Add queuing timing test to test-sir.R

inst/tinytest/test-sir.R

@@ -1,6 +1,24 @@
-# Run just this file with command:
-# - tinytest::run_test_file("inst/tinytest/test-sir.R")
-# Adding a Small world population without queuing ------------------------------
+# Test just this file: tinytest::run_test_file("inst/tinytest/test-sir.R")
+
+# Create function to test transition probability matrix ------------------------
+test_tmat_matches_expected <- function(tmat) {
+  tmat_expected <- structure(
+    c(
+      0.961843, 0, 0,
+      0.03815696, 0.69985167, 0,
+      0, 0.3001483, 1
+    ),
+    dim = c(3L, 3L),
+    dimnames = list(
+      c("Susceptible", "Infected", "Recovered"),
+      c("Susceptible", "Infected", "Recovered")
+    )
+  )
+
+  expect_equal(tmat, tmat_expected, tolerance = 0.0000001)
+}
+
+# Create small world population SIR Model --------------------------------------
 sir_0 <- ModelSIR(
   name = "COVID-19",
   prevalence = .01,
@@ -11,9 +29,6 @@ sir_0 <- ModelSIR(
 # Check model initialized correctly
 expect_inherits(sir_0,"epiworld_sir")
 expect_inherits(sir_0,"epiworld_model")
-# Check can't plot before model is run
-expect_warning(expect_error(plot(sir_0)))
-
 expect_silent(agents_smallworld(
   sir_0,
   n = 50000,
@@ -22,37 +37,36 @@ expect_silent(agents_smallworld(
   p = .01
 ))
 
-# Initializing 
-queuing_off(sir_0)
-
-# Running
-verbose_off(sir_0)
-run(sir_0, ndays = 50, seed = 1912)
-
-# Check plots without issue after running model
+# Running with queuing
+# - Suppressing print output
+expect_silent(verbose_off(sir_0))
+# - Check plot fails before model is run
+expect_warning(expect_error(plot(sir_0)))
+# - Run model
+expect_silent(run(sir_0, ndays = 50, seed = 1912))
+# - Check plot succeeded after running model
 expect_silent(plot(sir_0))
 
-tmat_0 <- get_transition_probability(sir_0)
+# Check transition probability matrix
+tmat_0_queuing <- get_transition_probability(sir_0)
+test_tmat_matches_expected(tmat_0_queuing)
 
-expected_dimnames <- list(
-  c("Susceptible", "Infected", "Recovered"),
-  c("Susceptible", "Infected", "Recovered")
-)
-expected_dim <- c(3L, 3L)
+# Run again without queuing and verify output is the same
+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_equal(dimnames(tmat_0), expected_dimnames)
-expect_equal(dim(tmat_0), expected_dim)
+expect_identical(tmat_0_noqueuing, tmat_0_queuing)
 
-# Creating a SIR model with queuing --------------------------------------------
-# TODO: Can we simply reset the model and run again?
+# Create new SIR model without queuing -----------------------------------------
 sir_1 <- ModelSIR(
   name = "COVID-19",
   prevalence = .01,
   transmission_rate = .9,
   recovery_rate = .3
 )
 
-# Adding a Small world population 
 agents_smallworld(
   sir_1,
   n = 50000,
@@ -61,28 +75,17 @@ agents_smallworld(
   p = .01
 )
 
-# Running and printing
+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)
 
-tmat_1 <- get_transition_probability(sir_1)
-
-# Expected
-tmat_expected <- structure(
-  c(
-    0.961843, 0, 0,
-    0.03815696, 0.69985167, 0,
-    0, 0.3001483, 1
-  ),
-  dim = c(3L, 3L),
-  dimnames = list(
-    c("Susceptible", "Infected", "Recovered"),
-    c("Susceptible", "Infected", "Recovered")
-  )
-)
+expect_identical(tmat_1_noqueuing, tmat_0_queuing)
 
-# Check matches expected output
-expect_equal(tmat_0, tmat_expected, tolerance = 0.0000001)
-# Check SIR produces same output with and without queuing
-# TODO: why is this the case?
-expect_equal(tmat_0, tmat_1)
+# Check queuing is faster ------------------------------------------------------
+runtime_0_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"])