build based on 1129b8e

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-04-26T01:46:07","documenter_version":"1.4.0"}}
+{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-04-27T09:31:35","documenter_version":"1.4.0"}}

dev/assets/Manifest.toml

@@ -58,9 +58,9 @@ weakdeps = ["StaticArrays"]
 
 [[deps.AliasTables]]
 deps = ["Random"]
-git-tree-sha1 = "ca95b2220ef440817963baa71525a8f2f4ae7f8f"
+git-tree-sha1 = "6f186dadec4d7725aa88d18487139d512f02db7b"
 uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8"
-version = "1.0.0"
+version = "1.1.0"
 
 [[deps.Antic_jll]]
 deps = ["Artifacts", "FLINT_jll", "GMP_jll", "JLLWrappers", "Libdl", "MPFR_jll", "Pkg"]
@@ -811,9 +811,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[deps.LinearSolve]]
 deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"]
-git-tree-sha1 = "bdf5c9162ff9ba8b320d8bbaa076d11dcf8a6c8b"
+git-tree-sha1 = "c55172df0d19b34db93c410cfcd79dbc3e52ba6f"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "2.29.0"
+version = "2.29.1"
 
     [deps.LinearSolve.extensions]
     LinearSolveBandedMatricesExt = "BandedMatrices"

dev/index.html

@@ -30,11 +30,11 @@
 Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)</code></pre></details><details><summary>A more complete overview of all dependencies and their versions is also provided.</summary><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Status `~/work/StructuralIdentifiability.jl/StructuralIdentifiability.jl/docs/Manifest.toml`
 ⌅ [47edcb42] ADTypes v0.2.7
   [a4c015fc] ANSIColoredPrinters v0.0.1
-  [c3fe647b] AbstractAlgebra v0.40.9
+⌅ [c3fe647b] AbstractAlgebra v0.40.9
   [1520ce14] AbstractTrees v0.4.5
   [7d9f7c33] Accessors v0.1.36
   [79e6a3ab] Adapt v4.0.4
-  [66dad0bd] AliasTables v1.0.0
+  [66dad0bd] AliasTables v1.1.0
   [ec485272] ArnoldiMethod v0.4.0
   [4fba245c] ArrayInterface v7.10.0
   [4c555306] ArrayLayouts v1.9.2
@@ -119,7 +119,7 @@
   [0e77f7df] LazilyInitializedFields v1.2.2
   [5078a376] LazyArrays v1.10.0
   [d3d80556] LineSearches v7.2.0
-  [7ed4a6bd] LinearSolve v2.29.0
+  [7ed4a6bd] LinearSolve v2.29.1
   [2ab3a3ac] LogExpFunctions v0.3.27
   [bdcacae8] LoopVectorization v0.12.169
   [d8e11817] MLStyle v0.4.17
@@ -275,4 +275,4 @@
   [3f19e933] p7zip_jll v17.4.0+2
 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints 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="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 1.4.0 on <span class="colophon-date" title="Friday 26 April 2024 01:46">Friday 26 April 2024</span>. Using Julia version 1.10.2.</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="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 1.4.0 on <span class="colophon-date" title="Saturday 27 April 2024 09:31">Saturday 27 April 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/input/input/index.html

@@ -9,10 +9,10 @@
     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-independent parameters</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/8d3f4c686bacdcdc1b3db80998b8fe302aed34a8/src/input_macro.jl#L242-L268">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/8d3f4c686bacdcdc1b3db80998b8fe302aed34a8/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/8d3f4c686bacdcdc1b3db80998b8fe302aed34a8/src/ODE.jl#L87-L96">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/8d3f4c686bacdcdc1b3db80998b8fe302aed34a8/src/lincomp.jl#L16-L27">source</a></section></article><h2 id="Discrete-time-systems"><a class="docs-heading-anchor" href="#Discrete-time-systems">Discrete-time systems</a><a id="Discrete-time-systems-1"></a><a class="docs-heading-anchor-permalink" href="#Discrete-time-systems" 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.@DDSmodel" href="#StructuralIdentifiability.@DDSmodel"><code>StructuralIdentifiability.@DDSmodel</code></a> — <span class="docstring-category">Macro</span></header><section><div><pre><code class="language-julia hljs">macro DDSmodel</code></pre><p>Macro for creating a DDS (discrete dynamical system)  from a list of equations. It also injects all variables into the global scope.</p><p><strong>Example</strong></p><p>Creating a simple <code>DDS</code>:</p><pre><code class="language-julia hljs">using StructuralIdentifiability
+)</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-independent parameters</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/1129b8ea5a62e666609a7633fcdad7dfa3855965/src/input_macro.jl#L242-L268">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/1129b8ea5a62e666609a7633fcdad7dfa3855965/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/1129b8ea5a62e666609a7633fcdad7dfa3855965/src/ODE.jl#L87-L96">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/1129b8ea5a62e666609a7633fcdad7dfa3855965/src/lincomp.jl#L16-L27">source</a></section></article><h2 id="Discrete-time-systems"><a class="docs-heading-anchor" href="#Discrete-time-systems">Discrete-time systems</a><a id="Discrete-time-systems-1"></a><a class="docs-heading-anchor-permalink" href="#Discrete-time-systems" 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.@DDSmodel" href="#StructuralIdentifiability.@DDSmodel"><code>StructuralIdentifiability.@DDSmodel</code></a> — <span class="docstring-category">Macro</span></header><section><div><pre><code class="language-julia hljs">macro DDSmodel</code></pre><p>Macro for creating a DDS (discrete dynamical system)  from a list of equations. It also injects all variables into the global scope.</p><p><strong>Example</strong></p><p>Creating a simple <code>DDS</code>:</p><pre><code class="language-julia hljs">using StructuralIdentifiability
 
 dds = @DDSmodel(
     x1(t + 1) = a * x1(t) + u(t),
     x2(t + 1) = 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-independent parameters</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/8d3f4c686bacdcdc1b3db80998b8fe302aed34a8/src/input_macro.jl#L275-L302">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/reparametrization/">« Reparametrizations</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="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 1.4.0 on <span class="colophon-date" title="Friday 26 April 2024 01:46">Friday 26 April 2024</span>. Using Julia version 1.10.2.</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-independent parameters</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/1129b8ea5a62e666609a7633fcdad7dfa3855965/src/input_macro.jl#L275-L302">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/reparametrization/">« Reparametrizations</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="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 1.4.0 on <span class="colophon-date" title="Saturday 27 April 2024 09:31">Saturday 27 April 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>