update ODEProcess benchmark

CDCgov · Nov 6, 2024 · fcb2501 · fcb2501
1 parent 692a0bd
commit fcb2501
Show file tree

Hide file tree

Showing 3 changed files with 21 additions and 24 deletions.
diff --git a/benchmark/Project.toml b/benchmark/Project.toml
@@ -3,6 +3,7 @@ BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 EpiAware = "b2eeebe4-5992-4301-9193-7ebc9f62c855"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 TuringBenchmarking = "0db1332d-5c25-4deb-809f-459bc696f94f"
diff --git a/benchmark/bench/EpiInfModels/InfectionODEProcess.jl b/benchmark/bench/EpiInfModels/InfectionODEProcess.jl
diff --git a/benchmark/bench/EpiInfModels/ODEProcess.jl b/benchmark/bench/EpiInfModels/ODEProcess.jl
@@ -0,0 +1,20 @@
+let
+    # Create an instance of SIRParams
+    sirparams = SIRParams(
+        tspan = (0.0, 30.0),
+        infectiousness = LogNormal(log(0.3), 0.05),
+        recovery_rate = LogNormal(log(0.1), 0.05),
+        initial_prop_infected = Beta(1, 99)
+    )
+
+    # Define the ODEProcess
+    sir_process = ODEProcess(
+        params = sirparams,
+        sol2infs = sol -> sol[2, :],
+        solver_options = Dict(:verbose => false, :saveat => 1.0)
+    )
+
+    # Generate the latent infections
+    mdl = generate_latent_infs(sir_process, nothing)
+    suite["ODEProcess"] = make_epiaware_suite(mdl)
+end