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Api doc proposed changes #862

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merged 4 commits into from
Jun 4, 2024
Merged

Api doc proposed changes #862

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TorkelE May 22, 2024
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TorkelE May 29, 2024
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TorkelE May 29, 2024
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Merge branch 'master' into api_doc_proposed_changes
TorkelE Jun 1, 2024
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2 changes: 1 addition & 1 deletion docs/pages.jl
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Expand Up @@ -66,5 +66,5 @@ pages = Any[
# # Repository structure.
# ],
#"FAQs" => "faqs.md",
#"API" => "api.md"
"API" => "api.md"
]
12 changes: 8 additions & 4 deletions docs/src/api.md
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Expand Up @@ -35,37 +35,41 @@ corresponding chemical reaction ODE models, chemical Langevin equation SDE
models, and stochastic chemical kinetics jump process models.

```@example ex1
using Catalyst, DifferentialEquations, Plots
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I have tried to remove all cases of DifferentialEquations

using Catalyst, OrdinaryDiffEq, StochasticDiffEq, JumpProcesses, Plots
t = default_t()
@parameters β γ
@species S(t) I(t) R(t)

rxs = [Reaction(β, [S,I], [I], [1,1], [2])
Reaction(γ, [I], [R])]
@named rs = ReactionSystem(rxs, t)
rs = complete(rs)
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completeness is now required for all systems.


u₀map = [S => 999.0, I => 1.0, R => 0.0]
parammap = [β => 1/10000, γ => 0.01]
tspan = (0.0, 250.0)

# solve as ODEs
odesys = convert(ODESystem, rs)
odesys = complete(odesys)
oprob = ODEProblem(odesys, u₀map, tspan, parammap)
sol = solve(oprob, Tsit5())
p1 = plot(sol, title = "ODE")

# solve as SDEs
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)
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When going through the doc build times, the rendering of large figures was the biggest problem. When building the docs (containing only the API) locally, reducing the saveat for these stochastic simulations reduced the build time from over 250 seconds to 15 seconds.

p3 = plot(sol, title = "jump")

plot(p1, p2, p3; layout = (3,1))
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