Fix bug with pev min_wait:

 * Update pev-epi min_wait test to directly check sample population
 * Update pe-epi  min_wait test to check that pev_timestep is being updated
   on the first dose
 * Copy pev-epi min_wait test to mass pev
 * Update pev and epi processes to calculate targets based on time of first dose
 * Update infection immunity function to calculate pev immunity only
   after 3rd dose

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: malariasimulation
 Title: An individual based model for malaria
-Version: 1.6.0
+Version: 1.6.1
 Authors@R: c(
   person(
     given = "Giovanni",

NEWS.md

@@ -1,3 +1,9 @@
+
+# malariasimulation 1.6.1 (wip)
+
+ * Fix bug with min_wait. Min wait was working off of the final primary dose. It
+   now works of of the first dose.
+
 # malariasimulation 1.6.0
 
   * Fix MDA bug where undetectable asymptomatics are treated

R/human_infection.R

@@ -130,8 +130,10 @@ calculate_infections <- function(
   # calculate vaccine efficacy
   vaccine_efficacy <- rep(0, length(source_vector))
   vaccine_times <- variables$pev_timestep$get_values(source_vector)
-  vaccinated <- vaccine_times > -1
   pev_profile <- variables$pev_profile$get_values(source_vector)
+  # get vector of individuals who have been vaccinated
+  # and received their 3rd dose
+  vaccinated <- pev_profile > -1
   pev_profile <- pev_profile[vaccinated]
   if (length(vaccinated) > 0) {
     antibodies <- calculate_pev_antibodies(

R/pev.R

@@ -48,6 +48,11 @@ create_epi_pev_process <- function(
       )
     ]
 
+    # Update the latest vaccination time
+    variables$pev_timestep$queue_update(timestep, target)
+    # Reset the pev_profile so that we are not yet efficacious
+    variables$pev_profile$queue_update(-1, target)
+
     schedule_vaccination(
       target,
       events,
@@ -99,6 +104,13 @@ create_mass_pev_listener <- function(
         correlations
       )
     ]
+
+    # Update the latest vaccination time
+    variables$pev_timestep$queue_update(timestep, target)
+    # Reset the pev_profile so that we are not yet efficacious
+    variables$pev_profile$queue_update(-1, target)
+
+    # Schedule future doses
     schedule_vaccination(
       target,
       events,

R/variables.R

@@ -20,8 +20,10 @@
 #' * zeta_group - Discretised heterogeneity of human individuals
 #' * pev_timestep - The timestep of the last pev vaccination (-1 if there
 #' haven't been any)
-#' * pev_profile - The index of the profile of the last administered pev vaccine 
-#' (-1 if there haven't been any)
+#' * pev_profile - The index of the profile of the last administered pev
+#' vaccine.
+#' This is only set on the final primary dose and subsequent booster doses
+#' (-1 otherwise)
 #' * tbv_vaccinated - The timstep of the last tbv vaccination (-1 if there
 #' haven't been any
 #' * net_time - The timestep when a net was last put up (-1 if never)

tests/testthat/test-pev-epi.R

@@ -89,46 +89,52 @@ test_that('pev epi targets correct age and respects min_wait', {
   variables$pev_timestep <- mock_integer(
     c(50, -1, -1, 4*365, -1)
   )
+  variables$pev_profile <- mock_integer(
+    c(1, -1, -1, 1, -1)
+  )
 
-  events$pev_epi_doses <- lapply(events$pev_epi_doses, mock_event)
-
+  correlations <- get_correlation_parameters(parameters)
   process <- create_epi_pev_process(
     variables,
     events,
     parameters,
-    get_correlation_parameters(parameters),
+    correlations,
     parameters$pev_epi_coverages,
     parameters$pev_epi_timesteps
   )
 
+  sample_mock <- mockery::mock(c(TRUE, TRUE, FALSE))
   mockery::stub(
     process,
     'sample_intervention',
-    mockery::mock(c(TRUE, TRUE, FALSE))
+    sample_mock
   )
 
   process(timestep)
 
   mockery::expect_args(
-    events$pev_epi_doses[[1]]$schedule,
+    sample_mock,
     1,
-    c(1, 2),
-    parameters$pev_doses[[1]]
+    c(1, 2, 5),
+    'pev',
+    .8,
+    correlations
   )
 
   mockery::expect_args(
-    events$pev_epi_doses[[2]]$schedule,
+    variables$pev_timestep$queue_update_mock(),
     1,
-    c(1, 2),
-    parameters$pev_doses[[2]]
+    timestep,
+    c(1, 2)
   )
 
   mockery::expect_args(
-    events$pev_epi_doses[[3]]$schedule,
+    variables$pev_profile$queue_update_mock(),
     1,
-    c(1, 2),
-    parameters$pev_doses[[3]]
+    -1,
+    c(1, 2)
   )
+
 })
 
 test_that('pev EPI respects min_wait when scheduling seasonal boosters', {

tests/testthat/test-pev.R

@@ -345,6 +345,75 @@ test_that('Mass booster coverages sample subpopulations correctly', {
   )
 })
 
+test_that('mass pev targets correct age and respects min_wait', {
+  timestep <- 5*365 
+  parameters <- get_parameters(list(human_population = 5))
+  parameters <- set_mass_pev(
+    parameters,
+    profile = rtss_profile,
+    timesteps = c(4, 5) * 365,
+    coverages = c(0.8, 0.8),
+    min_ages = 0,
+    max_ages = 19 * 365,
+    min_wait = 2*365,
+    booster_timestep = c(1, 6) * 30,
+    booster_coverage = c(.9, .8),
+    booster_profile = list(rtss_booster_profile, rtss_booster_profile)
+  )
+  events <- create_events(parameters)
+  variables <- create_variables(parameters)
+  variables$birth <- individual::IntegerVariable$new(
+    -c(18, 18, 30, 18, 18) * 365 + timestep
+  )
+  variables$pev_timestep <- mock_integer(
+    c(50, -1, -1, 4*365, -1)
+  )
+
+  variables$pev_profile <- mock_integer(
+    c(1, -1, -1, 1, -1)
+  )
+
+  correlations <- get_correlation_parameters(parameters)
+  listener <- create_mass_pev_listener(
+    variables,
+    events,
+    parameters,
+    get_correlation_parameters(parameters)
+  )
+
+  sample_mock <- mockery::mock(c(TRUE, TRUE, FALSE))
+  mockery::stub(
+    listener,
+    'sample_intervention',
+    sample_mock
+  )
+
+  listener(timestep)
+
+  mockery::expect_args(
+    sample_mock,
+    1,
+    c(1, 2, 5),
+    'pev',
+    .8,
+    correlations
+  )
+
+  mockery::expect_args(
+    variables$pev_timestep$queue_update_mock(),
+    1,
+    timestep,
+    c(1, 2)
+  )
+
+  mockery::expect_args(
+    variables$pev_profile$queue_update_mock(),
+    1,
+    -1,
+    c(1, 2)
+  )
+})
+
 test_that('Mass efficacy listener works correctly', {
   timestep <- 50
   parameters <- get_parameters()