Merge pull request #317 from mrc-ide/vivax_competing_hazards_main_no_…

…blood_immunity

Remove blood immunity from p.v model

R/human_infection.R

@@ -22,13 +22,15 @@ simulate_infection <- function(
     infection_outcome
 ) {
   if (bitten_humans$size() > 0) {
-    boost_immunity(
-      variables$ib,
-      bitten_humans,
-      variables$last_boosted_ib,
-      timestep,
-      parameters$ub
-    )
+    if(parameters$parasite == "falciparum"){
+      boost_immunity(
+        variables$ib,
+        bitten_humans,
+        variables$last_boosted_ib,
+        timestep,
+        parameters$ub
+      )
+    }
   }
 
   # Calculate Infected
@@ -61,7 +63,14 @@ calculate_infections <- function(
   source_humans <- variables$state$get_index_of(
     c('S', 'A', 'U'))$and(bitten_humans)
 
-  b <- blood_immunity(variables$ib$get_values(source_humans), parameters)
+  if(parameters$parasite == "falciparum"){
+    ## p.f models blood immunity
+    b <- blood_immunity(variables$ib$get_values(source_humans), parameters)
+
+  } else if (parameters$parasite == "vivax"){
+    ## p.v does not model blood immunity
+    b <- parameters$b
+  }
 
   source_vector <- source_humans$to_vector()
 

R/mortality_processes.R

@@ -91,15 +91,18 @@ reset_target <- function(variables, events, target, state, parameters, timestep)
     variables$birth$queue_update(timestep, target)
 
     # non-maternal immunity
-    variables$last_boosted_ib$queue_update(-1, target)
     variables$last_boosted_ica$queue_update(-1, target)
     variables$last_boosted_iva$queue_update(-1, target)
     variables$last_boosted_id$queue_update(-1, target)
-    variables$ib$queue_update(0, target)
     variables$ica$queue_update(0, target)
     variables$iva$queue_update(0, target)
     variables$id$queue_update(0, target)
     variables$state$queue_update(state, target)
+
+    if(parameters$parasite == "falciparum"){
+      variables$last_boosted_ib$queue_update(-1, target)
+      variables$ib$queue_update(0, target)
+    }
 
     # treatment
     variables$drug$queue_update(0, target)

R/processes.R

@@ -45,9 +45,6 @@ create_processes <- function(
                                                         parameters$rm),
     immunity_process = create_exponential_decay_process(variables$ivm,
                                                         parameters$rvm),
-    # Blood immunity
-    immunity_process = create_exponential_decay_process(variables$ib,
-                                                        parameters$rb),
     # Acquired immunity
     immunity_process = create_exponential_decay_process(variables$ica,
                                                         parameters$rc),
@@ -56,6 +53,15 @@ create_processes <- function(
     immunity_process = create_exponential_decay_process(variables$id,
                                                         parameters$rid)
   )
+
+  if(parameters$parasite == "falciparum"){
+    processes <- c(
+      processes,
+      # Blood immunity
+      immunity_process = create_exponential_decay_process(variables$ib,
+                                                          parameters$rb)
+    )
+  }
 
   if (parameters$individual_mosquitoes) {
     processes <- c(
@@ -179,7 +185,10 @@ create_processes <- function(
   # Rendering
   # =========
 
-  imm_var_names <- c('ica', 'icm', 'id', 'ib', 'iva', 'ivm')
+  imm_var_names <- c('ica', 'icm', 'id', 'iva', 'ivm')
+  if(parameters$parasite == "falciparum"){
+    imm_var_names <- c(imm_var_names, 'ib')
+  }
 
   processes <- c(
     processes,

R/variables.R

@@ -12,7 +12,7 @@
 #' boosted for tracking grace periods in the boost of immunity
 #' * ICM - Maternal immunity to clinical disease
 #' * IVM - Maternal immunity to severe disease
-#' * IB  - Pre-erythoctic immunity
+#' * IB  - Pre-erythrocytic immunity (p.f only)
 #' * ICA  - Acquired immunity to clinical disease
 #' * IVA  - Acquired immunity to severe disease
 #' * ID - Acquired immunity to detectability
@@ -96,7 +96,6 @@ create_variables <- function(parameters) {
   initial_states <- initial_state(parameters, initial_age, groups, eq, states)
   state <- individual::CategoricalVariable$new(states, initial_states)
   birth <- individual::IntegerVariable$new(-initial_age)
-  last_boosted_ib <- individual::DoubleVariable$new(rep(-1, size))
   last_boosted_ica <- individual::DoubleVariable$new(rep(-1, size))
   last_boosted_iva <- individual::DoubleVariable$new(rep(-1, size))
   last_boosted_id <- individual::DoubleVariable$new(rep(-1, size))
@@ -124,17 +123,21 @@ create_variables <- function(parameters) {
     )
   )
 
-  # Pre-erythoctic immunity
-  ib  <- individual::DoubleVariable$new(
-    initial_immunity(
-      parameters$init_ib,
-      initial_age,
-      groups,
-      eq,
-      parameters,
-      'IB'
+  if(parameters$parasite == "falciparum"){
+    # Pre-erythrocytic immunity
+    last_boosted_ib <- individual::DoubleVariable$new(rep(-1, size))
+    ib  <- individual::DoubleVariable$new(
+      initial_immunity(
+        parameters$init_ib,
+        initial_age,
+        groups,
+        eq,
+        parameters,
+        'IB'
+      )
     )
-  )
+  }
+
   # Acquired immunity to clinical disease
   ica <- individual::DoubleVariable$new(
     initial_immunity(
@@ -224,13 +227,11 @@ create_variables <- function(parameters) {
   variables <- list(
     state = state,
     birth = birth,
-    last_boosted_ib = last_boosted_ib,
     last_boosted_ica = last_boosted_ica,
     last_boosted_iva = last_boosted_iva,
     last_boosted_id = last_boosted_id,
     icm = icm,
     ivm = ivm,
-    ib = ib,
     ica = ica,
     iva = iva,
     id = id,
@@ -248,7 +249,13 @@ create_variables <- function(parameters) {
     spray_time = spray_time
   )
 
-
+  if(parameters$parasite == "falciparum"){
+    variables <- c(variables,
+                   last_boosted_ib = last_boosted_ib,
+                   ib = ib
+    )
+  }
+
   # Add variables for individual mosquitoes
   if (parameters$individual_mosquitoes) {
     species_values <- NULL

data-raw/parasite_parameters.csv

@@ -89,20 +89,13 @@ vivax,kmax,10, White (2018); doi: 10.1038/s41467-018-05860-8
 vivax,du,110,to_be_removed
 vivax,init_iva,0,to_be_removed
 vivax,init_ivm,0,to_be_removed
-vivax,init_ib,0,to_be_removed
 vivax,init_id,0,to_be_removed
-vivax,ub,7.2,to_be_removed
 vivax,uv,11.4321,to_be_removed
 vivax,ud,9.44512,to_be_removed
 vivax,pvm,0.195768,to_be_removed
 vivax,rvm,76.8365,to_be_removed
-vivax,rb,3650,to_be_removed
 vivax,rva,10950,to_be_removed
 vivax,rid,3650,to_be_removed
-vivax,b0,0.59,to_be_removed
-vivax,b1,0.5,to_be_removed
-vivax,ib0,43.9,to_be_removed
-vivax,kb,2.16,to_be_removed
 vivax,theta0,0.0749886,to_be_removed
 vivax,theta1,0.0001191,to_be_removed
 vivax,iv0,1.09629,to_be_removed

tests/testthat/test-vivax.R

@@ -24,7 +24,8 @@ test_that('Test difference between falciparum and vivax parameter lists', {
 
   expect_identical(
     in_falciparum_not_vivax,
-    c("gamma1") # asymptomatic infected infectivity towards mosquitos parameter
+    c("init_ib", "rb", "ub", "b0", "b1", "ib0", "kb", # blood immunity parameters
+    "gamma1") # asymptomatic infected infectivity towards mosquitos parameter
   )
 
   expect_identical(

vignettes/Plasmodium_vivax.Rmd

@@ -53,9 +53,15 @@ The *P. falciparum* model has five human disease compartments: susceptible (S),
 
 The *P. vivax* model follows a similar structure to the *P. falciparum* model, and also has five human disease compartments. However, the human disease states modeled explicitly focus on parasite density and detectability, such that we have: susceptible (S), clinical disease (D), **light-microscopy detectable infection (A)**, **PCR detectable infection (U)**, and treated (Tr).
 
+### Immunity
+
+The *P. falciparum* model tracks four kinds of immunity: immunity to blood stage infection (IB), clinical disease (acquired and maternal, ICA and ICM), to severe disease (acquired and maternal, IVA and IVM), and to detectability (ID).
+
+The *P. vivax* model tracks two kinds of immunity: immunity to clinical infection (acquired and maternal, ICA and ICM) and anti-parasite immunity (acquired and maternal, IAA and IAM). We do not track immunity to blood stage infections, severe immunity or immunity to detectability.
+
 ### Infectivity of LM-detectable infections
 
-While the *P. falciparum* model calculates the onward infectivity of asymptomatic infections (`ca`) using the age and detectability immunity of each individual, the *P. vivax* model uses a constant infectivity for LM-detectable infections (`ca = 0.1`).
+While the *P. falciparum* model calculates the onward infectivity of asymptomatic infections (`ca`) using the age and detectability immunity of each individual, the *P. vivax* model uses a constant onwards infectivity for LM-detectable infections (`ca = 0.1`).
 
 ### Key Model References