build based on 9d910f2

previews/PR249/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-11-22T21:07:47","documenter_version":"1.1.2"}}
+{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-11-23T21:46:35","documenter_version":"1.1.2"}}

previews/PR249/assets/Manifest.toml

@@ -267,9 +267,9 @@ version = "1.9.1"
 
 [[deps.DiffEqBase]]
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+version = "6.141.0"
 
     [deps.DiffEqBase.extensions]
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@@ -878,9 +878,9 @@ version = "0.2.4"
 
 [[deps.MultivariatePolynomials]]
 deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"]
-git-tree-sha1 = "6c2e970692b6f4fed2508865c43a0f67f3820cf4"
+git-tree-sha1 = "6ffb234d6d7c866a75c1879d2099049d3a35a83a"
 uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3"
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+version = "0.5.3"
 
 [[deps.MutableArithmetics]]
 deps = ["LinearAlgebra", "SparseArrays", "Test"]
@@ -961,9 +961,9 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
 version = "0.5.5+0"
 
 [[deps.OrderedCollections]]
-git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3"
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 [[deps.OrdinaryDiffEq]]
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@@ -1192,9 +1192,9 @@ version = "0.6.42"
 
 [[deps.SciMLBase]]
 deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "QuasiMonteCarlo", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"]
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-version = "2.8.2"
+version = "2.9.0"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"

previews/PR249/index.html

@@ -59,7 +59,7 @@
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   [459566f4] DiffEqCallbacks v2.34.0
   [163ba53b] DiffResults v1.1.0
   [b552c78f] DiffRules v1.15.1
@@ -126,15 +126,15 @@
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   [961ee093] ModelingToolkit v8.73.1
   [46d2c3a1] MuladdMacro v0.2.4
-  [102ac46a] MultivariatePolynomials v0.5.2
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   [d8a4904e] MutableArithmetics v1.3.3
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   [2774e3e8] NLsolve v4.5.1
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-  [2edaba10] Nemo v0.37.5
+⌅ [2edaba10] Nemo v0.37.5
   [8913a72c] NonlinearSolve v2.8.2
   [6fe1bfb0] OffsetArrays v1.12.10
-  [bac558e1] OrderedCollections v1.6.2
+  [bac558e1] OrderedCollections v1.6.3
   [1dea7af3] OrdinaryDiffEq v6.59.2
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@@ -164,7 +164,7 @@
   [fdea26ae] SIMD v3.4.6
   [94e857df] SIMDTypes v0.1.0
   [476501e8] SLEEFPirates v0.6.42
-  [0bca4576] SciMLBase v2.8.2
+  [0bca4576] SciMLBase v2.9.0
   [e9a6253c] SciMLNLSolve v0.1.9
   [c0aeaf25] SciMLOperators v0.3.7
   [efcf1570] Setfield v1.1.1
@@ -264,4 +264,4 @@
   [3f19e933] p7zip_jll v17.4.0+0
 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`</code></pre></details>You can also download the 
 <a href="">manifest</a> file and the
-<a href="">project</a> file.</article><nav class="docs-footer"><a class="docs-footer-nextpage" href="tutorials/creating_ode/">Creating ODE System »</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="Wednesday 22 November 2023 21:07">Wednesday 22 November 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+<a href="">project</a> file.</article><nav class="docs-footer"><a class="docs-footer-nextpage" href="tutorials/creating_ode/">Creating ODE System »</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="Thursday 23 November 2023 21:46">Thursday 23 November 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR249/input/input/index.html

@@ -9,4 +9,4 @@
     x1'(t) = a * x1(t) + u(t),
     x2'(t) = b * x2(t) + c*x1(t)*x2(t),
     y(t) = x1(t)
-)</code></pre><p>Here,</p><ul><li><code>x1</code>, <code>x2</code> are state variables</li><li><code>y</code> is an output variable</li><li><code>u</code> is an input variable</li><li><code>a</code>, <code>b</code>, <code>c</code> are time-indepdendent parameters</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/a5d01bf71bbf18e881688c04c28643b928a87e88/src/ODE.jl#L338-L364">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="StructuralIdentifiability.ODE" href="#StructuralIdentifiability.ODE"><code>StructuralIdentifiability.ODE</code></a> — <span class="docstring-category">Type</span></header><section><div><p>The main structure that represents input ODE system.</p><p>Stores information about states (<code>x_vars</code>), outputs (<code>y_vars</code>), inputs (<code>u_vars</code>), parameters (<code>parameters</code>) and the equations.</p><p>This structure is constructed via <code>@ODEmodel</code> macro.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/a5d01bf71bbf18e881688c04c28643b928a87e88/src/ODE.jl#L1-L7">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="StructuralIdentifiability.set_parameter_values" href="#StructuralIdentifiability.set_parameter_values"><code>StructuralIdentifiability.set_parameter_values</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">set_parameter_values(ode, param_values)</code></pre><p>Input:</p><ul><li><code>ode</code> - an ODE as above</li><li><code>param_values</code> - values for (possibly, some of) the parameters as dictionary <code>parameter</code> =&gt; <code>value</code></li></ul><p>Output:</p><ul><li>new ode with the parameters in param_values plugged with the given numbers</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/a5d01bf71bbf18e881688c04c28643b928a87e88/src/ODE.jl#L84-L93">source</a></section></article><h2 id="Create-Compartmental-Model"><a class="docs-heading-anchor" href="#Create-Compartmental-Model">Create Compartmental Model</a><a id="Create-Compartmental-Model-1"></a><a class="docs-heading-anchor-permalink" href="#Create-Compartmental-Model" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="StructuralIdentifiability.linear_compartment_model" href="#StructuralIdentifiability.linear_compartment_model"><code>StructuralIdentifiability.linear_compartment_model</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">linear_compartment_model(graph, inputs, outputs, leaks)</code></pre><p>Input: defines a linear compartment model with nodes numbered from 1 to <code>n</code> by</p><ul><li><code>graph</code> - and array of integer arrays representing the adjacency lists of the graph</li><li><code>inputs</code> - array of input nodes</li><li><code>outputs</code> - array of output nodes</li><li><code>leaks</code> - array of sink nodes</li></ul><p>Output:</p><ul><li>the corresponding ODE system in the notation of https://doi.org/10.1007/s11538-015-0098-0</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/a5d01bf71bbf18e881688c04c28643b928a87e88/src/lincomp.jl#L16-L27">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/discrete_time/">« Identifiability of Discrete-Time Models (Local)</a><a class="docs-footer-nextpage" href="../../identifiability/identifiability/">Functions to Assess Identifiability »</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="Wednesday 22 November 2023 21:07">Wednesday 22 November 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+)</code></pre><p>Here,</p><ul><li><code>x1</code>, <code>x2</code> are state variables</li><li><code>y</code> is an output variable</li><li><code>u</code> is an input variable</li><li><code>a</code>, <code>b</code>, <code>c</code> are time-indepdendent parameters</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/9d910f285d7c6d6bbe7e95940961eaa036d429cd/src/ODE.jl#L338-L364">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="StructuralIdentifiability.ODE" href="#StructuralIdentifiability.ODE"><code>StructuralIdentifiability.ODE</code></a> — <span class="docstring-category">Type</span></header><section><div><p>The main structure that represents input ODE system.</p><p>Stores information about states (<code>x_vars</code>), outputs (<code>y_vars</code>), inputs (<code>u_vars</code>), parameters (<code>parameters</code>) and the equations.</p><p>This structure is constructed via <code>@ODEmodel</code> macro.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/9d910f285d7c6d6bbe7e95940961eaa036d429cd/src/ODE.jl#L1-L7">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="StructuralIdentifiability.set_parameter_values" href="#StructuralIdentifiability.set_parameter_values"><code>StructuralIdentifiability.set_parameter_values</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">set_parameter_values(ode, param_values)</code></pre><p>Input:</p><ul><li><code>ode</code> - an ODE as above</li><li><code>param_values</code> - values for (possibly, some of) the parameters as dictionary <code>parameter</code> =&gt; <code>value</code></li></ul><p>Output:</p><ul><li>new ode with the parameters in param_values plugged with the given numbers</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/9d910f285d7c6d6bbe7e95940961eaa036d429cd/src/ODE.jl#L84-L93">source</a></section></article><h2 id="Create-Compartmental-Model"><a class="docs-heading-anchor" href="#Create-Compartmental-Model">Create Compartmental Model</a><a id="Create-Compartmental-Model-1"></a><a class="docs-heading-anchor-permalink" href="#Create-Compartmental-Model" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="StructuralIdentifiability.linear_compartment_model" href="#StructuralIdentifiability.linear_compartment_model"><code>StructuralIdentifiability.linear_compartment_model</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">linear_compartment_model(graph, inputs, outputs, leaks)</code></pre><p>Input: defines a linear compartment model with nodes numbered from 1 to <code>n</code> by</p><ul><li><code>graph</code> - and array of integer arrays representing the adjacency lists of the graph</li><li><code>inputs</code> - array of input nodes</li><li><code>outputs</code> - array of output nodes</li><li><code>leaks</code> - array of sink nodes</li></ul><p>Output:</p><ul><li>the corresponding ODE system in the notation of https://doi.org/10.1007/s11538-015-0098-0</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/9d910f285d7c6d6bbe7e95940961eaa036d429cd/src/lincomp.jl#L16-L27">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/discrete_time/">« Identifiability of Discrete-Time Models (Local)</a><a class="docs-footer-nextpage" href="../../identifiability/identifiability/">Functions to Assess Identifiability »</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="Thursday 23 November 2023 21:46">Thursday 23 November 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>