Remove severe immunity for P.v

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()

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,

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"){

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(

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"){

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

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