Merge pull request #249 from mrc-ide/vivax_pre_eryth_imm

Vivax pre eryth imm
mrc-ide · Jul 21, 2023 · 37aa34f · 37aa34f
2 parents 7e5af02 + 8d99d2d
commit 37aa34f
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Showing 5 changed files with 9 additions and 97 deletions.
diff --git a/R/human_infection.R b/R/human_infection.R
@@ -109,8 +109,12 @@ 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$parasite == "falciparum"){ ## P. falciparum models blood immunity
+    b <- blood_immunity(variables$ib$get_values(source_humans), parameters)
+  } else if (parameters$parasite == "vivax"){ ## P. vivax does not model blood immunity
+    b <- parameters$b
+  }
+
   source_vector <- source_humans$to_vector()
 
   # calculate prophylaxis

diff --git a/data-raw/parasite_parameters.csv b/data-raw/parasite_parameters.csv
@@ -76,10 +76,6 @@ vivax,rb,3650,TO BE REMOVED: NOT VIVAX: Job 4: Immunity
 vivax,rid,3650,
 vivax,rc,10950,
 vivax,rva,10950,TO BE REMOVED: NOT VIVAX: Job 4: Immunity
-vivax,b0,0.59,TO BE REMOVED: NOT VIVAX: Job 2: FOI
-vivax,b1,0.5,TO BE REMOVED: NOT VIVAX: Job 2: FOI
-vivax,ib0,43.9,TO BE REMOVED: NOT VIVAX: Job 2: FOI
-vivax,kb,2.16,TO BE REMOVED: NOT VIVAX: Job 2: FOI
 vivax,b,0.5,
 vivax,fd0,0.007055,TO BE REMOVED: NOT VIVAX: Job 4: Immunity/detectability
 vivax,ad,7993.5,TO BE REMOVED: NOT VIVAX: Job 4: Immunity/detectability

diff --git a/data/parasite_parameters.rda b/data/parasite_parameters.rda
diff --git a/man/get_parameters.Rd b/man/get_parameters.Rd
diff --git a/tests/testthat/test-vivax.R b/tests/testthat/test-vivax.R
@@ -24,93 +24,3 @@ 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)
-  )
-})