Merge pull request #248 from mrc-ide/vivax_asymp_infectivity

Vivax asymp infectivity

R/human_infection.R

@@ -347,12 +347,22 @@ schedule_infections <- function(
   }
 
   if(to_infect_asym$size() > 0) {
-    update_to_asymptomatic_infection(
-      variables,
-      parameters,
-      timestep,
-      to_infect_asym
-    )
+    if(parameters$parasite == "falciparum"){ ## P. falciparum has an age-dependent asymptomatic infectivity
+      update_to_asymptomatic_infection(
+        variables,
+        parameters,
+        timestep,
+        to_infect_asym
+      )
+    } else if (parameters$parasite == "vivax"){ ## P. vivax has a constant asymptomatic infectivity
+      update_infection(
+        variables$state,
+        'A',
+        variables$infectivity,
+        parameters$ca,
+        to_infect_asym
+      )
+    }
   }
 }
 

R/processes.R

@@ -81,12 +81,23 @@ create_processes <- function(
       mixing_index
     ),
     create_mortality_process(variables, events, renderer, parameters),
-    create_asymptomatic_progression_process(
-      variables$state,
-      parameters$dd,
-      variables,
-      parameters
-    ),
+    if(parameters$parasite == "falciparum"){ ## P. falciparum has an age-dependent asymptomatic infectivity
+      create_asymptomatic_progression_process(
+        variables$state,
+        parameters$dd,
+        variables,
+        parameters
+      )
+    } else if (parameters$parasite == "vivax"){ ## P. vivax has a constant asymptomatic infectivity
+      create_progression_process(
+        variables$state,
+        'D',
+        'A',
+        parameters$da,
+        variables$infectivity,
+        parameters$ca
+      )  
+    },
     create_progression_process(
       variables$state,
       'A',

R/variables.R

@@ -175,11 +175,14 @@ create_variables <- function(parameters) {
 
   # Set the initial infectivity values for each individual
   infectivity_values[diseased] <- parameters$cd
-  infectivity_values[asymptomatic] <- asymptomatic_infectivity(
-    initial_age[asymptomatic],
-    id$get_values(asymptomatic),
-    parameters
-  )
+  if(parameters$parasite == "falciparum"){ ## P. falciparum has an age-dependent asymptomatic infectivity
+    infectivity_values[asymptomatic] <- asymptomatic_infectivity(
+      initial_age[asymptomatic],
+      id$get_values(asymptomatic),
+      parameters)
+    } else if (parameters$parasite == "vivax"){ ## P. vivax has a constant asymptomatic infectivity
+      infectivity_values[asymptomatic] <- parameters$ca
+    }
   infectivity_values[subpatent] <- parameters$cu
 
   # Initialise the infectivity variable

data-raw/parasite_parameters.csv

@@ -104,7 +104,6 @@ vivax,av,2493.41,TO BE REMOVED: NOT VIVAX: Job 4: Immunity/severity
 vivax,gammav,2.91282,TO BE REMOVED: NOT VIVAX: Job 4: Immunity/severity
 vivax,cd,0.8,
 vivax,ca,0.1,
-vivax,gamma1,1.82425,TO BE REMOVED: NOT VIVAX: Job 1: asymptomatic infectivity
 vivax,cu,0.035,
 vivax,ct,0.4,
 vivax,de,10,

tests/testthat/test-vivax.R

@@ -24,3 +24,93 @@ test_that('Test difference between falciparum and vivax parameter lists', {
   expect_true(all(names(vivax_parameters[!names(vivax_parameters) %in% names(falciparum_parameters)]) %in%
                     c("du_max","du_min","ku","au50","b","phi0lm","phi1lm","ic0lm","kclm","d0","ca","init_idm","f","gammal")))
 })
+
+test_that('Test age structure should not change vivax infectivity', {
+
+  # Set all individuals to asymptomatic
+  # And ID immunity to not 0 (ID impacts age-specific asymptomatic infectivity)
+  parameters <- get_parameters(overrides = list(s_proportion = 0,
+                                                d_proportion = 0,
+                                                a_proportion = 1,
+                                                u_proportion = 0,
+                                                t_proportion = 0,
+                                                init_id  = 0.5))
+
+  vivax_parameters <- get_parameters(parasite = "vivax",
+                                     overrides = list(s_proportion = 0,
+                                                      d_proportion = 0,
+                                                      a_proportion = 1,
+                                                      u_proportion = 0,
+                                                      t_proportion = 0,
+                                                      init_id  = 0.5))
+
+  # Generate different age structure
+  year <- 365
+  ages <- round(c(0.083333, 1, 5, 10, 15, 20, 25, 30, 35, 40, 45,
+                  50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 200) * year)
+
+  deathrates <- rep(.1, length(ages)) / 365
+
+  dem_parameters <- set_demography(
+    parameters,
+    agegroups = ages,
+    timesteps = 0,
+    deathrates = matrix(deathrates, nrow = 1)
+  )
+
+  vivax_dem_parameters <- set_demography(
+    vivax_parameters,
+    agegroups = ages,
+    timesteps = 0,
+    deathrates = matrix(deathrates, nrow = 1)
+  )
+
+  # vivax asymptomatic infectivity should equal ca
+  expect_true(all(
+    c(create_variables(vivax_parameters)$infectivity$get_values(),
+      create_variables(vivax_dem_parameters)$infectivity$get_values())==vivax_parameters$ca))
+
+  # falciparum asymptomatic infectivity should not equal ca
+  expect_false(any(
+    c(create_variables(parameters)$infectivity$get_values(),
+      create_variables(dem_parameters)$infectivity$get_values())==vivax_parameters$ca))
+
+  # falciparum asymptomatic infectivity should change with age structure
+  expect_false(any(
+    c(create_variables(parameters)$infectivity$get_values() == create_variables(dem_parameters)$infectivity$get_values())))
+})
+
+test_that('vivax schedule_infections correctly schedules new infections', {
+  parameters <- get_parameters(list(human_population = 20), parasite = "vivax")
+  variables <- create_variables(parameters)
+
+  infections <- individual::Bitset$new(20)$insert(1:20)
+  clinical_infections <- individual::Bitset$new(20)$insert(5:15)
+  treated <- individual::Bitset$new(20)$insert(7:12)
+
+  infection_mock <- mockery::mock()
+
+  mockery::stub(schedule_infections, 'update_infection', infection_mock)
+
+  schedule_infections(
+    variables,
+    clinical_infections,
+    treated,
+    infections,
+    parameters,
+    42 
+  )
+
+  actual_infected <- mockery::mock_args(infection_mock)[[1]][[5]]$to_vector()
+  actual_asymp_infected <- mockery::mock_args(infection_mock)[[2]][[5]]$to_vector()
+
+  expect_equal(
+    actual_infected,
+    c(5, 6, 13, 14, 15)
+  )
+
+  expect_equal(
+    actual_asymp_infected,
+    c(1, 2, 3, 4, 16, 17, 18, 19, 20)
+  )
+})