Removed code redundancies. Adjusted extra arguments inputted into com…

…peting hazards object and reverting to previous competing hazard tests.

R/competing_hazards.R

@@ -25,7 +25,7 @@ CompetingOutcome <- R6::R6Class(
       self$args <- list(...)
     },
     execute = function(t, target){
-      do.call(private$targeted_process, list(t, target, self$args))
+      do.call(private$targeted_process, c(t, list(target), self$args))
     },
     reset = function() {
       self$target$clear()

R/human_infection.R

@@ -181,9 +181,6 @@ calculate_vivax_infections <- function(
       infection_rates[hyp_source_index] <- infection_rates[hyp_source_index] + relapse_rates
       # Get and store relative rates for bite/relapse competing hazards resolution
       relative_rates <- relapse_rates/infection_rates[hyp_source_index]
-      # infection_outcome$set_relative_rates(
-      # hypnozoites_humans, 
-      # relative_rates)
     }
 
     prob <- rate_to_prob(infection_rates) * (1 - prophylaxis) * (1 - vaccine_efficacy)
@@ -944,7 +941,7 @@ severe_immunity <- function(age, acquired_immunity, maternal_immunity, parameter
   parameters$theta0 * (parameters$theta1 + (1 - parameters$theta1) / (
     1 + fv * (
       (acquired_immunity + maternal_immunity) / parameters$iv0) ** parameters$kv
-  )
+    )
   )
 }
 

R/processes.R

@@ -96,7 +96,7 @@ create_processes <- function(
 
   if(parameters$parasite == "falciparum"){
     infection_outcome <- CompetingOutcome$new(
-      targeted_process = function(timestep, target, args){
+      targeted_process = function(timestep, target){
         falciparum_infection_outcome_process(timestep, target, 
                                   variables, renderer, parameters
         )
@@ -106,18 +106,18 @@ create_processes <- function(
 
   } else if (parameters$parasite == "vivax"){
     infection_outcome <- CompetingOutcome$new(
-      targeted_process = function(timestep, target, args){
+      targeted_process = function(timestep, target, relative_rates){
         vivax_infection_outcome_process(timestep, target, 
                                   variables, renderer, parameters, 
-                                  args$relative_rates
+                                  relative_rates
         )
       },
       size = parameters$human_population
     )
   }
 
   progression_outcome <- CompetingOutcome$new(
-    targeted_process = function(timestep, target, ...){
+    targeted_process = function(timestep, target){
       progression_outcome_process(timestep, target, variables, parameters, renderer)
     },
     size = parameters$human_population

tests/testthat/test-competing-hazards.R

@@ -26,14 +26,15 @@ test_that("hazard resolves two disjoint outcomes", {
 
   outcome_1$set_rates(population, c(10, 0, 10, 0))
   outcome_2$set_rates(population, c(0, 10, 0, 10))
-  
+
   hazard$resolve(0)
+
   mockery::expect_args(outcome_1_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(1, 3)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(1, 3)))
+
   mockery::expect_args(outcome_2_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(2, 4)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(2, 4)))
+
 })
 
 test_that("hazard resolves two competing outcomes", {
@@ -63,11 +64,9 @@ test_that("hazard resolves two competing outcomes", {
   hazard$resolve(0)
 
   mockery::expect_args(outcome_1_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(2, 3)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(2, 3)))
   mockery::expect_args(outcome_2_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(1, 4)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(1, 4)))
 })
 
 test_that("hazard may resolve to neither outcome", {
@@ -97,11 +96,9 @@ test_that("hazard may resolve to neither outcome", {
   hazard$resolve(0)
 
   mockery::expect_args(outcome_1_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(3)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(3)))
   mockery::expect_args(outcome_2_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(2, 4)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(2, 4)))
 })
 
 test_that("outcomes can define a partial set of rates", {
@@ -133,11 +130,9 @@ test_that("outcomes can define a partial set of rates", {
   hazard$resolve(0)
 
   mockery::expect_args(outcome_1_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(1, 3)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(1, 3)))
   mockery::expect_args(outcome_2_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(4)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(4)))
 })
 
 test_that("hazard resolves three competing outcomes", {
@@ -173,12 +168,9 @@ test_that("hazard resolves three competing outcomes", {
   hazard$resolve(0)
 
   mockery::expect_args(outcome_1_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(1)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(1)))
   mockery::expect_args(outcome_2_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(2)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(2)))
   mockery::expect_args(outcome_3_process, 1, 0,
-                       individual::Bitset$new(size)$insert(c(3, 4)),
-                       list())
+                       individual::Bitset$new(size)$insert(c(3, 4)))
 })