From 5077d4b8991e97346d01851b116baf0bd2a16c15 Mon Sep 17 00:00:00 2001
From: RJSheppard <rjs11@ic.ac.uk>
Date: Mon, 15 Apr 2024 13:33:36 +0100
Subject: [PATCH] Moved mortality to the end of processes to resolve order of
 competing hazards.

---
 R/processes.R | 34 +++++++++++++++++++---------------
 1 file changed, 19 insertions(+), 15 deletions(-)

diff --git a/R/processes.R b/R/processes.R
index 6109490f..cb6674e7 100644
--- a/R/processes.R
+++ b/R/processes.R
@@ -46,7 +46,7 @@ create_processes <- function(
     create_exponential_decay_process(variables$iva, parameters$rva),
     create_exponential_decay_process(variables$id, parameters$rid)
   )
-  
+
   if (parameters$individual_mosquitoes) {
     processes <- c(
       processes,
@@ -59,7 +59,7 @@ create_processes <- function(
       )
     )
   }
-  
+
   # ==============================
   # Biting and mortality processes
   # ==============================
@@ -80,7 +80,6 @@ create_processes <- function(
       mixing,
       mixing_index
     ),
-    create_mortality_process(variables, events, renderer, parameters),
     create_asymptomatic_progression_process(
       variables$state,
       parameters$dd,
@@ -112,7 +111,7 @@ create_processes <- function(
       0
     )
   )
-  
+
   # ===============
   # ODE integration
   # ===============
@@ -120,7 +119,7 @@ create_processes <- function(
     processes,
     create_solver_stepping_process(solvers, parameters)
   )
-  
+
   # =========
   # RTS,S EPI
   # =========
@@ -137,7 +136,7 @@ create_processes <- function(
       )
     )
   }
-  
+
   # =========
   # PMC
   # =========
@@ -156,7 +155,7 @@ create_processes <- function(
       )
     )
   }
-  
+
   # =========
   # Rendering
   # =========
@@ -186,7 +185,7 @@ create_processes <- function(
     ),
     create_compartmental_rendering_process(renderer, solvers, parameters)
   )
-  
+
   if (parameters$individual_mosquitoes) {
     processes <- c(
       processes,
@@ -208,11 +207,11 @@ create_processes <- function(
       )
     )
   }
-  
+
   # ======================
   # Intervention processes
   # ======================
-  
+
   if (parameters$bednets) {
     processes <- c(
       processes,
@@ -225,14 +224,14 @@ create_processes <- function(
       net_usage_renderer(variables$net_time, renderer)
     )
   }
-  
+
   if (parameters$spraying) {
     processes <- c(
       processes,
       indoor_spraying(variables$spray_time, parameters, correlations)
     )
   }
-  
+
   # ======================
   # Progress bar process
   # ======================
@@ -242,7 +241,12 @@ create_processes <- function(
       create_progress_process(timesteps)
     )
   }
-  
+
+  # Mortality step
+  processes <- c(
+    processes,
+    create_mortality_process(variables, events, renderer, parameters))
+
   processes
 }
 
@@ -266,7 +270,7 @@ create_exponential_decay_process <- function(variable, rate) {
 #' @title Create and initialise lagged_infectivity object
 #'
 #' @param variables model variables for initialisation
-#' @param parameters model parameters 
+#' @param parameters model parameters
 #' @noRd
 create_lagged_infectivity <- function(variables, parameters) {
   age <- get_age(variables$birth$get_values(), 0)
@@ -283,7 +287,7 @@ create_lagged_infectivity <- function(variables, parameters) {
 #'
 #' @param variables model variables for initialisation
 #' @param solvers model differential equation solvers
-#' @param parameters model parameters 
+#' @param parameters model parameters
 #' @noRd
 create_lagged_eir <- function(variables, solvers, parameters) {
   lapply(