Immunity to severe disease is not modelled in vivax. Switches are inc…

…luded to set and use severe immunity variables. Relevant severe immunity parameters removed from the pv parameters in the parameters csv file.
mrc-ide · Sep 18, 2024 · 5ff8fc6 · 5ff8fc6
1 parent e3e404c
commit 5ff8fc6
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Showing 8 changed files with 90 additions and 95 deletions.
diff --git a/R/disease_progression.R b/R/disease_progression.R
@@ -6,9 +6,9 @@
 #' @param progression_outcome competing hazards object for disease progression rates
 #' @noRd
 create_progression_rates_process <- function(
-  parameters,
-  variables,
-  progression_outcome
+    parameters,
+    variables,
+    progression_outcome
 ) {
   function(timestep){
     target <- variables$state$get_index_of("S")$not()
@@ -33,7 +33,6 @@ create_progression_rates_process <- function(
     progression_outcome$set_rates(
       target,
       progression_rates)
-
   }
 }
 

diff --git a/R/human_infection.R b/R/human_infection.R
@@ -199,13 +199,15 @@ infection_outcome_process <- function(
     timestep
   )
 
-  update_severe_disease(
-    timestep,
-    infected_humans,
-    variables,
-    parameters,
-    renderer
-  )
+  if(parameters$parasite == "falciparum"){
+    update_severe_disease(
+      timestep,
+      infected_humans,
+      variables,
+      parameters,
+      renderer
+    )
+  }
 
   treated <- calculate_treated(
     variables,

diff --git a/R/mortality_processes.R b/R/mortality_processes.R
@@ -66,10 +66,12 @@ sample_maternal_immunity <- function(variables, target, timestep, parameters) {
 
         # set their maternal immunities
         birth_icm <- variables$ica$get_values(mothers) * parameters$pcm
-        birth_ivm <- variables$iva$get_values(mothers) * parameters$pvm
         variables$icm$queue_update(birth_icm, target_group)
-        variables$ivm$queue_update(birth_ivm, target_group)
-        if(parameters$parasite == "vivax"){
+        if(parameters$parasite == "falciparum"){
+          birth_ivm <- variables$iva$get_values(mothers) * parameters$pvm
+          variables$ivm$queue_update(birth_ivm, target_group)
+
+        } else if(parameters$parasite == "vivax"){
           birth_iam <- variables$iaa$get_values(mothers) * parameters$pcm
           variables$iam$queue_update(birth_iam, target_group)
         }
@@ -96,15 +98,15 @@ reset_target <- function(variables, events, target, state, parameters, timestep)
 
     # non-maternal immunity
     variables$last_boosted_ica$queue_update(-1, target)
-    variables$last_boosted_iva$queue_update(-1, target)
     variables$ica$queue_update(0, target)
-    variables$iva$queue_update(0, target)
     variables$state$queue_update(state, target)
 
     if(parameters$parasite == "falciparum"){
       variables$last_boosted_ib$queue_update(-1, target)
+      variables$last_boosted_iva$queue_update(-1, target)
       variables$last_boosted_id$queue_update(-1, target)
       variables$ib$queue_update(0, target)
+      variables$iva$queue_update(0, target)
       variables$id$queue_update(0, target)
 
     } else if (parameters$parasite == "vivax"){

diff --git a/R/processes.R b/R/processes.R
@@ -40,24 +40,26 @@ create_processes <- function(
   # Immunity
   # ========
   processes <- list(
-    # Maternal immunity
+    # Immunity to clinical disease (maternal)
     immunity_process = create_exponential_decay_process(variables$icm,
                                                         parameters$rm),
-    immunity_process = create_exponential_decay_process(variables$ivm,
-                                                        parameters$rvm),
-    # Acquired immunity
+    # Immunity to clinical disease (acquired)
     immunity_process = create_exponential_decay_process(variables$ica,
-                                                        parameters$rc),
-    immunity_process = create_exponential_decay_process(variables$iva,
-                                                        parameters$rva)
+                                                        parameters$rc)
   )
-  
+
   if(parameters$parasite == "falciparum"){
     processes <- c(
       processes,
       # Blood immunity
       immunity_process = create_exponential_decay_process(variables$ib,
                                                           parameters$rb),
+      # Immunity to severe disease (maternal)
+      immunity_process = create_exponential_decay_process(variables$ivm,
+                                                          parameters$rvm),
+      # Immunity to severe disease (acquired)
+      immunity_process = create_exponential_decay_process(variables$iva,
+                                                          parameters$rva),
       # Immunity to detectability
       immunity_process = create_exponential_decay_process(variables$id, parameters$rid)
     )
@@ -193,13 +195,13 @@ create_processes <- function(
   # Rendering
   # =========
 
-  imm_var_names <- c('ica', 'icm', 'iva', 'ivm')
+  imm_var_names <- c('ica', 'icm')
   if(parameters$parasite == "falciparum"){
-    imm_var_names <- c(imm_var_names, 'ib', 'id')
+    imm_var_names <- c(imm_var_names, 'ib', 'iva', 'ivm', 'id')
   } else if (parameters$parasite == "vivax"){
     imm_var_names <- c(imm_var_names, 'iaa', 'iam')
   }
-  
+
   processes <- c(
     processes,
     categorical_renderer = individual::categorical_count_renderer_process(

diff --git a/R/variables.R b/R/variables.R
@@ -99,10 +99,7 @@ create_variables <- function(parameters) {
   state <- individual::CategoricalVariable$new(states, initial_states)
   birth <- individual::IntegerVariable$new(-initial_age)
 
-  last_boosted_ica <- individual::DoubleVariable$new(rep(-1, size))
-  last_boosted_iva <- individual::DoubleVariable$new(rep(-1, size))
-
-  # Maternal immunity
+  # Maternal immunity to clinical disease
   icm <- individual::DoubleVariable$new(
     initial_immunity(
       parameters$init_icm,
@@ -113,20 +110,22 @@ create_variables <- function(parameters) {
       'ICM'
     )
   )
-
-  ivm <- individual::DoubleVariable$new(
+
+  # Acquired immunity to clinical disease
+  last_boosted_ica <- individual::DoubleVariable$new(rep(-1, size))
+  ica <- individual::DoubleVariable$new(
     initial_immunity(
-      parameters$init_ivm,
+      parameters$init_ica,
       initial_age,
       groups,
       eq,
       parameters,
-      'IVM'
+      'ICA'
     )
   )
 
   if(parameters$parasite == "falciparum"){
-    # Pre-erythrocytic immunity
+    # Pre-erythoctic immunity
     last_boosted_ib <- individual::DoubleVariable$new(rep(-1, size))
     ib  <- individual::DoubleVariable$new(
       initial_immunity(
@@ -138,8 +137,33 @@ create_variables <- function(parameters) {
         'IB'
       )
     )
-
-    # Acquired immunity to detectability
+
+    # Maternal immunity to severe disease
+    ivm <- individual::DoubleVariable$new(
+      initial_immunity(
+        parameters$init_ivm,
+        initial_age,
+        groups,
+        eq,
+        parameters,
+        'IVM'
+      )
+    )
+
+    # Acquired immunity to severe disease
+    last_boosted_iva <- individual::DoubleVariable$new(rep(-1, size))
+    iva <- individual::DoubleVariable$new(
+      initial_immunity(
+        parameters$init_iva,
+        initial_age,
+        groups,
+        eq,
+        parameters,
+        'IVA'
+      )
+    )
+
+    # Acquired immunity to lm detectability
     last_boosted_id <- individual::DoubleVariable$new(rep(-1, size))
     id <- individual::DoubleVariable$new(
       initial_immunity(
@@ -153,56 +177,32 @@ create_variables <- function(parameters) {
     )
 
   } else if (parameters$parasite == "vivax"){
-    # Acquired anti-parasite immunity
-    last_boosted_iaa <- individual::DoubleVariable$new(rep(-1, size))
-    iaa <- individual::DoubleVariable$new(
+    # Maternal anti-parasite immunity
+    iam <- individual::DoubleVariable$new(
       initial_immunity(
-        parameters$init_iaa,
+        parameters$init_iam,
         initial_age,
         groups,
         eq,
         parameters,
-        'IAA'
+        'IAM'
       )
     )
 
-    # Maternal anti-parasite immunity
-    iam <- individual::DoubleVariable$new(
+    # Acquired anti-parasite immunity
+    last_boosted_iaa <- individual::DoubleVariable$new(rep(-1, size))
+    iaa <- individual::DoubleVariable$new(
       initial_immunity(
-        parameters$init_iam,
+        parameters$init_iaa,
         initial_age,
         groups,
         eq,
         parameters,
-        'IAM'
+        'IAA'
       )
     )
   }
 
-  # Acquired immunity to clinical disease
-  ica <- individual::DoubleVariable$new(
-    initial_immunity(
-      parameters$init_ica,
-      initial_age,
-      groups,
-      eq,
-      parameters,
-      'ICA'
-    )
-  )
-
-  # Acquired immunity to severe disease
-  iva <- individual::DoubleVariable$new(
-    initial_immunity(
-      parameters$init_iva,
-      initial_age,
-      groups,
-      eq,
-      parameters,
-      'IVA'
-    )
-  )
-
   # Initialise infectiousness of humans -> mosquitoes
   # NOTE: not yet supporting initialisation of infectiousness of Treated individuals
   infectivity_values <- rep(0, get_human_population(parameters, 0))
@@ -269,11 +269,8 @@ create_variables <- function(parameters) {
     state = state,
     birth = birth,
     last_boosted_ica = last_boosted_ica,
-    last_boosted_iva = last_boosted_iva,
     icm = icm,
-    ivm = ivm,
     ica = ica,
-    iva = iva,
     zeta = zeta,
     zeta_group = zeta_group,
     infectivity = infectivity,
@@ -291,8 +288,11 @@ create_variables <- function(parameters) {
   if(parameters$parasite == "falciparum"){
     variables <- c(variables,
                    last_boosted_ib = last_boosted_ib,
+                   last_boosted_iva = last_boosted_iva,
                    last_boosted_id = last_boosted_id,
+                   ivm = ivm,
                    ib = ib,
+                   iva = iva,
                    id = id
     )
   } else if (parameters$parasite == "vivax"){

diff --git a/data-raw/parasite_parameters.csv b/data-raw/parasite_parameters.csv
@@ -86,16 +86,3 @@ vivax,f,0.02439024, White (2018); doi: 10.1186/s12936-018-2318-1
 vivax,gammal,0.002610966, White (2018): doi: 10.1186/s12936-018-2318-1
 vivax,init_hyp,0,
 vivax,kmax,10, White (2018); doi: 10.1038/s41467-018-05860-8
-vivax,init_iva,0,to_be_removed
-vivax,init_ivm,0,to_be_removed
-vivax,uv,11.4321,to_be_removed
-vivax,pvm,0.195768,to_be_removed
-vivax,rvm,76.8365,to_be_removed
-vivax,rva,10950,to_be_removed
-vivax,theta0,0.0749886,to_be_removed
-vivax,theta1,0.0001191,to_be_removed
-vivax,iv0,1.09629,to_be_removed
-vivax,kv,2.00048,to_be_removed
-vivax,fv0,0.141195,to_be_removed
-vivax,av,2493.41,to_be_removed
-vivax,gammav,2.91282,to_be_removed
diff --git a/data/parasite_parameters.rda b/data/parasite_parameters.rda
diff --git a/tests/testthat/test-vivax.R b/tests/testthat/test-vivax.R
@@ -24,15 +24,18 @@ test_that('Test difference between falciparum and vivax parameter lists', {
 
   expect_identical(
     in_falciparum_not_vivax,
-    c("du", # human delays
-      "init_ib", "init_id", ## initial immunities
-      "rb", "rid", # rates of immune loss
-      "ub", "ud", # immunity non-boosting periods
+    c("du",
+      "init_ib", "init_iva", "init_ivm", "init_id", # initial immunity parameters
+      "rb", "rva", "rid", "rvm", # rates of immune loss
+      "ub", "uv", "ud", # immunity non-boosting periods
+      "pvm", # maternal immunity parameters
       "b0", "b1", "ib0", "kb", # blood immunity parameters
-      "fd0", "ad", "gammad", "d1", "id0", "kd", # immunity to detectability parameters
-      "gamma1") # asymptomatic infected infectivity towards mosquitos parameter
-  )
-
+      "fd0", "ad", "gammad", "d1", "id0", "kd", # asymptomatic detection by light microscopy parameters
+      "theta0", "theta1", "iv0", "kv", "fv0", "av", "gammav", # severe immunity parameters
+      "gamma1" # asymptomatic infected infectivity towards mosquitos parameter
+      )
+    )
+
   expect_identical(
     in_vivax_not_falciparum,
     c("dpcr_max", "dpcr_min", "kpcr", "apcr50", # human sub-patent state delay