haitipkg: R Package for Haiti Article

#### Build Models ##############################################################
#### Goal: test an assortment of possible model builds/configurations

## default model: no vaccinations, epidemic period
novac_epi <- haiti1()

## no vaccinations, endemic period
novac_end <- haiti1(period = "endemic")

## 3 department vaccination campaigns, epidemic period
vac3_epi <- haiti1(vacscen = "id4", period = "epidemic")

## national vaccination campaigns, endemic period
vacnat_end <- haiti1(vacscen = "id3", period = "endemic")


#### Tests #####################################################################

#### Test 1: check that models have the appropriate subset of data according to
####         time period
test_that("check time period", {
  ## no vacs, epi
  expect_equal(head(novac_epi@times, n = 1), 1) ## first time in data is 1 week
  expect_equal(tail(novac_epi@times, n = 1), 232) ## last time in data is 232 weeks
  ## no vacs, end
  expect_equal(head(novac_end@times, n = 1), 233) ## first time in data is 233 weeks
  expect_equal(tail(novac_end@times, n = 1), 430) ## last time in data is 430
  ## 3 dept vacs, epi
  expect_equal(head(vac3_epi@times, n = 1), 1) ## first time in data is 1 week
  expect_equal(tail(vac3_epi@times, n = 1), 232) ## last time in data is 232 weeks
  ## nat vacs, end
  expect_equal(head(vacnat_end@times, n = 1), 233) ## first time in data is 233 weeks
  expect_equal(tail(vacnat_end@times, n = 1), 430) ## last time in data is 430
})

#### Test 2: check that models have the appropriate initial time
test_that("check initial time", {
  ## no vacs, epi
  expect_equal(novac_epi@t0, 0) ## initial time is 0 weeks
  ## no vacs, end
  expect_equal(novac_end@t0, 232) ## initial time is 232 weeks
  ## 3 dept vacs, epi
  expect_equal(vac3_epi@t0, 0) ## initial time is 0 weeks
  ## nat vacs, end
  expect_equal(vacnat_end@t0, 232) ## initial time is 232 weeks
})

#### Test 3: check that models have the appropriate parameters
test_that("check parameters", {
  ## get parameter values
  epi_params <- MODEL1_INPUT_PARAMETERS$adj_pars_epi
  end_params <- MODEL1_INPUT_PARAMETERS$adj_pars_end
  ## append extra values for more depts
  depts <- 3
  param_names <- names(epi_params)
  extra_inits <- rep(0, 5*depts)
  epi3_params <- c(unlist(epi_params), 0, extra_inits)
  names(epi3_params) <- c(param_names, "kappa",
                          paste0("S", 1:depts, "_0"),
                          paste0("E", 1:depts, "_0"),
                          paste0("I", 1:depts, "_0"),
                          paste0("A", 1:depts, "_0"),
                          paste0("R", 1:depts, "_0"))
  depts <- 10
  param_names <- names(end_params)
  extra_inits <- rep(0, 5*depts)
  endnat_params <- c(unlist(end_params), 0, extra_inits)
  names(endnat_params) <- c(param_names, "kappa",
                            paste0("S", 1:depts, "_0"),
                            paste0("E", 1:depts, "_0"),
                            paste0("I", 1:depts, "_0"),
                            paste0("A", 1:depts, "_0"),
                            paste0("R", 1:depts, "_0"))

  ## no vacs, epi
  expect_identical(novac_epi@params, unlist(epi_params))
  ## no vacs, end
  expect_identical(novac_end@params, unlist(end_params))
  ## 3 dept vacs, epi
  expect_identical(vac3_epi@params, unlist(epi3_params))
  ## nat vacs, end
  expect_identical(vacnat_end@params, unlist(endnat_params))
})