confirm all changed functions return identical values as the originals

R/FUN_arrivals.R

@@ -28,11 +28,6 @@ arrivals.FUN <- function(dat, at, seed = NULL) {
   nOld <- dat$epi$num[at - 1]
   type <- dat$control$type
   nsteps <- dat$control$nsteps
-  a.rate.g2 <- dat$param$a.rate.g2
-  a.prop.e.g2 <- dat$param$a.prop.e.g2
-  a.prop.i.g2 <- dat$param$a.prop.i.g2
-  a.prop.q.g2 <- dat$param$a.prop.q.g2
-  
   
   # Process: partition arrivals into compartments -----------------------------------------------------------------
   nArrivals <- ifelse(a.rand, sum(stats::rbinom(nOld, 1, a.rate)), round(nOld * a.rate))

R/icm_seiqhrf.R

@@ -68,7 +68,8 @@ merge.seiqhrf.icm <- function(x, y, ...) {
 #' @importFrom EpiModel verbose.icm
 #' @importFrom future availableCores
 #' @export
-icm.seiqhrf <- function(param, init, control) {
+icm.seiqhrf <- function(param, init, control, seed = NULL) {
+
 
   crosscheck.seiqhrf.icm(param, init, control)
   EpiModel::verbose.icm(control, type = "startup")
@@ -83,7 +84,7 @@ icm.seiqhrf <- function(param, init, control) {
 
         ## Initialization module
         if (!is.null(control[["initialize.FUN"]])) {
-          dat <- do.call(control[["initialize.FUN"]], list(param, init, control))
+          dat <- do.call(control[["initialize.FUN"]], list(param, init, control, seed))
         }
 
 
@@ -94,31 +95,31 @@ icm.seiqhrf <- function(param, init, control) {
           um <- control$user.mods
           if (length(um) > 0) {
             for (i in 1:length(um)) {
-              dat <- do.call(control[[um[i]]], list(dat, at))
+              dat <- do.call(control[[um[i]]], list(dat, at, seed))
             }
           }
 
           ## Infection
           if (!is.null(control[["infection.FUN"]])) {
-            dat <- do.call(control[["infection.FUN"]], list(dat, at))
+            dat <- do.call(control[["infection.FUN"]], list(dat, at, seed))
           }
 
 
           ## Recovery
           if (!is.null(control[["recovery.FUN"]])) {
-            dat <- do.call(control[["recovery.FUN"]], list(dat, at))
+            dat <- do.call(control[["recovery.FUN"]], list(dat, at, seed))
           }
 
 
           ## Departure Module
           if (!is.null(control[["departures.FUN"]])) {
-            dat <- do.call(control[["departures.FUN"]], list(dat, at))
+            dat <- do.call(control[["departures.FUN"]], list(dat, at, seed))
           }
 
 
           ## Arrival Module
           if (!is.null(control[["arrivals.FUN"]])) {
-            dat <- do.call(control[["arrivals.FUN"]], list(dat, at))
+            dat <- do.call(control[["arrivals.FUN"]], list(dat, at, seed))
           }
 
 
@@ -155,7 +156,7 @@ icm.seiqhrf <- function(param, init, control) {
 
         ## Initialization module
         if (!is.null(control[["initialize.FUN"]])) {
-          dat <- do.call(control[["initialize.FUN"]], list(param, init, control))
+          dat <- do.call(control[["initialize.FUN"]], list(param, init, control, seed))
         }
 
         # Timestep loop
@@ -165,31 +166,31 @@ icm.seiqhrf <- function(param, init, control) {
           um <- control$user.mods
           if (length(um) > 0) {
             for (i in 1:length(um)) {
-              dat <- do.call(control[[um[i]]], list(dat, at))
+              dat <- do.call(control[[um[i]]], list(dat, at, seed))
             }
           }
 
           ## Infection
           if (!is.null(control[["infection.FUN"]])) {
-            dat <- do.call(control[["infection.FUN"]], list(dat, at))
+            dat <- do.call(control[["infection.FUN"]], list(dat, at, seed))
           }
 
 
           ## Recovery
           if (!is.null(control[["recovery.FUN"]])) {
-            dat <- do.call(control[["recovery.FUN"]], list(dat, at))
+            dat <- do.call(control[["recovery.FUN"]], list(dat, at, seed))
           }
 
 
           ## Departure Module
           if (!is.null(control[["departures.FUN"]])) {
-            dat <- do.call(control[["departures.FUN"]], list(dat, at))
+            dat <- do.call(control[["departures.FUN"]], list(dat, at, seed))
           }
 
 
           ## Arrival Module
           if (!is.null(control[["arrivals.FUN"]])) {
-            dat <- do.call(control[["arrivals.FUN"]], list(dat, at))
+            dat <- do.call(control[["arrivals.FUN"]], list(dat, at, seed))
           }
 
 

tests/testthat/test-icm-seiqhrf.R

+test_that("Identical output as Churches' original function: icm_seiqhrf", {
+    
+    full_params <- set_param(s.num = 1000, nsteps = 10)
+    param <- full_params$param
+    init <- full_params$init
+    
+    #### default functions: initialize.FUN, infection.FUN, recovery.FUN, departures.FUN, arrivals.FUN
+    control1 <- full_params$control
+    ### Churches' original function:
+    control2 <- control1
+    control2$initialize.FUN <- "initialize.icm"
+    control2$infection.FUN <- "infection.seiqhrf.icm"
+    control2$recovery.FUN <- "progress.seiqhrf.icm"
+    control2$departures.FUN <- "departures.seiqhrf.icm"
+    control2$arrivals.FUN <- "arrivals.seiqhrf.icm"
+    
+    No_seeds <- 10
+    seed_list <- sample(1:1000, No_seeds)
+    comp <- rep(NA, No_seeds)
+    i <- 1
+    for(seed in seed_list){
+        sim1 <- icm.seiqhrf(param, init, control1, seed)
+        sim2 <- icm.seiqhrf(param, init, control2, seed)
+        comp[i] <- identical(sim1, sim2)
+        i <- i + 1
+    }
+    
+    expect_equal(sum(comp), No_seeds)
+})