build based on b4d7f51

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-02-09T20:11:34","documenter_version":"1.2.1"}}
+{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-02-10T17:32:20","documenter_version":"1.2.1"}}

dev/assets/Manifest.toml

@@ -620,10 +620,10 @@ uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.4"
 
 [[deps.JuliaFormatter]]
-deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"]
-git-tree-sha1 = "8f5295e46f594ad2d8652f1098488a77460080cd"
+deps = ["CSTParser", "Combinatorics", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"]
+git-tree-sha1 = "9b909bdf638f192c42e83bc9300700577f304a82"
 uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-version = "1.0.45"
+version = "1.0.46"
 
 [[deps.JumpProcesses]]
 deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "UnPack"]
@@ -1039,9 +1039,9 @@ weakdeps = ["Requires", "TOML"]
 
 [[deps.ParamPunPam]]
 deps = ["AbstractAlgebra", "Groebner", "Logging", "Nemo", "Primes", "ProgressMeter", "Random"]
-git-tree-sha1 = "2bd3ab4ca4402e338b782ff6edf6503305ac89d2"
+git-tree-sha1 = "fe331ac345fab37234ca59cb54ba3a646f5d47cc"
 uuid = "3e851597-e36f-45a9-af0a-b7781937992f"
-version = "0.3.1"
+version = "0.3.2"
 
 [[deps.Parameters]]
 deps = ["OrderedCollections", "UnPack"]
@@ -1080,9 +1080,9 @@ version = "0.2.1"
 
 [[deps.PreallocationTools]]
 deps = ["Adapt", "ArrayInterface", "ForwardDiff"]
-git-tree-sha1 = "9d6e62d1ea6ab709142b42d3be4bd1db495bc4e0"
+git-tree-sha1 = "e5c09a13d66652fa62b39db3f8997a57f421fa69"
 uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
-version = "0.4.18"
+version = "0.4.19"
 
     [deps.PreallocationTools.extensions]
     PreallocationToolsReverseDiffExt = "ReverseDiff"
@@ -1286,9 +1286,9 @@ uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
 
 [[deps.SimpleNonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"]
-git-tree-sha1 = "df8266e0d4960d61325db8c54fad3fa95712b57e"
+git-tree-sha1 = "87c13d788c01aba75a66d1129b1a600860ad73a5"
 uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7"
-version = "1.4.0"
+version = "1.4.1"
 
     [deps.SimpleNonlinearSolve.extensions]
     SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore"

dev/index.html

@@ -102,7 +102,7 @@
   [82899510] IteratorInterfaceExtensions v1.0.0
   [692b3bcd] JLLWrappers v1.5.0
   [682c06a0] JSON v0.21.4
-  [98e50ef6] JuliaFormatter v1.0.45
+  [98e50ef6] JuliaFormatter v1.0.46
   [ccbc3e58] JumpProcesses v9.10.1
 ⌅ [ef3ab10e] KLU v0.4.1
   [ba0b0d4f] Krylov v0.9.5
@@ -139,13 +139,13 @@
   [1dea7af3] OrdinaryDiffEq v6.70.1
   [90014a1f] PDMats v0.11.31
   [65ce6f38] PackageExtensionCompat v1.0.2
-  [3e851597] ParamPunPam v0.3.1
+  [3e851597] ParamPunPam v0.3.2
   [d96e819e] Parameters v0.12.3
   [69de0a69] Parsers v2.8.1
   [e409e4f3] PoissonRandom v0.4.4
   [f517fe37] Polyester v0.7.9
   [1d0040c9] PolyesterWeave v0.2.1
-  [d236fae5] PreallocationTools v0.4.18
+  [d236fae5] PreallocationTools v0.4.19
   [aea7be01] PrecompileTools v1.2.0
   [21216c6a] Preferences v1.4.1
   [08abe8d2] PrettyTables v2.3.1
@@ -167,7 +167,7 @@
   [0bca4576] SciMLBase v2.23.2
   [c0aeaf25] SciMLOperators v0.3.7
   [efcf1570] Setfield v1.1.1
-  [727e6d20] SimpleNonlinearSolve v1.4.0
+  [727e6d20] SimpleNonlinearSolve v1.4.1
   [699a6c99] SimpleTraits v0.9.4
   [ce78b400] SimpleUnPack v1.1.0
   [a2af1166] SortingAlgorithms v1.2.1
@@ -268,4 +268,4 @@
   [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="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 1.2.1 on <span class="colophon-date" title="Friday 9 February 2024 20:11">Friday 9 February 2024</span>. Using Julia version 1.10.0.</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 1.2.1 on <span class="colophon-date" title="Saturday 10 February 2024 17:32">Saturday 10 February 2024</span>. Using Julia version 1.10.0.</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/9e0052ca92d47c35ea0f4f1041a146acec1d561f/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/9e0052ca92d47c35ea0f4f1041a146acec1d561f/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/9e0052ca92d47c35ea0f4f1041a146acec1d561f/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/9e0052ca92d47c35ea0f4f1041a146acec1d561f/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/b4d7f51f278bbfdb2cb0fdcce0aebb7b657e0a1e/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/b4d7f51f278bbfdb2cb0fdcce0aebb7b657e0a1e/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/b4d7f51f278bbfdb2cb0fdcce0aebb7b657e0a1e/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/b4d7f51f278bbfdb2cb0fdcce0aebb7b657e0a1e/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/9e0052ca92d47c35ea0f4f1041a146acec1d561f/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="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 1.2.1 on <span class="colophon-date" title="Friday 9 February 2024 20:11">Friday 9 February 2024</span>. Using Julia version 1.10.0.</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/b4d7f51f278bbfdb2cb0fdcce0aebb7b657e0a1e/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="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 1.2.1 on <span class="colophon-date" title="Saturday 10 February 2024 17:32">Saturday 10 February 2024</span>. Using Julia version 1.10.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>