Rewritten competing hazards resoltion so that it does not call itself…

… within the function. This also removed the "set_relative_rates" part of the competing hazards, and now we have args, such that the competing hazards object can still store the relative rates it needs, but retains flexibility.

Calculate_infections has been rewritten as four functions: calculate_falciparum_infections, calculate_vivax_infections, treatment_prophylaxis_efficacy and pev_efficacy.

Infection_outcome_process has been split into falciparum and vivax _infection_outcome_process.

Tests have been adjusted to reflect these changes.

R/competing_hazards.R

@@ -16,31 +16,25 @@ CompetingOutcome <- R6::R6Class(
 
       self$target <- individual::Bitset$new(size)
       self$rates <- NULL
-      self$relative_rates <- NULL
+      self$args <- NULL
     },
-    set_rates = function(target, rates){
+    set_rates = function(target, rates, ...){
       stopifnot(target$size() == length(rates))
-
       self$target$copy_from(target)
       self$rates <- rates
-    },
-    set_relative_rates = function(target, relative_rates){
-      stopifnot(target$size() == length(relative_rates))
-
-      self$target$copy_from(target)
-      self$relative_rates <- relative_rates
+      self$args <- list(...)
     },
     execute = function(t, target){
-      private$targeted_process(t, target)
+      do.call(private$targeted_process, list(t, target, self$args))
     },
     reset = function() {
       self$target$clear()
       self$rates <- NULL
-      self$relative_rates <- NULL
+      self$args <- NULL
     },
     target = NULL,
     rates = NULL,
-    relative_rates = NULL
+    args = NULL
   )
 )