Merge pull request #864 from SciML/param_stoich

proposed param stoich doc changes

Author: TorkelE

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.
         "model_creation/model_file_loading_and_export.md",# Distributed parameters, rates, and initial conditions.
         # Loading and writing models to files.
         "model_creation/model_visualisation.md",

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
 ```