Clean up test-sir.R

inst/tinytest/test-sir.R

@@ -26,7 +26,7 @@ sir_0 <- ModelSIR(
   recovery_rate = .3
 )
 
-# Check model initialized correctly
+# Check model initialization
 expect_inherits(sir_0,"epiworld_sir")
 expect_inherits(sir_0,"epiworld_model")
 expect_silent(agents_smallworld(
@@ -37,55 +37,24 @@ expect_silent(agents_smallworld(
   p = .01
 ))
 
-# Running with queuing
-# - Suppressing print output
+# Check model run with queuing -------------------------------------------------
 expect_silent(verbose_off(sir_0))
-# - Check plot fails before model is run
-expect_warning(expect_error(plot(sir_0)))
-# - Run model
+expect_warning(expect_error(plot(sir_0))) # Plot fails before model is run
 expect_silent(run(sir_0, ndays = 50, seed = 1912))
-# - Check plot succeeded after running model
-expect_silent(plot(sir_0))
+expect_silent(plot(sir_0)) # Plot succeeds after model is run
 
-# Check transition probability matrix
-tmat_0_queuing <- get_transition_probability(sir_0)
-test_tmat_matches_expected(tmat_0_queuing)
+tmat_queuing <- get_transition_probability(sir_0)
+test_tmat_matches_expected(tmat_queuing)
 
-# Run again without queuing and verify output is the same
+# Check model run without queuing ----------------------------------------------
 expect_silent(queuing_off(sir_0))
 run(sir_0, ndays = 50, seed = 1912)
-tmat_0_noqueuing <- get_transition_probability(sir_0)
-test_tmat_matches_expected(tmat_0_noqueuing)
 
-expect_identical(tmat_0_noqueuing, tmat_0_queuing)
-
-# Create new SIR model without queuing -----------------------------------------
-sir_1 <- ModelSIR(
-  name = "COVID-19",
-  prevalence = .01,
-  transmission_rate = .9,
-  recovery_rate = .3
-)
-
-agents_smallworld(
-  sir_1,
-  n = 50000,
-  k = 5,
-  d = FALSE,
-  p = .01
-)
-
-queuing_off(sir_1)
-
-# Run the model and check output
-verbose_off(sir_1)
-run(sir_1, ndays = 50, seed = 1912)
-tmat_1_noqueuing <- get_transition_probability(sir_1)
-
-expect_identical(tmat_1_noqueuing, tmat_0_queuing)
+tmat_noqueuing <- get_transition_probability(sir_0)
+expect_identical(tmat_noqueuing, tmat_queuing)
 
 # Check queuing is faster ------------------------------------------------------
-runtime_0_noqueuing <- system.time(run(sir_0, ndays = 50, seed = 1912))
+runtime_noqueuing <- system.time(run(sir_0, ndays = 50, seed = 1912))
 queuing_on(sir_0)
-runtime_0_queuing <- system.time(run(sir_0, ndays = 50, seed = 1912))
-expect_true(runtime_0_queuing["elapsed"] < runtime_0_noqueuing["elapsed"])
+runtime_queuing <- system.time(run(sir_0, ndays = 50, seed = 1912))
+expect_true(runtime_queuing["elapsed"] < runtime_noqueuing["elapsed"])