diff --git a/docs/pages.jl b/docs/pages.jl index bd716f4327..a93b09ad43 100644 --- a/docs/pages.jl +++ b/docs/pages.jl @@ -12,7 +12,7 @@ pages = Any[ #"model_creation/compositional_modeling.md", #"model_creation/constraint_equations.md", # Events. - #"model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions. + "model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions. # Loading and writing models to files. #"model_creation/model_visualisation.md", #"model_creation/network_analysis.md", diff --git a/docs/src/model_creation/parametric_stoichiometry.md b/docs/src/model_creation/parametric_stoichiometry.md index 434002f72c..a0d370ef0d 100644 --- a/docs/src/model_creation/parametric_stoichiometry.md +++ b/docs/src/model_creation/parametric_stoichiometry.md @@ -7,7 +7,7 @@ use symbolic stoichiometries, and discuss several caveats to be aware of. Let's first consider a simple reversible reaction where the number of reactants is a parameter, and the number of products is the product of two parameters. ```@example s1 -using Catalyst, Latexify, DifferentialEquations, ModelingToolkit, Plots +using Catalyst, Latexify, OrdinaryDiffEq, ModelingToolkit, Plots revsys = @reaction_network revsys begin k₊, m*A --> (m*n)*B k₋, B --> A @@ -58,6 +58,7 @@ stoichiometries `(F,2*H,2)`. Let's now convert `revsys` to ODEs and look at the resulting equations: ```@example s1 osys = convert(ODESystem, revsys) +osys = complete(osys) equations(osys) show(stdout, MIME"text/plain"(), equations(osys)) # hide ``` @@ -88,6 +89,7 @@ converting to an `ODESystem`). For the previous example this gives the following (different) system of ODEs ```@example s1 osys = convert(ODESystem, revsys; combinatoric_ratelaws = false) +osys = complete(osys) equations(osys) show(stdout, MIME"text/plain"(), equations(osys)) # hide ``` @@ -139,7 +141,9 @@ The parameter `b` does not need to be explicitly declared in the We next convert our network to a jump process representation ```@example s1 +using JumpProcesses jsys = convert(JumpSystem, burstyrn; combinatoric_ratelaws = false) +jsys = complete(jsys) equations(jsys) show(stdout, MIME"text/plain"(), equations(jsys)) # hide ```