Function Evaluation Timing - Logistic Model »</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="Monday 28 October 2024 05:16">Monday 28 October 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/examples/index.html
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addprocs(Threads.nthreads()-2, env=[&quot;JULIA_NUM_THREADS&quot;=&gt;&quot;1&quot;]) # the number of parallel workers to use - on the author&#39;s system Threads.nthreads() returns 10
# addprocs(8, env=[&quot;JULIA_NUM_THREADS&quot;=&gt;&quot;1&quot;]) # add 8 workers - total number of workers will be 9</code></pre><p>We can now check how many workers are allocated.</p><pre><code class="language-julia hljs">nprocs() # use to check the total number of worker processes allocated
workers() # the ids of the allocated workers
# Threads.nthreads() # the number of execution threads allocated to Julia at startup</code></pre><p>We import our package with the annotation <code>@everywhere</code>, letting Julia know that we wish to load the package on all allocated workers.</p><div class="admonition is-warning"><header class="admonition-header">Use of `@everywhere`</header><div class="admonition-body"><p>If <code>@everywhere</code> is not used at the beginning of the package import, then the package <code>LikelihoodBasedProfileWiseAnalysis</code> is only loaded onto the master worker&#39;s environment and cannot be seen by the other workers we wish to parallelise the simulation on. Similarly, any other functions that need to be loaded onto all workers, such as those that define the log-likelihood function, also need to have the annotation <code>@everywhere</code>. Resultantly, Julia will throw an error if <code>nprocs()&gt;1</code>. However, an error won&#39;t be thrown if we haven&#39;t added any worker processes (if <code>nprocs()==1</code>) using the above multiprocessing arguments (this package can run on a single thread).</p></div></div><pre><code class="language-julia hljs">@everywhere using LikelihoodBasedProfileWiseAnalysis</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../user_interface/coverage/predictions_and_realisations/">« Predictions and Realisations</a><a class="docs-footer-nextpage" href="logistic/">Logistic Model »</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="Monday 28 October 2024 04:46">Monday 28 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
# Threads.nthreads() # the number of execution threads allocated to Julia at startup</code></pre><p>We import our package with the annotation <code>@everywhere</code>, letting Julia know that we wish to load the package on all allocated workers.</p><div class="admonition is-warning"><header class="admonition-header">Use of `@everywhere`</header><div class="admonition-body"><p>If <code>@everywhere</code> is not used at the beginning of the package import, then the package <code>LikelihoodBasedProfileWiseAnalysis</code> is only loaded onto the master worker&#39;s environment and cannot be seen by the other workers we wish to parallelise the simulation on. Similarly, any other functions that need to be loaded onto all workers, such as those that define the log-likelihood function, also need to have the annotation <code>@everywhere</code>. Resultantly, Julia will throw an error if <code>nprocs()&gt;1</code>. However, an error won&#39;t be thrown if we haven&#39;t added any worker processes (if <code>nprocs()==1</code>) using the above multiprocessing arguments (this package can run on a single thread).</p></div></div><pre><code class="language-julia hljs">@everywhere using LikelihoodBasedProfileWiseAnalysis</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../user_interface/coverage/predictions_and_realisations/">« Predictions and Realisations</a><a class="docs-footer-nextpage" href="logistic/">Logistic Model »</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="Monday 28 October 2024 05:16">Monday 28 October 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/examples/logistic/index.html
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collect(combinations(1:model.core.num_pars, 2)),
dof=model.core.num_pars,
method=IterativeBoundaryMethod(10, 5, 5, 0.15, 0.1, use_ellipse=true),
optimizationsettings=opt_settings)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Distributed Environment Setup</a><a class="docs-footer-nextpage" href="../lotka-volterra/">Lotka-Volterra Model »</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="Monday 28 October 2024 04:46">Monday 28 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
optimizationsettings=opt_settings)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Distributed Environment Setup</a><a class="docs-footer-nextpage" href="../lotka-volterra/">Lotka-Volterra Model »</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="Monday 28 October 2024 05:16">Monday 28 October 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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TO.reset_timer!(LikelihoodBasedProfileWiseAnalysis.timer)
end

TO.disable_debug_timings(LikelihoodBasedProfileWiseAnalysis)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../binomial_normal_approximation/">« Gaussian Approximation of a Binomial Distribution</a><a class="docs-footer-nextpage" href="../../internal_library/common/">Common Functions »</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="Monday 28 October 2024 04:46">Monday 28 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
TO.disable_debug_timings(LikelihoodBasedProfileWiseAnalysis)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../binomial_normal_approximation/">« Gaussian Approximation of a Binomial Distribution</a><a class="docs-footer-nextpage" href="../../internal_library/common/">Common Functions »</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="Monday 28 October 2024 05:16">Monday 28 October 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/examples/lotka-volterra/index.html
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collect(combinations(1:model.core.num_pars, 2)),
dof=model.core.num_pars,
method=IterativeBoundaryMethod(20, 5, 5, 0.15, 0.1, use_ellipse=true),
optimizationsettings=opt_settings)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../logistic/">« Logistic Model</a><a class="docs-footer-nextpage" href="../two-species_logistic/">Two-Species Logistic Model »</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="Monday 28 October 2024 04:46">Monday 28 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
optimizationsettings=opt_settings)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../logistic/">« Logistic Model</a><a class="docs-footer-nextpage" href="../two-species_logistic/">Two-Species Logistic Model »</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="Monday 28 October 2024 05:16">Monday 28 October 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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