build based on 5caadd9

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-29T00:31:38","documenter_version":"1.1.2"}}
+{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-30T14:41:06","documenter_version":"1.1.2"}}

dev/generated/covid/bilayerconversion/index.html

@@ -2028,4 +2028,4 @@
 │ 6.52941 │  1.26071 │  0.87633 │   0.243074 │  2.09047 │
 │ 6.40594 │  1.27708 │ 0.877557 │   0.258154 │  2.18127 │
 │ 6.28322 │   1.2926 │ 0.877852 │   0.273717 │  2.27261 │
-└─────────┴──────────┴──────────┴────────────┴──────────┘</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../enzymes/enzyme_reactions/">« Cathepsin Enzyme Reactions</a><a class="docs-footer-nextpage" href="../stratification/">Stratification of COVID Models »</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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Sunday 29 October 2023 00:31">Sunday 29 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+└─────────┴──────────┴──────────┴────────────┴──────────┘</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../enzymes/enzyme_reactions/">« Cathepsin Enzyme Reactions</a><a class="docs-footer-nextpage" href="../stratification/">Stratification of COVID Models »</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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 30 October 2023 14:40">Monday 30 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/generated/covid/disease_strains/index.html

@@ -651,4 +651,4 @@
 aug_sird_strain_vax = add_reflexives(sird_strain_vax_retyped, reflx, aug_inf_ontology);</code></pre><p>To the simple trip model, we add an <code>:nstrata</code> tranisiton for each state.</p><pre><code class="language-julia hljs">simple_trip_retyped = flatten_labels(compose(simple_trip_model,rgn_ont_act))
 aug_trip = add_reflexives(simple_trip_retyped, repeat([[:nstrata]],ns(dom(simple_trip_retyped))), aug_inf_ontology);</code></pre><h3 id="Stratify-the-SIRD-strain-vax-and-simple-trip-models"><a class="docs-heading-anchor" href="#Stratify-the-SIRD-strain-vax-and-simple-trip-models">Stratify the SIRD-strain-vax and simple trip models</a><a id="Stratify-the-SIRD-strain-vax-and-simple-trip-models-1"></a><a class="docs-heading-anchor-permalink" href="#Stratify-the-SIRD-strain-vax-and-simple-trip-models" title="Permalink"></a></h3><pre><code class="language-julia hljs">sird_strain_vax_trip = typed_product([aug_sird_strain_vax,aug_trip])
 
-to_graphviz(dom(sird_strain_vax_trip))</code></pre><img src="66c2dd49.svg" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../stratification/">« Stratification of COVID Models</a><a class="docs-footer-nextpage" href="../max_common_subobject/">Maximum Common Sub C-Set »</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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Sunday 29 October 2023 00:31">Sunday 29 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+to_graphviz(dom(sird_strain_vax_trip))</code></pre><img src="66c2dd49.svg" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../stratification/">« Stratification of COVID Models</a><a class="docs-footer-nextpage" href="../max_common_subobject/">Maximum Common Sub C-Set »</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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 30 October 2023 14:41">Monday 30 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/generated/covid/epidemiology/index.html

@@ -183,7 +183,7 @@
 p = LVector(inf=0.4, rec=0.4);</code></pre><p>The C-Set representation has direct support for generating a DiffEq vector field</p><pre><code class="language-julia hljs">prob = ODEProblem(vectorfield(p_sir),u0,(0.0,7.5),p);
 sol = solve(prob,Tsit5())
 
-plot(sol)</code></pre><img src="1d5d4184.svg" alt="Example block output"/><h4 id="SEIR-Model:"><a class="docs-heading-anchor" href="#SEIR-Model:">SEIR Model:</a><a id="SEIR-Model:-1"></a><a class="docs-heading-anchor-permalink" href="#SEIR-Model:" title="Permalink"></a></h4><p>define model</p><pre><code class="language-julia hljs">seir = @relation (s,e,i,r) begin
+plot(sol)</code></pre><img src="3e803f54.svg" alt="Example block output"/><h4 id="SEIR-Model:"><a class="docs-heading-anchor" href="#SEIR-Model:">SEIR Model:</a><a id="SEIR-Model:-1"></a><a class="docs-heading-anchor-permalink" href="#SEIR-Model:" title="Permalink"></a></h4><p>define model</p><pre><code class="language-julia hljs">seir = @relation (s,e,i,r) begin
     exposure(s,i,e)
     illness(e,i)
     recovery(i,r)
@@ -424,7 +424,7 @@
 prob = ODEProblem(vectorfield(p_seir),u0,(0.0,15.0),p);
 sol = solve(prob,Tsit5())
 
-plot(sol)</code></pre><img src="b23df9d0.svg" alt="Example block output"/><h4 id="SEIRD-Model:"><a class="docs-heading-anchor" href="#SEIRD-Model:">SEIRD Model:</a><a id="SEIRD-Model:-1"></a><a class="docs-heading-anchor-permalink" href="#SEIRD-Model:" title="Permalink"></a></h4><p>define model</p><pre><code class="language-julia hljs">seird = @relation (s,e,i,r,d) begin
+plot(sol)</code></pre><img src="55f06ab6.svg" alt="Example block output"/><h4 id="SEIRD-Model:"><a class="docs-heading-anchor" href="#SEIRD-Model:">SEIRD Model:</a><a id="SEIRD-Model:-1"></a><a class="docs-heading-anchor-permalink" href="#SEIRD-Model:" title="Permalink"></a></h4><p>define model</p><pre><code class="language-julia hljs">seird = @relation (s,e,i,r,d) begin
     exposure(s,i,e)
     illness(e,i)
     recovery(i,r)
@@ -721,4 +721,4 @@
 prob = ODEProblem(vectorfield(p_seird),u0,(0.0,15.0),p);
 sol = solve(prob,Tsit5())
 
-plot(sol)</code></pre><img src="bbe1cf53.svg" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../predation/lotka-volterra/">« Lotka-Volterra Model</a><a class="docs-footer-nextpage" href="../../enzymes/enzyme_reactions/">Cathepsin Enzyme Reactions »</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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Sunday 29 October 2023 00:31">Sunday 29 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plot(sol)</code></pre><img src="8e85dc1c.svg" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../predation/lotka-volterra/">« Lotka-Volterra Model</a><a class="docs-footer-nextpage" href="../../enzymes/enzyme_reactions/">Cathepsin Enzyme Reactions »</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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 30 October 2023 14:41">Monday 30 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/generated/covid/max_common_subobject/index.html

@@ -961,4 +961,4 @@
 </g>
 </g>
 </svg>
-'/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../disease_strains/">« Multiple-Strain Model of COVID and Vaccines</a><a class="docs-footer-nextpage" href="../../../api/">Library Reference »</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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Sunday 29 October 2023 00:31">Sunday 29 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+'/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../disease_strains/">« Multiple-Strain Model of COVID and Vaccines</a><a class="docs-footer-nextpage" href="../../../api/">Library Reference »</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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 30 October 2023 14:41">Monday 30 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>