bugs + last_year vars

mrc-ide · May 17, 2024 · bb3bb05 · bb3bb05
1 parent b7b4a12
commit bb3bb05
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Showing 4 changed files with 21 additions and 9 deletions.
diff --git a/R/mortality_processes.R b/R/mortality_processes.R
@@ -113,6 +113,9 @@ 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)
 

diff --git a/R/pev.R b/R/pev.R
@@ -25,7 +25,7 @@ create_epi_pev_process <- function(
     if(coverage == 0){
       return()
     }
-    
+
     to_vaccinate <- variables$birth$get_index_of(
       set = timestep - parameters$pev_epi_age
     )
@@ -77,6 +77,7 @@ create_epi_pev_process <- function(
 #' @param events a list of events in the model
 #' @param parameters the model parameters
 #' @param correlations correlation parameters
+#' @param renderer the model renderer object
 #' @noRd
 create_mass_pev_listener <- function(
   variables,
@@ -86,6 +87,7 @@ create_mass_pev_listener <- function(
   renderer
   ) {
   renderer$set_default('n_new_vaccinations', 0)
+  renderer$set_default('n_pev_last_year', 0)
   function(timestep) {
     in_age_group <- individual::Bitset$new(parameters$human_population)
     for (i in seq_along(parameters$mass_pev_min_ages)) {
@@ -111,7 +113,7 @@ create_mass_pev_listener <- function(
     } else {
       target <- target$to_vector()
     }
-    
+
     time_index = which(parameters$mass_pev_timesteps == timestep)
     target <- target[
       sample_intervention(
@@ -129,6 +131,7 @@ create_mass_pev_listener <- function(
     )$size()
 
     renderer$render('n_new_vaccinations', n_new_vaccinations, timestep)
+    renderer$render('n_pev_last_year', used_intervention(variables$last_pev_timestep, timestep, 365)$size(), timestep)
 
     # Update the latest vaccination time
     variables$last_pev_timestep$queue_update(timestep, target)

diff --git a/R/processes.R b/R/processes.R
@@ -143,7 +143,7 @@ create_processes <- function(
   )
 
   # =========
-  # RTS,S EPI
+  # PEV EPI
   # =========
   if (!is.null(parameters$pev_epi_coverage)) {
     processes <- c(
@@ -239,6 +239,7 @@ create_processes <- function(
       processes,
       distribute_nets(
         variables,
+        renderer,
         events$throw_away_net,
         parameters,
         correlations

diff --git a/R/vector_control.R b/R/vector_control.R
@@ -102,13 +102,13 @@ prob_bitten <- function(
 #' `get_correlation_parameters`
 #'
 #' @param spray_time the variable for the time of spraying
-#' @param renderer items to render
+#' @param renderer the model renderer object
 #' @param parameters the model parameters
 #' @param correlations correlation parameters
 #' @noRd
 indoor_spraying <- function(spray_time, renderer, parameters, correlations) {
-  renderer$set_default("n_spray", 0)
-  renderer$set_default("spray_last_year", 0)
+  renderer$set_default('n_spray', 0)
+  renderer$set_default('n_spray_last_year', 0)
   function(timestep) {
     matches <- timestep == parameters$spraying_timesteps
     if (any(matches)) {
@@ -119,9 +119,9 @@ indoor_spraying <- function(spray_time, renderer, parameters, correlations) {
         correlations
       ))
       spray_time$queue_update(timestep, target)
-      renderer$render("n_spray", length(target), timestep)
+      renderer$render('n_spray', length(target), timestep)
     }
-    renderer$render("spray_last_year", used_intervention(spray_time, timestep, 365)$size(), timestep)
+    renderer$render('n_spray_last_year', used_intervention(spray_time, timestep, 365)$size(), timestep)
   }
 }
 
@@ -132,11 +132,14 @@ indoor_spraying <- function(spray_time, renderer, parameters, correlations) {
 #' `get_correlation_parameters`
 #'
 #' @param variables list of variables in the model
+#' @param renderer the model renderer object
 #' @param throw_away_net an event to trigger when the net will be removed
 #' @param parameters the model parameters
 #' @param correlations correlation parameters
 #' @noRd
-distribute_nets <- function(variables, throw_away_net, parameters, correlations) {
+distribute_nets <- function(variables, renderer, throw_away_net, parameters, correlations) {
+  renderer$set_default('n_net', 0)
+  renderer$set_default('n_net_last_year', 0)
   function(timestep) {
     matches <- timestep == parameters$bednet_timesteps
     if (any(matches)) {
@@ -152,7 +155,9 @@ distribute_nets <- function(variables, throw_away_net, parameters, correlations)
         target,
         log_uniform(length(target), parameters$bednet_retention)
       )
+      renderer$render('n_net', length(target), timestep)
     }
+    renderer$render('n_net_last_year', used_intervention(variables$net_time, timestep, 365)$size(), timestep)
   }
 }