adding in n_spray output

- adding spraying to mortality processes
- renaming process from RTS,S to PEV

R/mortality_processes.R

@@ -111,9 +111,12 @@ reset_target <- function(variables, events, target, state, parameters, timestep)
     variables$pev_profile$queue_update(-1, target)
     variables$tbv_vaccinated$queue_update(-1, target)
 
+    # spraying
+    variables$spray_time$queue_update(-1, target)
+
     # onwards infectiousness
     variables$infectivity$queue_update(0, target)
-    
+
     # treated compartment residence time:
     if(!is.null(variables$dt)) {
       variables$dt$queue_update(parameters$dt, target)

R/processes.R

@@ -30,7 +30,7 @@ create_processes <- function(
     correlations,
     lagged_eir,
     lagged_infectivity,
-    timesteps, 
+    timesteps,
     mixing = 1,
     mixing_index = 1
 ) {
@@ -105,22 +105,22 @@ create_processes <- function(
       0
     )
   )
-  
+
   # =======================
   # 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$dt
-  
-  # If antimalarial resistance is switched on, assign dt variable values to the 
+
+  # If antimalarial resistance is switched on, assign dt variable values to the
   if(parameters$antimalarial_resistance) {
     dt_input <- variables$dt
   }
-  
+
   # Create the progression process for Tr --> S specifying dt_input as the rate:
   processes <- c(
     processes,
@@ -143,7 +143,7 @@ create_processes <- function(
   )
 
   # =========
-  # RTS,S EPI
+  # PEV EPI
   # =========
   if (!is.null(parameters$pev_epi_coverage)) {
     processes <- c(
@@ -250,7 +250,7 @@ create_processes <- function(
   if (parameters$spraying) {
     processes <- c(
       processes,
-      indoor_spraying(variables$spray_time, parameters, correlations)
+      indoor_spraying(variables$spray_time, renderer, parameters, correlations)
     )
   }
 

R/vector_control.R

@@ -105,7 +105,8 @@ prob_bitten <- function(
 #' @param parameters the model parameters
 #' @param correlations correlation parameters
 #' @noRd
-indoor_spraying <- function(spray_time, parameters, correlations) {
+indoor_spraying <- function(spray_time, render, parameters, correlations) {
+  renderer$set_default('n_spray', 0)
   function(timestep) {
     matches <- timestep == parameters$spraying_timesteps
     if (any(matches)) {
@@ -116,6 +117,7 @@ indoor_spraying <- function(spray_time, parameters, correlations) {
         correlations
       ))
       spray_time$queue_update(timestep, target)
+      renderer$render('n_spray', length(target), timestep)
     }
   }
 }