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SciML · May 29, 2024 · 007e809 · 007e809
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Showing 2 changed files with 27 additions and 27 deletions.
diff --git a/docs/pages.jl b/docs/pages.jl
@@ -1,61 +1,61 @@
 pages = Any[
     "Home" => "index.md",
     "Introduction to Catalyst" => Any[
-        "introduction_to_catalyst/catalyst_for_new_julia_users.md",
+        #"introduction_to_catalyst/catalyst_for_new_julia_users.md",
         # "introduction_to_catalyst/introduction_to_catalyst.md"
         # Advanced introduction.
     ],
     "Model Creation and Properties" => Any[
-        "model_creation/dsl_basics.md",
-        "model_creation/dsl_advanced.md",
+        #"model_creation/dsl_basics.md",
+        #"model_creation/dsl_advanced.md",
         #"model_creation/programmatic_CRN_construction.md",
         #"model_creation/compositional_modeling.md",
         #"model_creation/constraint_equations.md",
         # Events.
         #"model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions.
         # Loading and writing models to files.
-        "model_creation/model_visualisation.md",
+        #"model_creation/model_visualisation.md",
         #"model_creation/network_analysis.md",
-        "model_creation/chemistry_related_functionality.md",
+        #"model_creation/chemistry_related_functionality.md",
         "Model creation examples" => Any[
-            "model_creation/examples/basic_CRN_library.md",
-            "model_creation/examples/programmatic_generative_linear_pathway.md",
+            #"model_creation/examples/basic_CRN_library.md",
+            #"model_creation/examples/programmatic_generative_linear_pathway.md",
             #"model_creation/examples/hodgkin_huxley_equation.md",
             #"model_creation/examples/smoluchowski_coagulation_equation.md"
         ]
     ],
     "Model simulation" => Any[
-        "model_simulation/simulation_introduction.md",
+        #"model_simulation/simulation_introduction.md",
         # Simulation introduction.
-        "model_simulation/simulation_plotting.md",
-        "model_simulation/simulation_structure_interfacing.md",
-        "model_simulation/ensemble_simulations.md",
+        #"model_simulation/simulation_plotting.md",
+        #"model_simulation/simulation_structure_interfacing.md",
+        #"model_simulation/ensemble_simulations.md",
         # Stochastic simulation statistical analysis.
-        "model_simulation/ode_simulation_performance.md",
+        #"model_simulation/ode_simulation_performance.md",
         # ODE Performance considerations/advice.
         # SDE Performance considerations/advice.
         # Jump Performance considerations/advice.
         # Finite state projection
     ],
     "Steady state analysis" => Any[
-        "steady_state_functionality/homotopy_continuation.md",
-        "steady_state_functionality/nonlinear_solve.md",
-        "steady_state_functionality/steady_state_stability_computation.md",        
-        "steady_state_functionality/bifurcation_diagrams.md",
-        "steady_state_functionality/dynamical_systems.md"
+        #"steady_state_functionality/homotopy_continuation.md",
+        #"steady_state_functionality/nonlinear_solve.md",
+        #"steady_state_functionality/steady_state_stability_computation.md",        
+        #"steady_state_functionality/bifurcation_diagrams.md",
+        #"steady_state_functionality/dynamical_systems.md"
     ],
     "Inverse Problems" => Any[
         # Inverse problems introduction.
-        "inverse_problems/optimization_ode_param_fitting.md",
+        #"inverse_problems/optimization_ode_param_fitting.md",
         # "inverse_problems/petab_ode_param_fitting.md",
         # ODE parameter fitting using Turing.
         # SDE/Jump fitting.
-        "inverse_problems/behaviour_optimisation.md",
-        "inverse_problems/structural_identifiability.md",
+        #"inverse_problems/behaviour_optimisation.md",
+        #"inverse_problems/structural_identifiability.md",
         # Practical identifiability.
-        "inverse_problems/global_sensitivity_analysis.md",
+        #"inverse_problems/global_sensitivity_analysis.md",
         "Inverse problem examples" => Any[
-            "inverse_problems/examples/ode_fitting_oscillation.md"
+            #"inverse_problems/examples/ode_fitting_oscillation.md"
         ]
     ],
     "Spatial modelling" => Any[
@@ -68,5 +68,5 @@ pages = Any[
     #     # Repository structure.
     # ],
     #"FAQs" => "faqs.md",
-    #"API" => "api.md"
+    "API" => "api.md"
 ]
diff --git a/docs/src/api.md b/docs/src/api.md
@@ -35,7 +35,7 @@ corresponding chemical reaction ODE models, chemical Langevin equation SDE
 models, and stochastic chemical kinetics jump process models.
 
 ```@example ex1
-using Catalyst, DifferentialEquations, Plots
+using Catalyst, OrdinaryDiffEq, StochasticDiffEq, JumpProcesses, Plots
 t = default_t()
 @parameters β γ
 @species S(t) I(t) R(t)
@@ -60,16 +60,16 @@ p1 = plot(sol, title = "ODE")
 sdesys = convert(SDESystem, rs)
 sdesys = complete(sdesys)
 sprob = SDEProblem(sdesys, u₀map, tspan, parammap)
-sol = solve(sprob, EM(), dt=.01)
+sol = solve(sprob, EM(), dt=.01, saveat = 2.0)
 p2 = plot(sol, title = "SDE")
 
 # solve as jump process
 jumpsys = convert(JumpSystem, rs)
 jumpsys = complete(jumpsys)
 u₀map    = [S => 999, I => 1, R => 0]
 dprob = DiscreteProblem(jumpsys, u₀map, tspan, parammap)
-jprob = JumpProblem(jumpsys, dprob, Direct())
-sol = solve(jprob, SSAStepper())
+jprob = JumpProblem(jumpsys, dprob, Direct(); save_positions = (false,false))
+sol = solve(jprob, SSAStepper(), saveat = 2.0)
 p3 = plot(sol, title = "jump")
 
 plot(p1, p2, p3; layout = (3,1))