From f5287d3b07196c6dd2dea00e31ada1377aac29c2 Mon Sep 17 00:00:00 2001
From: "Documenter.jl" <documenter@juliadocs.github.io>
Date: Wed, 17 May 2023 13:17:33 +0000
Subject: [PATCH] build based on e8f0f06
---
dev/api/abc.html | 2 +-
dev/api/model.html | 2 +-
dev/api/plots.html | 2 +-
dev/api/trajectory.html | 2 +-
dev/create_model.html | 2 +-
dev/index.html | 2 +-
dev/search.html | 2 +-
dev/starting.html | 2 +-
8 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/dev/api/abc.html b/dev/api/abc.html
index 85f207e..2824e0a 100644
--- a/dev/api/abc.html
+++ b/dev/api/abc.html
@@ -9,4 +9,4 @@
k::Int, N_ref::Int; dir_results::Union{Nothing,String} = nothing)</code></pre><p>Creates a reference table for ABC model choice.</p><p>The mandatory arguments are:</p><ul><li><code>models</code> is a list of objects inherited from <code>Model</code> or <code>ParametricModel</code>,</li><li><code>models_prior</code>: the prior over the models (by default: discrete uniform distribution)</li><li><code>summary_stats_observations</code> are the summary statitics of the observations,</li><li><code>summary_stats_func::Function</code>: the function that computes the summary statistics over a model simulation,</li><li><code>distance_func</code>: the distance function over the summary statistics space,</li><li><code>N_ref</code>: the number of samples in the reference table,</li><li><code>k</code>: the k nearest samples from the observations to keep in the reference table (k < N_ref).</li></ul><p>The result is a <code>AbcModelChoiceDataset</code> with fields:</p><ul><li><code>summary_stats_matrix</code>: the (N<em>stats, N</em>ref) features matrix. Accessible via <code>.X</code>.</li><li><code>models_indexes</code>: the labels vector. Accessible via <code>.y</code>.</li></ul><p>If specified, <code>dir_results</code> is the directory where the summary statistics matrix and associated models are stored (CSV).</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.posterior_proba_model-Tuple{MarkovProcesses.RandomForestABC}" href="#MarkovProcesses.posterior_proba_model-Tuple{MarkovProcesses.RandomForestABC}"><code>MarkovProcesses.posterior_proba_model</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">posterior_proba_model(rf_abc::RandomForestABC)</code></pre><p>Estimates the posterior probability of the model <span>$P(M = \widehat{M}(s_{obs}) | s_{obs})$</span> with the Random Forest ABC method.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.rf_abc_model_choice-Tuple{Vector{<:Union{Model, ParametricModel}}, Any, Function, Int64}" href="#MarkovProcesses.rf_abc_model_choice-Tuple{Vector{<:Union{Model, ParametricModel}}, Any, Function, Int64}"><code>MarkovProcesses.rf_abc_model_choice</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">rf_abc_model_choice(models, summary_stats_observations,
summary_stats_func::Function, N_ref::Int;
k::Int = N_ref, distance_func::Function = (x,y) -> 1,
- hyperparameters_range::Dict)</code></pre><p>Run the Random Forest Approximate Bayesian Computation model choice method.</p><p>The mandatory arguments are:</p><ul><li><code>models</code> is a list of objects inherited from <code>Model</code> or <code>ParametricModel</code>,</li><li><code>summary_stats_observations</code> are the summary statitics of the observations</li><li><code>N_ref</code>: the number of samples in the reference table.</li><li><code>summary_stats_func::Function</code>: the function that computes the summary statistics over a model simulation.</li></ul><p>The optional arguments are:</p><ul><li><code>abc_trainset</code>: an already simulated dataset with `<code>abc_model_choice_dataset</code> (by default: nothing)</li><li><code>models_prior</code>: the prior over the models (by default: discrete uniform distribution)</li><li><code>k</code>: the k nearest samples from the observations to keep in the reference table (by default: k = N_ref)</li><li><code>distance_func</code>: the distance function, has to be defined if k < N_ref</li><li><code>hyperparameters_range</code>: a dict with the hyperparameters range values for the cross validation fit of the Random Forest (by default: <code>Dict(:n_estimators => [200], :min_samples_leaf => [1], :min_samples_split => [2])</code>). See scikit-learn documentation of RandomForestClassifier for the hyperparameters name.</li></ul><p>The result is a <code>RandomForestABC</code> object with fields:</p><ul><li><code>reference_table</code> an AbcModelChoiceDataset that corresponds to the reference table of the algorithm, </li><li><code>clf</code> a random forest classifier (PyObject from scikit-learn),</li><li><code>summary_stats_observations</code> are the summary statitics of the observations</li><li><code>estim_model</code> is the underlying model of the observations inferred with the RF-ABC method.</li></ul></div></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="trajectory.html">« Trajectory</a><a class="docs-footer-nextpage" href="plots.html">Plots »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 5 April 2023 08:47">Wednesday 5 April 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ hyperparameters_range::Dict)</code></pre><p>Run the Random Forest Approximate Bayesian Computation model choice method.</p><p>The mandatory arguments are:</p><ul><li><code>models</code> is a list of objects inherited from <code>Model</code> or <code>ParametricModel</code>,</li><li><code>summary_stats_observations</code> are the summary statitics of the observations</li><li><code>N_ref</code>: the number of samples in the reference table.</li><li><code>summary_stats_func::Function</code>: the function that computes the summary statistics over a model simulation.</li></ul><p>The optional arguments are:</p><ul><li><code>abc_trainset</code>: an already simulated dataset with `<code>abc_model_choice_dataset</code> (by default: nothing)</li><li><code>models_prior</code>: the prior over the models (by default: discrete uniform distribution)</li><li><code>k</code>: the k nearest samples from the observations to keep in the reference table (by default: k = N_ref)</li><li><code>distance_func</code>: the distance function, has to be defined if k < N_ref</li><li><code>hyperparameters_range</code>: a dict with the hyperparameters range values for the cross validation fit of the Random Forest (by default: <code>Dict(:n_estimators => [200], :min_samples_leaf => [1], :min_samples_split => [2])</code>). See scikit-learn documentation of RandomForestClassifier for the hyperparameters name.</li></ul><p>The result is a <code>RandomForestABC</code> object with fields:</p><ul><li><code>reference_table</code> an AbcModelChoiceDataset that corresponds to the reference table of the algorithm, </li><li><code>clf</code> a random forest classifier (PyObject from scikit-learn),</li><li><code>summary_stats_observations</code> are the summary statitics of the observations</li><li><code>estim_model</code> is the underlying model of the observations inferred with the RF-ABC method.</li></ul></div></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="trajectory.html">« Trajectory</a><a class="docs-footer-nextpage" href="plots.html">Plots »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 17 May 2023 13:17">Wednesday 17 May 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
diff --git a/dev/api/model.html b/dev/api/model.html
index 35d62dc..be38fbc 100644
--- a/dev/api/model.html
+++ b/dev/api/model.html
@@ -1,2 +1,2 @@
<!DOCTYPE html>
-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Model · MarkovProcesses.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../index.html"><img src="../assets/logo.png" alt="MarkovProcesses.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">MarkovProcesses.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><a class="tocitem" href="../starting.html">Getting Started</a></li><li><a class="tocitem" href="../create_model.html">Create a model</a></li><li><span class="tocitem">API</span><ul><li class="is-active"><a class="tocitem" href="model.html">Model</a></li><li><a class="tocitem" href="trajectory.html">Trajectory</a></li><li><a class="tocitem" href="abc.html">Approximate Bayesian Computation</a></li><li><a class="tocitem" href="plots.html">Plots</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">API</a></li><li class="is-active"><a href="model.html">Model</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="model.html">Model</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com//blob/master/docs/src/api/model.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Model-test-related-methods"><a class="docs-heading-anchor" href="#Model-test-related-methods">Model test related methods</a><a id="Model-test-related-methods-1"></a><a class="docs-heading-anchor-permalink" href="#Model-test-related-methods" title="Permalink"></a></h1><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.change_simulation_stop_criteria-Tuple{ContinuousTimeModel, Symbol}" href="#MarkovProcesses.change_simulation_stop_criteria-Tuple{ContinuousTimeModel, Symbol}"><code>MarkovProcesses.change_simulation_stop_criteria</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>change_simulation_stop_criteria(m::ContinuousTimeModel, isabsorbing_func::Symbol)</code></p><p>Change the simulation of the model <code>m</code> by adding a stop criteria based on the function named <code>isabsorbing_func::Symbol</code>. <code>isabsorbing_func</code> must have the type signature <code>isabsorbing_func(p::Vector{Float64}, x::Vector{Int})</code> where <code>p</code> is the parameter vector of the model and <code>x</code> a state (not an observed state) of the model.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.distribute_mean_value_lha-Tuple{SynchronizedModel, Symbol, Int64}" href="#MarkovProcesses.distribute_mean_value_lha-Tuple{SynchronizedModel, Symbol, Int64}"><code>MarkovProcesses.distribute_mean_value_lha</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>distribute_mean_value_lha(sm::SynchronizedModel, sym_var::Symbol, nbr_stim::Int)</code></p><p>Distribute over workers the computation of the mean value of an LHA over <code>nbr_sim</code> simulations of the model.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.draw!-Tuple{AbstractMatrix{Float64}, ParametricModel}" href="#MarkovProcesses.draw!-Tuple{AbstractMatrix{Float64}, ParametricModel}"><code>MarkovProcesses.draw!</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>draw!(mat_p, pm)</code></p><p>Draw <code>size(mat_p)[2]</code> (number of columns of <code>mat_p</code>) parameters from the prior distribution defined in <code>pm</code> and stores it in <code>mat_p</code>.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.draw!-Tuple{AbstractVector{Float64}, ParametricModel}" href="#MarkovProcesses.draw!-Tuple{AbstractVector{Float64}, ParametricModel}"><code>MarkovProcesses.draw!</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>draw!(vec_p, pm)</code></p><p>Draw a parameter from the prior distribution defined in pm and stores it in <code>vec_p</code>.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.draw_model!-Tuple{ParametricModel}" href="#MarkovProcesses.draw_model!-Tuple{ParametricModel}"><code>MarkovProcesses.draw_model!</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>draw_model!(pm::ParametricModel)</code></p><p>Draw a parameter from the prior disitribution defined in <code>pm::ParametricModel</code> and save it in the model contained in <code>pm</code>.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.prior_pdf!-Tuple{AbstractVector{Float64}, ParametricModel, AbstractMatrix{Float64}}" href="#MarkovProcesses.prior_pdf!-Tuple{AbstractVector{Float64}, ParametricModel, AbstractMatrix{Float64}}"><code>MarkovProcesses.prior_pdf!</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>prior_pdf(res_pdf, mat_p, pm)</code></p><p>Computes the density for each column of <code>mat_p</code> of the prior distribution defined in <code>pm</code>. Stores it in <code>res_pdf</code>. (<code>length(vec_res) == size(mat_p)[2]</code>)</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.prior_pdf-Tuple{ParametricModel, AbstractVector{Float64}}" href="#MarkovProcesses.prior_pdf-Tuple{ParametricModel, AbstractVector{Float64}}"><code>MarkovProcesses.prior_pdf</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>prior_pdf(p_prior, pm)</code></p><p>Computes the density at <code>p_prior</code> of the prior distribution defined in <code>pm</code>.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.probability_var_value_lha-Tuple{SynchronizedModel, Int64}" href="#MarkovProcesses.probability_var_value_lha-Tuple{SynchronizedModel, Int64}"><code>MarkovProcesses.probability_var_value_lha</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>distribute_var_value_lha(sm::SynchronizedModel, nbr_sim::Int, value = 0, sym_var = :d)</code></p><p>Compute the probability that the variable <code>sym_var</code> is equal to <code>value</code> of an LHA over <code>nbr_sim</code> simulations of the model.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.simulate-Tuple{ParametricModel, AbstractVector{Float64}}" href="#MarkovProcesses.simulate-Tuple{ParametricModel, AbstractVector{Float64}}"><code>MarkovProcesses.simulate</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>simulate(pm::ParametricModel, p_prior::AbstractVector{Float64})</code></p><p>Simulates the model contained in the parametric model <code>pm</code> with the <code>p_prior</code> parameters. It simulates the model by taking the parameters contained in <code>get_proba_model(pm).p</code> and replace the 1D parameters pm.params with <code>p_prior</code>.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.volatile_simulate-Tuple{ParametricModel, AbstractVector{Float64}}" href="#MarkovProcesses.volatile_simulate-Tuple{ParametricModel, AbstractVector{Float64}}"><code>MarkovProcesses.volatile_simulate</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>volatile_simulate(pm::ParametricModel, p_prior::AbstractVector{Float64})</code></p><p>A volatile version of <code>simulate(pm::ParametricModel, p_prior::AbstractVector{Float64})</code>. The model in <code>pm</code> should be of type SynchronizedModel (<code>typeof(pm.m) <: SynchronizedModel</code>). It returns <code>S::StateLHA</code>, not a trajectory.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.volatile_simulate-Tuple{SynchronizedModel}" href="#MarkovProcesses.volatile_simulate-Tuple{SynchronizedModel}"><code>MarkovProcesses.volatile_simulate</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>volatile_simulate(sm::SynchronizedModel; p, verbose)</code></p><p>Simulates a model synchronized with an automaton but does not store the values of the simulation in order to improve performance. It returns the last state of the simulation <code>S::StateLHA</code> not a trajectory <code>σ::SynchronizedTrajectory</code>.</p></div></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../create_model.html">« Create a model</a><a class="docs-footer-nextpage" href="trajectory.html">Trajectory »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 5 April 2023 08:47">Wednesday 5 April 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Model · MarkovProcesses.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../index.html"><img src="../assets/logo.png" alt="MarkovProcesses.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">MarkovProcesses.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><a class="tocitem" href="../starting.html">Getting Started</a></li><li><a class="tocitem" href="../create_model.html">Create a model</a></li><li><span class="tocitem">API</span><ul><li class="is-active"><a class="tocitem" href="model.html">Model</a></li><li><a class="tocitem" href="trajectory.html">Trajectory</a></li><li><a class="tocitem" href="abc.html">Approximate Bayesian Computation</a></li><li><a class="tocitem" href="plots.html">Plots</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">API</a></li><li class="is-active"><a href="model.html">Model</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="model.html">Model</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com//blob/master/docs/src/api/model.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Model-test-related-methods"><a class="docs-heading-anchor" href="#Model-test-related-methods">Model test related methods</a><a id="Model-test-related-methods-1"></a><a class="docs-heading-anchor-permalink" href="#Model-test-related-methods" title="Permalink"></a></h1><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.change_simulation_stop_criteria-Tuple{ContinuousTimeModel, Symbol}" href="#MarkovProcesses.change_simulation_stop_criteria-Tuple{ContinuousTimeModel, Symbol}"><code>MarkovProcesses.change_simulation_stop_criteria</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>change_simulation_stop_criteria(m::ContinuousTimeModel, isabsorbing_func::Symbol)</code></p><p>Change the simulation of the model <code>m</code> by adding a stop criteria based on the function named <code>isabsorbing_func::Symbol</code>. <code>isabsorbing_func</code> must have the type signature <code>isabsorbing_func(p::Vector{Float64}, x::Vector{Int})</code> where <code>p</code> is the parameter vector of the model and <code>x</code> a state (not an observed state) of the model.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.distribute_mean_value_lha-Tuple{SynchronizedModel, Symbol, Int64}" href="#MarkovProcesses.distribute_mean_value_lha-Tuple{SynchronizedModel, Symbol, Int64}"><code>MarkovProcesses.distribute_mean_value_lha</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>distribute_mean_value_lha(sm::SynchronizedModel, sym_var::Symbol, nbr_stim::Int)</code></p><p>Distribute over workers the computation of the mean value of an LHA over <code>nbr_sim</code> simulations of the model.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.draw!-Tuple{AbstractMatrix{Float64}, ParametricModel}" href="#MarkovProcesses.draw!-Tuple{AbstractMatrix{Float64}, ParametricModel}"><code>MarkovProcesses.draw!</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>draw!(mat_p, pm)</code></p><p>Draw <code>size(mat_p)[2]</code> (number of columns of <code>mat_p</code>) parameters from the prior distribution defined in <code>pm</code> and stores it in <code>mat_p</code>.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.draw!-Tuple{AbstractVector{Float64}, ParametricModel}" href="#MarkovProcesses.draw!-Tuple{AbstractVector{Float64}, ParametricModel}"><code>MarkovProcesses.draw!</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>draw!(vec_p, pm)</code></p><p>Draw a parameter from the prior distribution defined in pm and stores it in <code>vec_p</code>.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.draw_model!-Tuple{ParametricModel}" href="#MarkovProcesses.draw_model!-Tuple{ParametricModel}"><code>MarkovProcesses.draw_model!</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>draw_model!(pm::ParametricModel)</code></p><p>Draw a parameter from the prior disitribution defined in <code>pm::ParametricModel</code> and save it in the model contained in <code>pm</code>.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.prior_pdf!-Tuple{AbstractVector{Float64}, ParametricModel, AbstractMatrix{Float64}}" href="#MarkovProcesses.prior_pdf!-Tuple{AbstractVector{Float64}, ParametricModel, AbstractMatrix{Float64}}"><code>MarkovProcesses.prior_pdf!</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>prior_pdf(res_pdf, mat_p, pm)</code></p><p>Computes the density for each column of <code>mat_p</code> of the prior distribution defined in <code>pm</code>. Stores it in <code>res_pdf</code>. (<code>length(vec_res) == size(mat_p)[2]</code>)</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.prior_pdf-Tuple{ParametricModel, AbstractVector{Float64}}" href="#MarkovProcesses.prior_pdf-Tuple{ParametricModel, AbstractVector{Float64}}"><code>MarkovProcesses.prior_pdf</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>prior_pdf(p_prior, pm)</code></p><p>Computes the density at <code>p_prior</code> of the prior distribution defined in <code>pm</code>.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.probability_var_value_lha-Tuple{SynchronizedModel, Int64}" href="#MarkovProcesses.probability_var_value_lha-Tuple{SynchronizedModel, Int64}"><code>MarkovProcesses.probability_var_value_lha</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>distribute_var_value_lha(sm::SynchronizedModel, nbr_sim::Int, value = 0, sym_var = :d)</code></p><p>Compute the probability that the variable <code>sym_var</code> is equal to <code>value</code> of an LHA over <code>nbr_sim</code> simulations of the model.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.simulate-Tuple{ParametricModel, AbstractVector{Float64}}" href="#MarkovProcesses.simulate-Tuple{ParametricModel, AbstractVector{Float64}}"><code>MarkovProcesses.simulate</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>simulate(pm::ParametricModel, p_prior::AbstractVector{Float64})</code></p><p>Simulates the model contained in the parametric model <code>pm</code> with the <code>p_prior</code> parameters. It simulates the model by taking the parameters contained in <code>get_proba_model(pm).p</code> and replace the 1D parameters pm.params with <code>p_prior</code>.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.volatile_simulate-Tuple{ParametricModel, AbstractVector{Float64}}" href="#MarkovProcesses.volatile_simulate-Tuple{ParametricModel, AbstractVector{Float64}}"><code>MarkovProcesses.volatile_simulate</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>volatile_simulate(pm::ParametricModel, p_prior::AbstractVector{Float64})</code></p><p>A volatile version of <code>simulate(pm::ParametricModel, p_prior::AbstractVector{Float64})</code>. The model in <code>pm</code> should be of type SynchronizedModel (<code>typeof(pm.m) <: SynchronizedModel</code>). It returns <code>S::StateLHA</code>, not a trajectory.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.volatile_simulate-Tuple{SynchronizedModel}" href="#MarkovProcesses.volatile_simulate-Tuple{SynchronizedModel}"><code>MarkovProcesses.volatile_simulate</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>volatile_simulate(sm::SynchronizedModel; p, verbose)</code></p><p>Simulates a model synchronized with an automaton but does not store the values of the simulation in order to improve performance. It returns the last state of the simulation <code>S::StateLHA</code> not a trajectory <code>σ::SynchronizedTrajectory</code>.</p></div></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../create_model.html">« Create a model</a><a class="docs-footer-nextpage" href="trajectory.html">Trajectory »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 17 May 2023 13:17">Wednesday 17 May 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
diff --git a/dev/api/plots.html b/dev/api/plots.html
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+++ b/dev/api/plots.html
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-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Plots · MarkovProcesses.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" 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href="#Plots-related-methods" title="Permalink"></a></h1></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="abc.html">« Approximate Bayesian Computation</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> 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+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Plots · MarkovProcesses.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" 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diff --git a/dev/api/trajectory.html b/dev/api/trajectory.html
index 311bbd3..4b818b3 100644
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<!DOCTYPE html>
-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Trajectory · MarkovProcesses.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../index.html"><img src="../assets/logo.png" alt="MarkovProcesses.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">MarkovProcesses.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><a class="tocitem" href="../starting.html">Getting Started</a></li><li><a class="tocitem" href="../create_model.html">Create a model</a></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="model.html">Model</a></li><li class="is-active"><a class="tocitem" href="trajectory.html">Trajectory</a></li><li><a class="tocitem" href="abc.html">Approximate Bayesian Computation</a></li><li><a class="tocitem" href="plots.html">Plots</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">API</a></li><li class="is-active"><a href="trajectory.html">Trajectory</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="trajectory.html">Trajectory</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com//blob/master/docs/src/api/trajectory.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Trajectory-related-methods"><a class="docs-heading-anchor" href="#Trajectory-related-methods">Trajectory related methods</a><a id="Trajectory-related-methods-1"></a><a class="docs-heading-anchor-permalink" href="#Trajectory-related-methods" title="Permalink"></a></h1><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.dist_lp-Tuple{AbstractTrajectory, AbstractTrajectory, Symbol}" href="#MarkovProcesses.dist_lp-Tuple{AbstractTrajectory, AbstractTrajectory, Symbol}"><code>MarkovProcesses.dist_lp</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>dist_lp(σ1, σ2, var; verbose, p, str_stat)</code> </p><p>Function that computes Lp distance between two trajectories of any dimension. It computes Lp distances for each observed variable (contained in <code>get_obs_var(σ)</code>). and then apply a statistic on these distances. Requires <code>get_obs_var(σ1) == get_obs_var(σ2)</code>, it is verified if they are simulated from the same model. ...</p><p><strong>Arguments</strong></p><ul><li><code>σ1::AbstractTrajectory</code> is the first trajectory. σ2 is the second.</li><li><code>var::Symbol</code> is an observed variable. Have to be contained in <code>get_obs_var(σ1)</code> and <code>get_obs_var(σ2)</code>.</li><li><code>verbose::Bool</code> If <code>true</code>, launch a verbose execution of the computation. </li></ul><p>...</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.dist_lp-Tuple{AbstractTrajectory, AbstractTrajectory}" href="#MarkovProcesses.dist_lp-Tuple{AbstractTrajectory, AbstractTrajectory}"><code>MarkovProcesses.dist_lp</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>dist_lp(σ1, σ2; verbose, p, str_stat)</code> </p><p>Function that computes Lp distance between two trajectories of any dimension. It computes Lp distances for each observed variable (contained in <code>get_obs_var(σ)</code>). and then apply a statistic on these distances. Requires <code>get_obs_var(σ1) == get_obs_var(σ2)</code>, it is verified if they are simulated from the same model. ...</p><p><strong>Arguments</strong></p><ul><li><code>σ1::AbstractTrajectory</code> is the first trajectory. σ2 is the second.</li><li><code>verbose::Bool</code> If <code>true</code>, launch a verbose execution of the computation. </li><li><code>str_stat::String</code> allows to set the statistic to apply on the distances computed of the trajectories. </li></ul><p>Only "mean" is available for now on. ...</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.dist_lp-Tuple{Vector{<:AbstractTrajectory}, Vector{<:AbstractTrajectory}}" href="#MarkovProcesses.dist_lp-Tuple{Vector{<:AbstractTrajectory}, Vector{<:AbstractTrajectory}}"><code>MarkovProcesses.dist_lp</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>dist_lp(l_σ1, l_σ2; verbose, p, str_stat_list, str_stat_trajectory)</code> </p><p>Function that computes Lp distance between two set of any dimensional trajectories. ...</p><p><strong>Arguments</strong></p><ul><li><code>l_σ1::Vector{AbstractTrajectory}</code> is the first set of trajectories. l_σ2 is the second.</li><li><code>verbose::Bool</code> If <code>true</code>, launch a verbose execution of the computation. </li><li><code>str_stat_list::String</code> allows to set the statistic to apply on the distances of the trajectories. </li></ul><p>It is salso called linkage function in clustering field. Only "mean" is available for now on. ...</p></div></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="model.html">« Model</a><a class="docs-footer-nextpage" href="abc.html">Approximate Bayesian Computation »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 5 April 2023 08:47">Wednesday 5 April 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Trajectory · MarkovProcesses.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../index.html"><img src="../assets/logo.png" alt="MarkovProcesses.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">MarkovProcesses.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><a class="tocitem" href="../starting.html">Getting Started</a></li><li><a class="tocitem" href="../create_model.html">Create a model</a></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="model.html">Model</a></li><li class="is-active"><a class="tocitem" href="trajectory.html">Trajectory</a></li><li><a class="tocitem" href="abc.html">Approximate Bayesian Computation</a></li><li><a class="tocitem" href="plots.html">Plots</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">API</a></li><li class="is-active"><a href="trajectory.html">Trajectory</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="trajectory.html">Trajectory</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com//blob/master/docs/src/api/trajectory.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Trajectory-related-methods"><a class="docs-heading-anchor" href="#Trajectory-related-methods">Trajectory related methods</a><a id="Trajectory-related-methods-1"></a><a class="docs-heading-anchor-permalink" href="#Trajectory-related-methods" title="Permalink"></a></h1><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.dist_lp-Tuple{AbstractTrajectory, AbstractTrajectory, Symbol}" href="#MarkovProcesses.dist_lp-Tuple{AbstractTrajectory, AbstractTrajectory, Symbol}"><code>MarkovProcesses.dist_lp</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>dist_lp(σ1, σ2, var; verbose, p, str_stat)</code> </p><p>Function that computes Lp distance between two trajectories of any dimension. It computes Lp distances for each observed variable (contained in <code>get_obs_var(σ)</code>). and then apply a statistic on these distances. Requires <code>get_obs_var(σ1) == get_obs_var(σ2)</code>, it is verified if they are simulated from the same model. ...</p><p><strong>Arguments</strong></p><ul><li><code>σ1::AbstractTrajectory</code> is the first trajectory. σ2 is the second.</li><li><code>var::Symbol</code> is an observed variable. Have to be contained in <code>get_obs_var(σ1)</code> and <code>get_obs_var(σ2)</code>.</li><li><code>verbose::Bool</code> If <code>true</code>, launch a verbose execution of the computation. </li></ul><p>...</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.dist_lp-Tuple{AbstractTrajectory, AbstractTrajectory}" href="#MarkovProcesses.dist_lp-Tuple{AbstractTrajectory, AbstractTrajectory}"><code>MarkovProcesses.dist_lp</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>dist_lp(σ1, σ2; verbose, p, str_stat)</code> </p><p>Function that computes Lp distance between two trajectories of any dimension. It computes Lp distances for each observed variable (contained in <code>get_obs_var(σ)</code>). and then apply a statistic on these distances. Requires <code>get_obs_var(σ1) == get_obs_var(σ2)</code>, it is verified if they are simulated from the same model. ...</p><p><strong>Arguments</strong></p><ul><li><code>σ1::AbstractTrajectory</code> is the first trajectory. σ2 is the second.</li><li><code>verbose::Bool</code> If <code>true</code>, launch a verbose execution of the computation. </li><li><code>str_stat::String</code> allows to set the statistic to apply on the distances computed of the trajectories. </li></ul><p>Only "mean" is available for now on. ...</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="MarkovProcesses.dist_lp-Tuple{Vector{<:AbstractTrajectory}, Vector{<:AbstractTrajectory}}" href="#MarkovProcesses.dist_lp-Tuple{Vector{<:AbstractTrajectory}, Vector{<:AbstractTrajectory}}"><code>MarkovProcesses.dist_lp</code></a> — <span class="docstring-category">Method</span></header><section><div><p><code>dist_lp(l_σ1, l_σ2; verbose, p, str_stat_list, str_stat_trajectory)</code> </p><p>Function that computes Lp distance between two set of any dimensional trajectories. ...</p><p><strong>Arguments</strong></p><ul><li><code>l_σ1::Vector{AbstractTrajectory}</code> is the first set of trajectories. l_σ2 is the second.</li><li><code>verbose::Bool</code> If <code>true</code>, launch a verbose execution of the computation. </li><li><code>str_stat_list::String</code> allows to set the statistic to apply on the distances of the trajectories. </li></ul><p>It is salso called linkage function in clustering field. Only "mean" is available for now on. ...</p></div></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="model.html">« Model</a><a class="docs-footer-nextpage" href="abc.html">Approximate Bayesian Computation »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 17 May 2023 13:17">Wednesday 17 May 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
diff --git a/dev/create_model.html b/dev/create_model.html
index 6dddb59..278f7ef 100644
--- a/dev/create_model.html
+++ b/dev/create_model.html
@@ -78,4 +78,4 @@ tryhard_sir = TryhardSIRModel(dim_state_sir, dim_params_sir,
map_var_idx_sir, map_params_idx_sir,
transitions_sir, p_sir, x0_sir, t0_sir,
:sir_f!, :sir_isabsorbing; g = g_sir)
-σ = simulate(tryhard_sir)</code></pre><h2 id="List-of-pre-written-models"><a class="docs-heading-anchor" href="#List-of-pre-written-models">List of pre-written models</a><a id="List-of-pre-written-models-1"></a><a class="docs-heading-anchor-permalink" href="#List-of-pre-written-models" title="Permalink"></a></h2><ul><li><code>load_model("poisson")</code>: Poisson process</li><li><code>load_model("ER")</code>: Michaelis-Menten kinetics (Enzymatic Reactions)</li><li><code>load_model("SIR")</code>: Susceptible-Infected-Removed</li><li><code>load_model("doping_3way_oscillator")</code>: Three-way oscillator with doping reactions</li><li><code>load_model("repressilator")</code>: A repressilator model</li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="starting.html">« Getting Started</a><a class="docs-footer-nextpage" href="api/model.html">Model »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 5 April 2023 08:47">Wednesday 5 April 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+σ = simulate(tryhard_sir)</code></pre><h2 id="List-of-pre-written-models"><a class="docs-heading-anchor" href="#List-of-pre-written-models">List of pre-written models</a><a id="List-of-pre-written-models-1"></a><a class="docs-heading-anchor-permalink" href="#List-of-pre-written-models" title="Permalink"></a></h2><ul><li><code>load_model("poisson")</code>: Poisson process</li><li><code>load_model("ER")</code>: Michaelis-Menten kinetics (Enzymatic Reactions)</li><li><code>load_model("SIR")</code>: Susceptible-Infected-Removed</li><li><code>load_model("doping_3way_oscillator")</code>: Three-way oscillator with doping reactions</li><li><code>load_model("repressilator")</code>: A repressilator model</li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="starting.html">« Getting Started</a><a class="docs-footer-nextpage" href="api/model.html">Model »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 17 May 2023 13:17">Wednesday 17 May 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
diff --git a/dev/index.html b/dev/index.html
index bcef708..4ff8ae7 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -1,2 +1,2 @@
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-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · MarkovProcesses.jl</title><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="index.html"><img src="assets/logo.png" alt="MarkovProcesses.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">MarkovProcesses.jl</a></span></div><form class="docs-search" action="search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul 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title="Permalink"></a></h1><p><em>A package for simulation, verification and parameter estimation of Chemical Reaction Networks.</em></p><h2 id="Package-features"><a class="docs-heading-anchor" href="#Package-features">Package features</a><a id="Package-features-1"></a><a class="docs-heading-anchor-permalink" href="#Package-features" title="Permalink"></a></h2><ul><li>A core of simulation for Continuous-Time Markov Chains (CTMC) defined by Chemical Reaction Networks (CRN),</li><li>A simple interface for Biochemical Networks / Stochastic Petri Nets,</li><li>Synchronized simulation with Linear Hybrid Automata,</li><li>Approximate Bayesian Computation, a likelihood-free inference method,</li><li>Automaton-ABC: a statistical method for verification of parametric CTMCs.</li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="starting.html">Getting Started »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a 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Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · MarkovProcesses.jl</title><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script 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class="docs-menu"><li class="is-active"><a class="tocitem" href="index.html">Home</a><ul class="internal"><li><a class="tocitem" href="#Package-features"><span>Package features</span></a></li></ul></li><li><a class="tocitem" href="starting.html">Getting Started</a></li><li><a class="tocitem" href="create_model.html">Create a model</a></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="api/model.html">Model</a></li><li><a class="tocitem" href="api/trajectory.html">Trajectory</a></li><li><a class="tocitem" href="api/abc.html">Approximate Bayesian Computation</a></li><li><a class="tocitem" href="api/plots.html">Plots</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="index.html">Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="index.html">Home</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com//blob/master/docs/src/index.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="MarkovProcesses.jl"><a class="docs-heading-anchor" href="#MarkovProcesses.jl">MarkovProcesses.jl</a><a id="MarkovProcesses.jl-1"></a><a class="docs-heading-anchor-permalink" href="#MarkovProcesses.jl" title="Permalink"></a></h1><p><em>A package for simulation, verification and parameter estimation of Chemical Reaction Networks.</em></p><h2 id="Package-features"><a class="docs-heading-anchor" href="#Package-features">Package features</a><a id="Package-features-1"></a><a class="docs-heading-anchor-permalink" href="#Package-features" title="Permalink"></a></h2><ul><li>A core of simulation for Continuous-Time Markov Chains (CTMC) defined by Chemical Reaction Networks (CRN),</li><li>A simple interface for Biochemical Networks / Stochastic Petri Nets,</li><li>Synchronized simulation with Linear Hybrid Automata,</li><li>Approximate Bayesian Computation, a likelihood-free inference method,</li><li>Automaton-ABC: a statistical method for verification of parametric CTMCs.</li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="starting.html">Getting Started »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a 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Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
diff --git a/dev/search.html b/dev/search.html
index 0a57c1c..f2f65fa 100644
--- a/dev/search.html
+++ b/dev/search.html
@@ -1,2 +1,2 @@
<!DOCTYPE html>
-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Search · MarkovProcesses.jl</title><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="index.html"><img src="assets/logo.png" alt="MarkovProcesses.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">MarkovProcesses.jl</a></span></div><form class="docs-search" action="search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="index.html">Home</a></li><li><a class="tocitem" href="starting.html">Getting Started</a></li><li><a class="tocitem" href="create_model.html">Create a model</a></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="api/model.html">Model</a></li><li><a class="tocitem" href="api/trajectory.html">Trajectory</a></li><li><a class="tocitem" href="api/abc.html">Approximate Bayesian Computation</a></li><li><a class="tocitem" href="api/plots.html">Plots</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="search.html">Search</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="search.html">Search</a></li></ul></nav><div class="docs-right"><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article><p id="documenter-search-info">Loading search...</p><ul id="documenter-search-results"></ul></article><nav class="docs-footer"><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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 5 April 2023 08:47">Wednesday 5 April 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><script src="search_index.js"></script><script src="assets/search.js"></script></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Search · MarkovProcesses.jl</title><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="index.html"><img src="assets/logo.png" alt="MarkovProcesses.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">MarkovProcesses.jl</a></span></div><form class="docs-search" action="search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="index.html">Home</a></li><li><a class="tocitem" href="starting.html">Getting Started</a></li><li><a class="tocitem" href="create_model.html">Create a model</a></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="api/model.html">Model</a></li><li><a class="tocitem" href="api/trajectory.html">Trajectory</a></li><li><a class="tocitem" href="api/abc.html">Approximate Bayesian Computation</a></li><li><a class="tocitem" href="api/plots.html">Plots</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="search.html">Search</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="search.html">Search</a></li></ul></nav><div class="docs-right"><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article><p id="documenter-search-info">Loading search...</p><ul id="documenter-search-results"></ul></article><nav class="docs-footer"><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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 17 May 2023 13:17">Wednesday 17 May 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><script src="search_index.js"></script><script src="assets/search.js"></script></html>
diff --git a/dev/starting.html b/dev/starting.html
index b8cb3e5..66a4390 100644
--- a/dev/starting.html
+++ b/dev/starting.html
@@ -48,4 +48,4 @@ SIR.g = [:I]
(size(σ.values), length(σ[:I])) = ((1,), 196)</code></pre><p>The SIR model is by default unbounded, i.e. each trajectory is simulated until it reaches an absorbing state.</p><pre><code class="language-julia hljs">julia> @show isbounded(SIR)
@show isbounded(σ)
isbounded(SIR) = false
-isbounded(σ) = false</code></pre><p>We can bound the SIR's trajectories until time 120 by running <code>set_time_bound!(SIR, 120.0)</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="index.html">« Home</a><a class="docs-footer-nextpage" href="create_model.html">Create a model »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 5 April 2023 08:47">Wednesday 5 April 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+isbounded(σ) = false</code></pre><p>We can bound the SIR's trajectories until time 120 by running <code>set_time_bound!(SIR, 120.0)</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="index.html">« Home</a><a class="docs-footer-nextpage" href="create_model.html">Create a model »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Wednesday 17 May 2023 13:17">Wednesday 17 May 2023</span>. Using Julia version 1.7.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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