Changing create_progression_process() rates to probs

R/disease_progression.R

@@ -22,7 +22,7 @@ create_progression_process <- function(
     state,
     from_state,
     to_state,
-    rate,
+    prob,
     infectivity,
     new_infectivity
 ) {
@@ -31,13 +31,13 @@ create_progression_process <- function(
     # Retrieve the indices of all individuals in the to_move state:
     index <- state$get_index_of(from_state)
 
-    # If the length of rate is greater than 1 (when it's a variable):
-    if (inherits(rate, "DoubleVariable")) {
-      rate <- rate$get_values(index)
+    # If function receives a vector transition probabilities rather than a single value:
+    if (length(prob) > 1) {
+      prob <- prob[index$to_vector()]
     }
 
-    # Sample the individuals to be moved into a new Bitset using the transition rate(s):
-    to_move <- index$sample(1/rate)
+    # Sample the individuals to be moved into a new Bitset using the transition probabilities:
+    to_move <- index$sample(prob)
 
     # Update the infection status of those individuals who are moving:
     update_infection(
@@ -52,12 +52,12 @@ create_progression_process <- function(
 
 create_asymptomatic_progression_process <- function(
   state,
-  rate,
+  prob,
   variables,
   parameters
   ) {
   function(timestep) {
-    to_move <- state$get_index_of('D')$sample(1/rate)
+    to_move <- state$get_index_of('D')$sample(prob)
     update_to_asymptomatic_infection(
       variables,
       parameters,

R/processes.R

@@ -84,23 +84,23 @@ create_processes <- function(
     ),
     create_asymptomatic_progression_process(
       variables$state,
-      parameters$dd,
+      1 - exp(-1/parameters$dd),
       variables,
       parameters
     ),
     create_progression_process(
       variables$state,
       'A',
       'U',
-      parameters$da,
+      1 - exp(-1/parameters$da),
       variables$infectivity,
       parameters$cu
     ),
     create_progression_process(
       variables$state,
       'U',
       'S',
-      parameters$du,
+      1 - exp(-1/parameters$du),
       variables$infectivity,
       0
     )
@@ -109,16 +109,13 @@ create_processes <- function(
   # =======================
   # Antimalarial Resistance
   # =======================
-  # Add an a new process which governs the transition from Tr to S when
-  # antimalarial resistance is simulated. The rate of transition switches
-  # from a parameter to a variable when antimalarial resistance == TRUE.
 
   # Assign the dt input to a separate object with the default single parameter value:
   dt_input <- parameters$dt
 
   # If antimalarial resistance is switched on, assign dt variable values to the 
   if(parameters$antimalarial_resistance) {
-    dt_input <- variables$dt
+    dt_input <- variables$dt$get_values()
   }
 
   # Create the progression process for Tr --> S specifying dt_input as the rate:
@@ -128,7 +125,7 @@ create_processes <- function(
       variables$state,
       'Tr',
       'S',
-      dt_input,
+      1 - exp(-1/dt_input),
       variables$infectivity,
       0
     )