# WARNING - Generated by {fusen} from dev/flat_plots.Rmd: do not edit by hand # nolint: line_length_linter.

test_that("plot_dalys works", {
  library(dplyr)
  library(purrr)
  scenario_test <- create_scenario(system.file("input_1culture_2pop.xlsx", package = "ambre"))
  
  scenario_conc <- inflow_concentration(scenario = scenario_test,
   pathogenName = c("Campylobacter jejuni"))
  
  scenario_volume <-
    scenario_conc |>                     
    mutate(
      volume = map(
        .x = config,                                         
        .f = ~ simulate_exposure(config = .x)              
      )
    )

  scenario_dose_ini <- initial_dose_calculation(scenario_volume)
  
  scenario_scheme <- update_treatment_scheme(scenario_dose_ini)
  
  scenario_with_logreduc_and_co <- scenario_scheme |> 
    mutate( log_reduction = map(config, simulate_treatment))
  
  scenario_final_dose_and_co_test <- final_dose_calculation(scenario_with_logreduc_and_co)
  
  scenario_inf_proba_and_co <- infection_probability_calculation(scenario_final_dose_and_co_test)
  
  scenario_illness_proba_and_co <- illness_probability_calculation(scenario_inf_proba_and_co)
  
  scenario_dalys_and_co <- dalys_calculation(scenario_illness_proba_and_co)
  
  scenario_risk_total_and_co <-get_risk_total(scenario_dalys_and_co)
  
  result <- plot_dalys(scenario_risk_total_and_co)
  expect_type(result, "list")
})

test_that("plot_dalys multiple pathogen works", {
  library(dplyr)
  library(purrr)
  scenario_test <- create_scenario(system.file("input_1culture_2pop.xlsx", package = "ambre"))
  
  scenario_conc <- inflow_concentration(scenario = scenario_test,
   pathogenName = c("Campylobacter jejuni", "Escherichia coli", "Norovirus", "Rotavirus"))
  
  scenario_volume <-
    scenario_conc |>                     
    mutate(
      volume = map(
        .x = config,                                         
        .f = ~ simulate_exposure(config = .x)              
      )
    )

  scenario_dose_ini <- initial_dose_calculation(scenario_volume)
  
  scenario_scheme <- update_treatment_scheme(scenario_dose_ini)
  
  scenario_with_logreduc_and_co <- scenario_scheme |> 
    mutate( log_reduction = map(config, simulate_treatment))
  
  scenario_final_dose_and_co_test <- final_dose_calculation(scenario_with_logreduc_and_co)
  
  scenario_inf_proba_and_co <- infection_probability_calculation(scenario_final_dose_and_co_test)
  
  scenario_illness_proba_and_co <- illness_probability_calculation(scenario_inf_proba_and_co)
  
  scenario_dalys_and_co <- dalys_calculation(scenario_illness_proba_and_co)
  
  scenario_risk_total_and_co <-get_risk_total(scenario_dalys_and_co)
  
  result <- plot_dalys(scenario_risk_total_and_co)
  expect_equal(object=names(result),
               expected = c("Campylobacter jejuni", "Escherichia coli", "Norovirus", "Rotavirus"))
})