Merge pull request #139 from mrc-ide/dev

Dev

.github/workflows/R-CMD-check.yaml

@@ -3,7 +3,7 @@
 on:
   pull_request:
     branches:
-      - dev
+      - dev 
       - master
 
 name: R-CMD-check
@@ -21,19 +21,21 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
       - name: Query dependencies
         run: |
@@ -42,35 +44,38 @@ jobs:
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - name: Restore R package cache
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
       - name: Install dependencies
         run: |
-          install.packages(c("remotes"))
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload code coverage
-        if: runner.os == 'Linux'
-        run: covr::codecov()
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          path: check

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: malariasimulation
 Title: An individual based model for malaria
-Version: 1.0.2
+Version: 1.1.0
 Authors@R: c(
   person(
     given = "Giovanni",
@@ -19,7 +19,6 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Remotes:
-  mrc-ide/individual,
   mrc-ide/malariaEquilibrium
 Imports:
   individual,
@@ -29,7 +28,8 @@ Imports:
   MASS,
   dqrng,
   sitmo,
-  BH
+  BH,
+  R6
 Suggests: 
   testthat,
   mockery,

NAMESPACE

@@ -17,8 +17,9 @@ export(set_bednets)
 export(set_clinical_treatment)
 export(set_drugs)
 export(set_equilibrium)
+export(set_mass_rtss)
 export(set_mda)
-export(set_rtss)
+export(set_rtss_epi)
 export(set_smc)
 export(set_species)
 export(set_spraying)

R/RcppExports.R

@@ -1,16 +1,28 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-create_adult_mosquito_model <- function(growth_model, mu, tau, susceptible) {
-    .Call(`_malariasimulation_create_adult_mosquito_model`, growth_model, mu, tau, susceptible)
+create_adult_mosquito_model <- function(growth_model, mu, tau, susceptible, foim) {
+    .Call(`_malariasimulation_create_adult_mosquito_model`, growth_model, mu, tau, susceptible, foim)
 }
 
 adult_mosquito_model_update <- function(model, mu, foim, susceptible, f) {
     invisible(.Call(`_malariasimulation_adult_mosquito_model_update`, model, mu, foim, susceptible, f))
 }
 
-create_adult_solver <- function(model, init, r_tol, a_tol) {
-    .Call(`_malariasimulation_create_adult_solver`, model, init, r_tol, a_tol)
+create_adult_solver <- function(model, init, r_tol, a_tol, max_steps) {
+    .Call(`_malariasimulation_create_adult_solver`, model, init, r_tol, a_tol, max_steps)
+}
+
+create_aquatic_mosquito_model <- function(beta, de, mue, K0, gamma, dl, mul, dp, mup, total_M, model_seasonality, g0, g, h, R_bar, mum, f) {
+    .Call(`_malariasimulation_create_aquatic_mosquito_model`, beta, de, mue, K0, gamma, dl, mul, dp, mup, total_M, model_seasonality, g0, g, h, R_bar, mum, f)
+}
+
+aquatic_mosquito_model_update <- function(model, total_M, f, mum) {
+    invisible(.Call(`_malariasimulation_aquatic_mosquito_model_update`, model, total_M, f, mum))
+}
+
+create_aquatic_solver <- function(model, init, r_tol, a_tol, max_steps) {
+    .Call(`_malariasimulation_create_aquatic_solver`, model, init, r_tol, a_tol, max_steps)
 }
 
 create_history <- function(size, default_value) {
@@ -37,18 +49,6 @@ rainfall <- function(t, g0, g, h) {
     .Call(`_malariasimulation_rainfall`, t, g0, g, h)
 }
 
-create_mosquito_model <- function(beta, de, mue, K0, gamma, dl, mul, dp, mup, total_M, model_seasonality, g0, g, h, R_bar) {
-    .Call(`_malariasimulation_create_mosquito_model`, beta, de, mue, K0, gamma, dl, mul, dp, mup, total_M, model_seasonality, g0, g, h, R_bar)
-}
-
-mosquito_model_update <- function(model, total_M, f, mum) {
-    invisible(.Call(`_malariasimulation_mosquito_model_update`, model, total_M, f, mum))
-}
-
-create_solver <- function(model, init, r_tol, a_tol) {
-    .Call(`_malariasimulation_create_solver`, model, init, r_tol, a_tol)
-}
-
 solver_get_states <- function(solver) {
     .Call(`_malariasimulation_solver_get_states`, solver)
 }

R/biting_process.R

@@ -135,7 +135,12 @@ simulate_bites <- function(
 
     if (parameters$individual_mosquitoes) {
       # update the ODE with stats for ovoposition calculations
-      mosquito_model_update(models[[s_i]], species_index$size(), f, mu)
+      aquatic_mosquito_model_update(
+        models[[s_i]],
+        species_index$size(),
+        f,
+        mu
+      )
 
       # update the individual mosquitoes
       susceptible_species_index <- susceptible_index$copy()$and(species_index)

R/ode.R → R/compartmental.R

@@ -7,7 +7,7 @@ parameterise_mosquito_models <- function(parameters) {
     function(i) {
       p <- parameters$species_proportions[[i]]
       m <- p * parameters$total_M
-      growth_model <- create_mosquito_model(
+      growth_model <- create_aquatic_mosquito_model(
         parameters$beta,
         parameters$del,
         parameters$me,
@@ -22,7 +22,9 @@ parameterise_mosquito_models <- function(parameters) {
         parameters$g0,
         parameters$g,
         parameters$h,
-        calculate_R_bar(parameters)
+        calculate_R_bar(parameters),
+        parameters$mum[[i]],
+        parameters$blood_meal_rates[[i]]
       )
 
       if (!parameters$individual_mosquitoes) {
@@ -37,7 +39,8 @@ parameterise_mosquito_models <- function(parameters) {
             growth_model,
             parameters$mum[[i]],
             parameters$dem,
-            susceptible * parameters$init_foim
+            susceptible * parameters$init_foim,
+            parameters$init_foim
           )
         )
       }
@@ -58,15 +61,17 @@ parameterise_solvers <- function(models, parameters) {
             models[[i]],
             init,
             parameters$r_tol,
-            parameters$a_tol
+            parameters$a_tol,
+            parameters$ode_max_steps
           )
         )
       }
-      create_solver(
+      create_aquatic_solver(
         models[[i]],
         init[ODE_INDICES],
         parameters$r_tol,
-        parameters$a_tol
+        parameters$a_tol,
+        parameters$ode_max_steps
       )
     }
   )

R/correlation.R

@@ -130,14 +130,15 @@ CorrelationParameters <- R6::R6Class(
 #' parameters <- get_parameters()
 #' 
 #' # Set some rtss strategy
-#' parameters <- set_rtss(
+#' parameters <- set_mass_rtss(
 #'   parameters,
 #'   timesteps = 100,
 #'   coverages = .9,
+#'   min_wait = 0,
 #'   min_ages = 100,
 #'   max_ages = 1000,
-#'   boosters = NULL,
-#'   booster_coverage = NULL
+#'   boosters = numeric(0),
+#'   booster_coverage = numeric(0)
 #' )
 #' 
 #' # Set some smc strategy

R/events.R

@@ -12,18 +12,46 @@ create_events <- function(parameters) {
     # whether the infection is detected
     detection = individual::TargetedEvent$new(parameters$human_population), 
 
-    # Vaccination events
-    rtss_vaccination = individual::Event$new(),
-    rtss_booster = individual::TargetedEvent$new(parameters$human_population),
-    tbv_vaccination = individual::Event$new(),
-
     # MDA events
     mda_administer = individual::Event$new(),
     smc_administer = individual::Event$new(),
 
+    # TBV event
+    tbv_vaccination = individual::Event$new(),
+
     # Bednet events
     throw_away_net = individual::TargetedEvent$new(parameters$human_population)
   )
+
+  # Mass vaccination events
+  if (!is.null(parameters$rtss_mass_timesteps)) {
+    rtss_mass_doses <- lapply(
+      seq_along(parameters$rtss_doses),
+      function(.) individual::TargetedEvent$new(parameters$human_population)
+    )
+    rtss_mass_boosters <- lapply(
+      seq_along(parameters$rtss_mass_boosters),
+      function(.) individual::TargetedEvent$new(parameters$human_population)
+    )
+    events$rtss_mass_vaccination = individual::Event$new()
+    events$rtss_mass_doses <- rtss_mass_doses
+    events$rtss_mass_boosters <- rtss_mass_boosters
+  }
+
+  # EPI vaccination events
+  if (!is.null(parameters$rtss_epi_start)) {
+    rtss_epi_doses <- lapply(
+      seq_along(parameters$rtss_doses),
+      function(.) individual::TargetedEvent$new(parameters$human_population)
+    )
+    rtss_epi_boosters <- lapply(
+      seq_along(parameters$rtss_epi_boosters),
+      function(.) individual::TargetedEvent$new(parameters$human_population)
+    )
+    events$rtss_epi_doses <- rtss_epi_doses
+    events$rtss_epi_boosters <- rtss_epi_boosters
+  }
+
   if (parameters$individual_mosquitoes) {
     events <- c(
       events,
@@ -45,9 +73,9 @@ initialise_events <- function(events, variables, parameters) {
     )
   }
 
-  # Initialise interventions
-  if (parameters$rtss) {
-    events$rtss_vaccination$schedule(parameters$rtss_timesteps[[1]] - 1)
+  # Initialise scheduled interventions
+  if (!is.null(parameters$rtss_mass_timesteps)) {
+    events$rtss_mass_vaccination$schedule(parameters$rtss_mass_timesteps[[1]] - 1)
   }
   if (parameters$mda) {
     events$mda_administer$schedule(parameters$mda_timesteps[[1]] - 1)
@@ -175,22 +203,39 @@ attach_event_listeners <- function(
     )
   }
 
-  if (parameters$rtss == 1) {
-    events$rtss_vaccination$add_listener(
-      create_rtss_vaccination_listener(
+  # RTS,S listeners
+  if (!is.null(events$rtss_mass_doses)) {
+    # set up distribution
+    events$rtss_mass_vaccination$add_listener(
+      create_rtss_mass_listener(
         variables,
         events,
         parameters,
-        correlations,
-        renderer
+        correlations
       )
     )
-    events$rtss_booster$add_listener(
-      create_rtss_booster_listener(
-        variables,
-        events,
-        parameters
-      )
+    attach_rtss_dose_listeners(
+      variables,
+      parameters,
+      events$rtss_mass_doses,
+      events$rtss_mass_boosters,
+      parameters$rtss_mass_boosters,
+      parameters$rtss_mass_booster_coverage,
+      'mass',
+      renderer
+    )
+  }
+
+  if (!is.null(events$rtss_epi_doses)) {
+    attach_rtss_dose_listeners(
+      variables,
+      parameters,
+      events$rtss_epi_doses,
+      events$rtss_epi_boosters,
+      parameters$rtss_epi_boosters,
+      parameters$rtss_epi_booster_coverage,
+      'epi',
+      renderer
     )
   }