build based on 2ff1a9d

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-11-14T08:44:33","documenter_version":"1.1.2"}}
+{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-11-14T14:14:21","documenter_version":"1.1.2"}}

dev/assets/Manifest.toml

@@ -855,14 +855,16 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
 [[deps.ModelingToolkit]]
 deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "MacroTools", "NaNMath", "OrdinaryDiffEq", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"]
-git-tree-sha1 = "90b0d8395c9a8d3fcb5838f7f4f54b3f26e6f17a"
+git-tree-sha1 = "d014a44030d78626ff05c0348b3e9cb7cbd3d8be"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
-version = "8.72.2"
+version = "8.73.0"
 
     [deps.ModelingToolkit.extensions]
+    MTKBifurcationKitExt = "BifurcationKit"
     MTKDeepDiffsExt = "DeepDiffs"
 
     [deps.ModelingToolkit.weakdeps]
+    BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
     DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
 
 [[deps.MozillaCACerts_jll]]
@@ -965,9 +967,9 @@ version = "1.6.2"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "760558496b50017d10e1907244dc2c4fa4385963"
+git-tree-sha1 = "ea532499662b771442746811fa345a7ea516225c"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.59.0"
+version = "6.59.1"
 
 [[deps.PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]

dev/index.html

@@ -16,17 +16,17 @@
 }</code></pre><h2 id="Feature-Summary"><a class="docs-heading-anchor" href="#Feature-Summary">Feature Summary</a><a id="Feature-Summary-1"></a><a class="docs-heading-anchor-permalink" href="#Feature-Summary" title="Permalink"></a></h2><p><code>StructuralIdentifiability.jl</code> can assess local and global identifiability of ODE models. In addition to these straightforward identifiability queries on individual parameters, the package can distinguish between single- and multi-experiment identifiability.</p><h2 id="Feature-List"><a class="docs-heading-anchor" href="#Feature-List">Feature List</a><a id="Feature-List-1"></a><a class="docs-heading-anchor-permalink" href="#Feature-List" title="Permalink"></a></h2><ul><li>Local identifiability checks</li><li>Global identifiability checks</li><li>Assessment of identifiable functions of parameters and states</li><li>Model reparametrization (experimental)</li></ul><h2 id="Contributing"><a class="docs-heading-anchor" href="#Contributing">Contributing</a><a id="Contributing-1"></a><a class="docs-heading-anchor-permalink" href="#Contributing" title="Permalink"></a></h2><ul><li><p>Please refer to the <a href="https://github.com/SciML/ColPrac/blob/master/README.md">SciML ColPrac: Contributor&#39;s Guide on Collaborative Practices for Community Packages</a> for guidance on PRs, issues, and other matters relating to contributing to StructuralIdentifiability.</p></li><li><p>There are a few community forums:</p><ul><li>The #diffeq-bridged channel in the <a href="https://julialang.org/slack/">Julia Slack</a></li><li><a href="https://gitter.im/JuliaDiffEq/Lobby">JuliaDiffEq</a> on Gitter</li><li>On the Julia Discourse forums</li><li>See also <a href="https://sciml.ai/community/">SciML Community page</a></li></ul></li></ul><h2 id="Reproducibility"><a class="docs-heading-anchor" href="#Reproducibility">Reproducibility</a><a id="Reproducibility-1"></a><a class="docs-heading-anchor-permalink" href="#Reproducibility" title="Permalink"></a></h2><details><summary>The documentation of this SciML package was built using these direct dependencies,</summary><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Status `~/work/StructuralIdentifiability.jl/StructuralIdentifiability.jl/docs/Project.toml`
   [6e4b80f9] BenchmarkTools v1.3.2
   [e30172f5] Documenter v1.1.2
-  [961ee093] ModelingToolkit v8.72.2
+  [961ee093] ModelingToolkit v8.73.0
   [220ca800] StructuralIdentifiability v0.4.15 `~/work/StructuralIdentifiability.jl/StructuralIdentifiability.jl`</code></pre></details><details><summary>and using this machine and Julia version.</summary><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Julia Version 1.9.3
 Commit bed2cd540a1 (2023-08-24 14:43 UTC)
 Build Info:
   Official https://julialang.org/ release
 Platform Info:
   OS: Linux (x86_64-linux-gnu)
-  CPU: 2 × Intel(R) Xeon(R) Platinum 8370C CPU @ 2.80GHz
+  CPU: 2 × Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz
   WORD_SIZE: 64
   LIBM: libopenlibm
-  LLVM: libLLVM-14.0.6 (ORCJIT, icelake-server)
+  LLVM: libLLVM-14.0.6 (ORCJIT, skylake-avx512)
   Threads: 1 on 2 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 v0.2.4
   [a4c015fc] ANSIColoredPrinters v0.0.1
@@ -124,7 +124,7 @@
   [d125e4d3] ManualMemory v0.1.8
   [d0879d2d] MarkdownAST v0.1.2
   [e1d29d7a] Missings v1.1.0
-  [961ee093] ModelingToolkit v8.72.2
+  [961ee093] ModelingToolkit v8.73.0
   [46d2c3a1] MuladdMacro v0.2.4
   [102ac46a] MultivariatePolynomials v0.5.2
   [d8a4904e] MutableArithmetics v1.3.3
@@ -135,7 +135,7 @@
   [8913a72c] NonlinearSolve v2.8.0
   [6fe1bfb0] OffsetArrays v1.12.10
   [bac558e1] OrderedCollections v1.6.2
-  [1dea7af3] OrdinaryDiffEq v6.59.0
+  [1dea7af3] OrdinaryDiffEq v6.59.1
   [90014a1f] PDMats v0.11.29
   [65ce6f38] PackageExtensionCompat v1.0.2
   [3e851597] ParamPunPam v0.2.3
@@ -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="Tuesday 14 November 2023 08:44">Tuesday 14 November 2023</span>. Using Julia version 1.9.3.</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="Tuesday 14 November 2023 14:14">Tuesday 14 November 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/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/2f0c87180042979aba151ed03ba2a0c0e3dcb86e/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/2f0c87180042979aba151ed03ba2a0c0e3dcb86e/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/2f0c87180042979aba151ed03ba2a0c0e3dcb86e/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/2f0c87180042979aba151ed03ba2a0c0e3dcb86e/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="Tuesday 14 November 2023 08:44">Tuesday 14 November 2023</span>. Using Julia version 1.9.3.</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/2ff1a9dddcc19608399fa0a6e65638b884946b34/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/2ff1a9dddcc19608399fa0a6e65638b884946b34/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/2ff1a9dddcc19608399fa0a6e65638b884946b34/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/2ff1a9dddcc19608399fa0a6e65638b884946b34/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="Tuesday 14 November 2023 14:14">Tuesday 14 November 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>