Adding benchmarks

README.md

@@ -127,8 +127,8 @@ summary(sir)
 #> Number of entities  : 0
 #> Days (duration)     : 50 (of 50)
 #> Number of viruses   : 1
-#> Last run elapsed t  : 172.00ms
-#> Last run speed      : 29.03 million agents x day / second
+#> Last run elapsed t  : 170.00ms
+#> Last run speed      : 29.29 million agents x day / second
 #> Rewiring            : off
 #> 
 #> Global actions:

playground/benchmark-seir.R

@@ -0,0 +1,50 @@
+library(epiworldR)
+library(epiworldRfaster)
+
+library(microbenchmark)
+
+ns <- c(1e3, 5e3, 1e4, 5e4, 1e5, 5e5)
+ans <- vector("list", length(ns))
+names(ans) <- as.character(ns)
+for (n in ns) {
+
+  sir <- epiworldR::ModelSEIR(
+    name                = "COVID-19",
+    prevalence          = 0.01, 
+    incubation_days     = 7, 
+    transmission_rate   = 0.6,
+    recovery_rate       = 0.5
+  ) |> 
+    epiworldR::agents_smallworld(n = n, k = 20, p = 0.0, d = FALSE) |>
+    epiworldR::add_virus(
+      epiworldR::virus("COVID-19-beta", 0.01, 0.6, 0.5, 7), .2
+      ) |>
+    epiworldR::verbose_off()
+
+
+  sirfast <- epiworldRfaster::ModelSEIR(
+    name                = "COVID-19",
+    prevalence          = 0.01, 
+    incubation_days     = 7, 
+    transmission_rate   = 0.6,
+    recovery_rate       = 0.5
+  ) |> 
+    epiworldRfaster::agents_smallworld(n = n, k = 20, p = 0, d = FALSE) |>
+    epiworldRfaster::add_virus(
+      epiworldRfaster::virus("COVID-19-beta", 0.01, 0.6, 0.5, 7), .2
+      ) |>
+    epiworldRfaster::verbose_off()
+
+
+  ans[[as.character(n)]] <- microbenchmark(
+    old = epiworldR::run(sir, ndays = 100, seed = 1912),
+    new = epiworldRfaster::run(sirfast, ndays = 100, seed = 1912),
+    times = 10
+  )
+
+  message("Simulation with ", n, " individuals finished.")
+
+}
+
+saveRDS(ans, "playground/benchmark-seir.rds")
+

playground/benchmark-seirconn.R

@@ -0,0 +1,52 @@
+library(epiworldR)
+library(epiworldRfaster)
+
+library(microbenchmark)
+
+ns <- c(1e3, 5e3, 1e4, 5e4, 1e5, 5e5)
+ans <- vector("list", length(ns))
+names(ans) <- as.character(ns)
+for (n in ns) {
+
+  sir <- epiworldR::ModelSEIRCONN(
+    name                = "COVID-19",
+    prevalence          = 0.01, 
+    n                   = n,
+    contact_rate        = 4, 
+    incubation_days     = 7, 
+    transmission_rate   = 0.6,
+    recovery_rate       = 0.5
+  ) |> 
+    epiworldR::add_virus(
+      epiworldR::virus("COVID-19-beta", 0.01, 0.6, 0.5, 7), .2
+      ) |>
+    epiworldR::verbose_off()
+
+
+  sirfast <- epiworldRfaster::ModelSEIRCONN(
+    name                = "COVID-19",
+    prevalence          = 0.01, 
+    n                   = n,
+    contact_rate        = 4, 
+    incubation_days     = 7, 
+    transmission_rate   = 0.6,
+    recovery_rate       = 0.5
+  ) |> 
+    epiworldRfaster::add_virus(
+      epiworldRfaster::virus("COVID-19-beta", 0.01, 0.6, 0.5, 7), .2
+      ) |>
+    epiworldRfaster::verbose_off()
+
+
+  ans[[as.character(n)]] <- microbenchmark(
+    old = epiworldR::run(sir, ndays = 100, seed = 1912),
+    new = epiworldRfaster::run(sirfast, ndays = 100, seed = 1912),
+    times = 10
+  )
+
+  message("Simulation with ", n, " individuals finished.")
+
+}
+
+saveRDS(ans, "playground/benchmark-seirconn.rds")
+