Merge pull request #321 from mrc-ide/vivax_competing_hazards_main_hyp…

…nozoites

Add hypnozoites to the P.v model

R/biting_process.R

@@ -34,7 +34,7 @@ create_biting_process <- function(
   function(timestep) {
     # Calculate combined EIR
     age <- get_age(variables$birth$get_values(), timestep)
-    bitten_humans <- simulate_bites(
+    bitten <- simulate_bites(
       renderer,
       solvers,
       models,
@@ -52,7 +52,8 @@ create_biting_process <- function(
     simulate_infection(
       variables,
       events,
-      bitten_humans,
+      bitten$bitten_humans,
+      bitten$n_bites_per_person,
       age,
       parameters,
       timestep,
@@ -78,6 +79,7 @@ simulate_bites <- function(
   mixing_index = 1
   ) {
   bitten_humans <- individual::Bitset$new(parameters$human_population)
+  n_bites_per_person <- numeric(0)
 
   human_infectivity <- variables$infectivity$get_values()
   if (parameters$tbv) {
@@ -146,13 +148,24 @@ simulate_bites <- function(
 
     renderer$render(paste0('EIR_', species_name), species_eir, timestep)
     EIR <- EIR + species_eir
-    expected_bites <- species_eir * mean(psi)
+    if(parameters$parasite == "falciparum"){
+      # p.f model factors eir by psi
+      expected_bites <- species_eir * mean(psi)
+    } else if (parameters$parasite == "vivax"){
+      # p.v model standardises biting rate het to eir
+      expected_bites <- species_eir
+    }
+
     if (expected_bites > 0) {
       n_bites <- rpois(1, expected_bites)
       if (n_bites > 0) {
-        bitten_humans$insert(
-          fast_weighted_sample(n_bites, lambda)
-        )
+        bitten <- fast_weighted_sample(n_bites, lambda)
+        bitten_humans$insert(bitten)
+        renderer$render('n_bitten', bitten_humans$size(), timestep)
+        if(parameters$parasite == "vivax"){
+          # p.v must pass through the number of bites per person
+          n_bites_per_person <- tabulate(bitten, nbins = length(lambda))
+        }
       }
     }
 
@@ -202,9 +215,8 @@ simulate_bites <- function(
       )
     }
   }
-
-  renderer$render('n_bitten', bitten_humans$size(), timestep)
-  bitten_humans
+
+  list(bitten_humans = bitten_humans, n_bites_per_person = n_bites_per_person)
 }
 
 

R/competing_hazards.R

@@ -16,22 +16,25 @@ CompetingOutcome <- R6::R6Class(
 
       self$target <- individual::Bitset$new(size)
       self$rates <- NULL
+      self$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
+      self$args <- list(...)
     },
     execute = function(t, target){
-      private$targeted_process(t, target)
+      do.call(private$targeted_process, c(t, list(target), self$args))
     },
     reset = function() {
       self$target$clear()
       self$rates <- NULL
+      self$args <- NULL
     },
     target = NULL,
-    rates = NULL
+    rates = NULL,
+    args = NULL
   )
 )