build based on 7c6bf1f

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-31T11:00:29","documenter_version":"1.1.2"}}
+{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-31T22:51:00","documenter_version":"1.1.2"}}

dev/assets/Manifest.toml

@@ -239,9 +239,9 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
 [[deps.DiffEqBase]]
 deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"]
-git-tree-sha1 = "59842b690c2ed12428a741c1334f3c68d1377fb6"
+git-tree-sha1 = "c8bc8487a7987c13576f25959ac11b25d5da84e2"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.135.0"
+version = "6.136.0"
 
     [deps.DiffEqBase.extensions]
     DiffEqBaseDistributionsExt = "Distributions"
@@ -587,9 +587,9 @@ version = "0.21.4"
 
 [[deps.JuliaFormatter]]
 deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"]
-git-tree-sha1 = "b11c259ae111b08aabdc2ff5186dad12a95fedca"
+git-tree-sha1 = "3d5b5b539e4606dcca0e6a467b98a64c8da4850b"
 uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-version = "1.0.41"
+version = "1.0.42"
 
 [[deps.JumpProcesses]]
 deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"]
@@ -645,9 +645,9 @@ version = "0.16.1"
 
 [[deps.LayoutPointers]]
 deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"]
-git-tree-sha1 = "88b8f66b604da079a627b6fb2860d3704a6729a1"
+git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277"
 uuid = "10f19ff3-798f-405d-979b-55457f8fc047"
-version = "0.1.14"
+version = "0.1.15"
 
 [[deps.LazilyInitializedFields]]
 git-tree-sha1 = "410fe4739a4b092f2ffe36fcb0dcc3ab12648ce1"
@@ -1412,9 +1412,9 @@ version = "0.3.0"
 
 [[deps.TriangularSolve]]
 deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"]
-git-tree-sha1 = "31eedbc0b6d07c08a700e26d31298ac27ef330eb"
+git-tree-sha1 = "fadebab77bf3ae041f77346dd1c290173da5a443"
 uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf"
-version = "0.1.19"
+version = "0.1.20"
 
 [[deps.Tricks]]
 git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f"

dev/index.html

@@ -23,10 +23,10 @@
   Official https://julialang.org/ release
 Platform Info:
   OS: Linux (x86_64-linux-gnu)
-  CPU: 2 × Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz
+  CPU: 2 × Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz
   WORD_SIZE: 64
   LIBM: libopenlibm
-  LLVM: libLLVM-14.0.6 (ORCJIT, broadwell)
+  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
@@ -57,7 +57,7 @@
   [9a962f9c] DataAPI v1.15.0
   [864edb3b] DataStructures v0.18.15
   [e2d170a0] DataValueInterfaces v1.0.0
-  [2b5f629d] DiffEqBase v6.135.0
+  [2b5f629d] DiffEqBase v6.136.0
   [459566f4] DiffEqCallbacks v2.33.1
   [163ba53b] DiffResults v1.1.0
   [b552c78f] DiffRules v1.15.1
@@ -100,15 +100,15 @@
   [82899510] IteratorInterfaceExtensions v1.0.0
   [692b3bcd] JLLWrappers v1.5.0
   [682c06a0] JSON v0.21.4
-  [98e50ef6] JuliaFormatter v1.0.41
+  [98e50ef6] JuliaFormatter v1.0.42
   [ccbc3e58] JumpProcesses v9.8.0
   [ef3ab10e] KLU v0.4.1
   [ba0b0d4f] Krylov v0.9.4
   [b964fa9f] LaTeXStrings v1.3.0
   [2ee39098] LabelledArrays v1.14.0
   [984bce1d] LambertW v0.4.6
   [23fbe1c1] Latexify v0.16.1
-  [10f19ff3] LayoutPointers v0.1.14
+  [10f19ff3] LayoutPointers v0.1.15
   [0e77f7df] LazilyInitializedFields v1.2.1
   [50d2b5c4] Lazy v0.15.1
   [d3d80556] LineSearches v7.2.0
@@ -189,7 +189,7 @@
   [a759f4b9] TimerOutputs v0.5.23
   [0796e94c] Tokenize v0.5.25
   [a2a6695c] TreeViews v0.3.0
-  [d5829a12] TriangularSolve v0.1.19
+  [d5829a12] TriangularSolve v0.1.20
   [410a4b4d] Tricks v0.1.8
   [781d530d] TruncatedStacktraces v1.4.0
   [5c2747f8] URIs v1.5.1
@@ -259,4 +259,4 @@
   [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 31 October 2023 11:00">Tuesday 31 October 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 31 October 2023 22:51">Tuesday 31 October 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/6b55fa9ab8ed99b0646c5a6623037a8ef2fbfa3e/src/ODE.jl#L339-L365">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/6b55fa9ab8ed99b0646c5a6623037a8ef2fbfa3e/src/ODE.jl#L2-L8">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/6b55fa9ab8ed99b0646c5a6623037a8ef2fbfa3e/src/ODE.jl#L85-L94">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/6b55fa9ab8ed99b0646c5a6623037a8ef2fbfa3e/src/lincomp.jl#L16-L27">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/identifiable_functions/">« Globally Identifiable Functions</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 31 October 2023 11:00">Tuesday 31 October 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/7c6bf1f087ddd75c0387ad51bc7e3f937924c69d/src/ODE.jl#L339-L365">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/7c6bf1f087ddd75c0387ad51bc7e3f937924c69d/src/ODE.jl#L2-L8">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/7c6bf1f087ddd75c0387ad51bc7e3f937924c69d/src/ODE.jl#L85-L94">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/7c6bf1f087ddd75c0387ad51bc7e3f937924c69d/src/lincomp.jl#L16-L27">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/identifiable_functions/">« Globally Identifiable Functions</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 31 October 2023 22:51">Tuesday 31 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>