Add tests to test-sir.R

inst/tinytest/test-sir.R

@@ -1,3 +1,5 @@
+# Run just this file with command:
+# - tinytest::run_test_file("inst/tinytest/test-sir.R")
 # Adding a Small world population without queuing ------------------------------
 sir_0 <- ModelSIR(
   name = "COVID-19",
@@ -6,23 +8,45 @@ sir_0 <- ModelSIR(
   recovery_rate = .3
 )
 
-agents_smallworld(
+# Check model initialized correctly
+expect_inherits(sir_0,"epiworld_sir")
+expect_inherits(sir_0,"epiworld_model")
+# Check can't plot before model is run
+# TODO: Is this actually expected behavior?
+expect_error(plot(sir_0))
+
+expect_silent(agents_smallworld(
   sir_0,
   n = 50000,
   k = 5,
   d = FALSE,
   p = .01
-)
+))
 
 # Initializing 
 queuing_off(sir_0)
 
-# Running and printing
+# Running
+verbose_off(sir_0)
 run(sir_0, ndays = 50, seed = 1912)
 
+# Check plots without errors or warnings
+# TODO: Fix this check, it produces warnings but succeeds
+expect_silent(plot(sir_0))
+
 tmat_0 <- get_transition_probability(sir_0)
 
+expected_dimnames <- list(
+  c("Susceptible", "Infected", "Recovered"),
+  c("Susceptible", "Infected", "Recovered")
+)
+expected_dim <- c(3L, 3L)
+
+expect_equal(dimnames(tmat_0), expected_dimnames)
+expect_equal(dim(tmat_0), expected_dim)
+
 # Creating a SIR model with queuing --------------------------------------------
+# TODO: Can we simply reset the model and run again?
 sir_1 <- ModelSIR(
   name = "COVID-19",
   prevalence = .01,
@@ -40,16 +64,17 @@ agents_smallworld(
 )
 
 # Running and printing
+verbose_off(sir_1)
 run(sir_1, ndays = 50, seed = 1912)
 
 tmat_1 <- get_transition_probability(sir_1)
 
 # Expected
 tmat_expected <- structure(
   c(
-    0.962139427661896, 0, 0,
-    0.0378605611622334, 0.70049238204956, 
-    0, 0, 0.299507558345795, 1
+    0.961843, 0, 0,
+    0.03815696, 0.69985167, 0,
+    0, 0.3001483, 1
   ),
   dim = c(3L, 3L),
   dimnames = list(
@@ -58,8 +83,8 @@ tmat_expected <- structure(
   )
 )
 
-expect_equivalent(tmat_0, tmat_1)
-expect_equivalent(tmat_0, tmat_expected)
-expect_equivalent(tmat_1, tmat_expected)
-
-
+# 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)