cdc-model-reboot.Rmd

---
output:
  html_document:
    self_contained: yes
    smart: yes
    css: styles-reboot.css
runtime: shiny
---
```{r, echo=FALSE}
source("cdc_model_functions.R")
source("cdc_plotting_functions.R")
source("shiny-helpers.R")
source("pauseable.R")

with(defaults, {

transmission_rate <- makeVectorControl(
  control_prefixes, "transmission_rate",
  control_descriptions, control_transmission_rates,
  min = 0, step=0.01,
  tests = list(validators$positive("tranmission rates"))
)
stay_durations <- makeVectorControl(
  control_prefixes, "stay_duration",
  control_descriptions, control_durations,
  min = 0, step=1,
  tests = list(validators$positive("durations"), validators$integers("durations"))
)
hospitalization_rate <- makeVectorControl(
  control_prefixes, "hospitalization_rate",
  control_descriptions, control_hospitalization_rates,
  type = probabilityInput,
  tests = list(validators$positive("hospitalization rates"))
)

infection_pdf <- inputIntervalPDF('infection', 6)

# infection_pdf <- list(control=NULL, reactor = function() {
# 	defaults$I_day_PDF
# })
# incubation_pdf <- list(control=NULL, reactor = function() {
# 	defaults$E_day_PDF
# })
# output$incubation_download <- downloadHandler(
# 	filename='incubation_pdf.csv', contentType = 'text/csv', content = function(file) {
# 	  pdf <- defaults$E_day_PDF
# 	  res <- data.frame(pdf=pdf)
# 	  write.table(res, file, row.names=F, col.names=F)
# })
# 
# incubation_pdf_file_warning <- reactive({
# 	if(!is.null(input$incubation_upload)) {
# 		inputFile <- input$incubation_upload$datapath
# 		src <- drop(as.matrix(read.table(inputFile, header = F)))
# 		if (is.numeric(src)) {
# 			if (sum(src) == 1) {
# 				## pause pdf updating?
# 				## updateRadioButtons(session, incubation_pdf_type, selected="manual")
# 				## set incubation to manual
# 				## updateNumericInput(session, incubation_pdf_max, value=length(src))
# 				## set incubation max to length
# 				## for i in 1 to length, set inc_day_i to data[i]
# 				## unpause pdf updating
# 				''
# 			} else {
# 				'pdf does not sum to 1.'
# 			}
# 		} else {
# 			'did not provide numeric data.'
# 		}
# 	} else {
# 		''
# 	}
# })

# simulation <- reactive({
# 	sim_duration <- input$simulation_duration ## TODO validate
# 	N0 <- defaults$N0
#   simulate(list(
#     infective_treatments = defaults$infective_treatments,
#     treatment_durations = stay_durations$reactor(),
#     simulation_duration = sim_duration,
#     treatment_distribution = defaults$treatment_distribution, #yield_intervention(intervention_scenario()),
#     introductions = defaults$introductions, # yield_introduction(introduction_scenario()), 
#     treatment_transmissions = transmission_rate$reactor(),
#     hosp_proportions = hospitalization_rate$reactor(),
#     E_day_PDF = incubation_PDF$reactor(),
#     I_day_PDF = infection_PDF$reactor(),
#     N0 = N0
#   ))
# })
# 	

shinyUI(navbarPage("EbolaResponse v2",
  nestedTabPanel("Results",
    tabPanel("Symptomatic Individuals",
      renderPlot(dummyPlot(100)),
      tags$caption("Plot Caption")
    ),
    tabPanel("Occupied Beds",
      renderPlot(dummyPlot(100))
    ),
    tabPanel("Cumulative Incidence",
      renderPlot(dummyPlot(100))
    ),
    tabPanel("Cumulative Mortality",
      renderPlot(dummyPlot(100))
    )
#     ,
#     inputTabPanel("Display Options",
#       radioButtons("option_1", "Option 1", choices = c('a','b'), inline = T),
#       radioButtons("option_2", "Option 2", choices = c('a','b'), inline = T)
#     )
  ),
  nestedTabPanel("Change Model Settings",
    inputTabPanel("General",
    	customizeInput(
    		numericInput, "population","Population", value=10, min=0.1, step=0.1,
    		mouseover="The initial susceptible population.", units="millions"
    	),
      customizeInput(
      	dateInput, "start_date", "Start date", min="2014-01-01", max="2014-12-31", value="2014-02-03",
      	mouseover="The reference start date for initial incubation.", units="YYYY-MM-DD"
      ),
      customizeInput(
      	numericInput, "simulation_duration", "Simulation Duration", value=300, min=1, step=1,
      	mouseover="The number of days considered in the simulation.", units="days"
      )
    ),
    inputTabPanel("Transmission",
      h3("New Ebola Cases produced per capita-day from Infectious Individuals, by Treatment Setting:", title = "TODO"),
      transmission_rate$control,
      customizeInput(
      	numericInput, "beta_multiplier", "Transmission Coefficient Multiplier", value=1, min=0.01, step=0.01,
        mouseover = "This multiplier applies to all beta values.  The default value, 1, means that the transmission parameters are used directly.  A value of 2 means that all transmission rates are doubled, a value of 0.5 means that all rates are halved."
      )
    ),
    inputTabPanel("Incubation",
      #inputPDF("incubation"),
      inputCSV('incubation_upload', "Upload a file to fill in manual distribution."),
      div(renderText(incubation_pdf_file_warning()), class="warning"),
      view = renderPlot(plotIntervalDistribution(incubation_pdf$reactor())),
      download = "incubation_download"
    ),
    inputTabPanelSolid("Disease",
      #inputPDF("infection"),
      infection_pdf$control,
      customizeInput(
        probabilityInput, "case_fatality_rate", "Case Fatality Rate", value=0.7,
        mouseover = "The probability of dying from Ebola.",
        units = '%'
      ),
      customizeInput(
        probabilityInput, "asymptomatic_rate", "Asymptomatic Infection Rate", value=0.0,
        mouseover = "The probability of asymptomatic, immunizing exposure.",
        units = '%'
      )
      #, view = renderPlot(plotIntervalDistribution(infection_pdf$reactor()))
    ),
    inputTabPanel("Treatment",
      h3("Effective Bed-Days, by Treatment Setting:", title = "TODO"),
      stay_durations$control,
      renderPrint(stay_durations$reactor()),
      h3("Proportion Requiring Hospitalization, by Treatment Setting:", title = "TODO"),
      hospitalization_rate$control
    )
  ),
  nestedTabPanel("Model Description & Assumptions",
  	tabPanel("Overall", includeMarkdown("overall.md")),
  	tabPanel("Transmission", includeMarkdown("transmission.md")),
  	tabPanel("Incubation", includeMarkdown("incubation.md")),
  	tabPanel("Disease", includeMarkdown("disease.md")),
  	tabPanel("Treatment Logistics", includeMarkdown("treatment.md"))
  )
))
})
```