## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  message = FALSE,
  warning = FALSE,
  fig.width = 7,
  fig.height = 4.5,
  out.width = "100%"
)

## ----setup--------------------------------------------------------------------
library(ambre)
set.seed(2024)

## ----libs---------------------------------------------------------------------
library(dplyr)
library(purrr)

## ----default-exposure, results = "hide"---------------------------------------
scenario <- create_scenario(
  system.file("input_1culture_2pop.xlsx", package = "ambre")
)
scenario_conc <- inflow_concentration(
  scenario = scenario,
  pathogenName = "Campylobacter jejuni"
)

## ----default-exposure-show----------------------------------------------------
# Row 1 of this two-row scenario: irrigation-staff droplet ingestion
scenario_conc$config[[1]]$exposure

## ----default-concentration-show-----------------------------------------------
# Row 1 of this two-row scenario: Campylobacter jejuni concentration
dplyr::filter(scenario_conc$config[[1]]$inflow, PathogenName == "Campylobacter jejuni")

## ----inspect-pathid-----------------------------------------------------------
pid <- query_exp_path(
  pathName = "Ingestion of water droplets during maintenance of the irrigation system"
)
pid

## ----inspect-values-----------------------------------------------------------
scenario$PathID          # the two paths in this input file

query_volume(scenario$PathID)     # litres per event: min / max
query_frequency(scenario$PathID)  # events per year: min / max

## ----override-volume----------------------------------------------------------
scenario_ppe <- update_volume_with_desired_value(
  scenario = scenario,
  volume = data.frame(
    min = c(0.0005, 0.0005),   # 0.5 mL per event, one entry per row
    max = c(0.0005, 0.0005),
    type = c("triangle", "triangle")
  )
)

scenario_ppe$config[[1]]$exposure

## ----override-frequency-------------------------------------------------------
scenario_night <- update_frequency_with_desired_value(
  scenario = scenario,
  frequency = c(30L, 30L)   # cap both paths at 30 events / year
)

scenario_night$config[[1]]$exposure

## ----override-concentration---------------------------------------------------
concentration_custom <- data.frame(PathogenName = c("Campylobacter jejuni"),
                                   min = c(1),
                                   max = c(2),
                                   type = c("uniform"))

scenario_pathogen <- update_pathogen(scenario = scenario, pathoName = concentration_custom$PathogenName)
scenario_low_pathogen <- update_concentration(scenario = scenario_pathogen ,
                     concentration = concentration_custom)

dplyr::filter(scenario_low_pathogen$config[[1]]$inflow, PathogenName == "Campylobacter jejuni")


## ----qmra-custom, results = "hide"--------------------------------------------
sc <- create_scenario(system.file("input_1culture_2pop.xlsx", package = "ambre"))

regulation_reduction <- config_ambre$regulation$regulation_value |> 
  dplyr::filter(Country == "France") |>
  dplyr::select(-c(Concentration, Country, RegulationID))
regulation_concentration <- config_ambre$regulation$regulation_value |> 
  dplyr::filter(Country == "France") |>
  dplyr::select(-c(Country, RegulationID, Reduction))

concentration_custom <- data.frame(PathogenName = c("Rotavirus"),
                                   min = c(1000),
                                   max = c(2000),
                                   type = c("uniform"))

set.seed(2024)
bare <- run_qmra_custom(scenario = sc,
                  concentration = concentration_custom,
                  volume = data.frame(min=c(0.005,0.005), max = c(0.01, 0.01), type = c("triangle", "triangle")),
                  frequency = c(48L, 60L),
                  regulationLog = regulation_reduction,
                  regulationConcentration = regulation_concentration,
                  initialSituation = TRUE) # min 5 mL, max 10 mL

set.seed(2024)
ppe  <- run_qmra_custom(scenario = sc,
                  concentratio = concentration_custom,
                  volume = data.frame(min=c(0.0005,0.0005), max = c(0.001, 0.001), type = c("triangle", "triangle")),
                  frequency = c(48L, 60L),
                  regulationLog = regulation_reduction,
                  regulationConcentration = regulation_concentration,
                  initialSituation = TRUE) # min 0.5 mL min 0.1 mL


## ----qmra-custom-comparison, results = "hide"---------------------------------
library(ggplot2)
cowplot::plot_grid(
      bare$dalys$Rotavirus +
        labs(subtitle = "min 5 mL, max 10 mL") +
        theme(plot.subtitle = element_text(hjust = 0.5)),
      ppe$dalys$Rotavirus +
        labs(subtitle = "min 0.5 mL min 0.1 mL") +
        theme(plot.subtitle = element_text(hjust = 0.5)),
      ncol = 2,
      align = "h"
    )