inst/models/shiny_sirconn.R

In epiworldRShiny: A 'shiny' Wrapper of the R Package 'epiworldR'

# alt-name: SIR
shiny_sirconn <- function(input) {

  model_sirconn <- epiworldR::ModelSIRCONN(
    name              = input$sirconn_disease_name,
    prevalence        = input$sirconn_prevalence,
    transmission_rate = input$sirconn_transmission_rate,
    recovery_rate     = input$sirconn_recovery_rate,
    contact_rate      = input$sirconn_contact_rate,
    n                 = input$sirconn_population_size
    )

  # NPIs -----------------------------------------------------------------------
  interventions_add_all(model_sirconn, "sirconn", input)
  
  # Running and printing
  epiworldR::verbose_off(model_sirconn)
  epiworldR::run(model_sirconn, ndays = input$sirconn_n_days, seed = input$sirconn_seed)

  # Plot, summary, and reproductive number
  plot_sirconn <- function() plot_epi(model_sirconn)
  summary_sirconn <- function() summary(model_sirconn)
  reproductive_sirconn <- function() plot_reproductive_epi(model_sirconn)
  # Table
  table_sirconn <- function() {
    df <- as.data.frame(epiworldR::get_hist_total(model_sirconn))
    # Subset to only include "infection" state
    infection_data <- df[df$state == "Infected", ]
    # Row with the maximum count
    max_infection_row <- infection_data[which.max(infection_data$count), ]
    # Row number of the maximum count in the original data frame
    max_row_number <- which(df$date == max_infection_row$date &
                              df$state == "Infected")
    df[max_row_number,] <- sprintf("<strong>%s</strong>",
                                       df[max_row_number,])
    df
  }
  # Output list
  return(
    list(
      epicurves_plot     = plot_sirconn,
      reproductive_plot  = reproductive_sirconn,
      model_summary      = summary_sirconn,
      model_table        = table_sirconn
    )
  )
}

sirconn_panel <- function(model_alt) {
  shiny::conditionalPanel(
    simulate_button("sirconn"),
    condition = sprintf("input.model == '%s'", model_alt),
    text_input_disease_name("sirconn"),
    slider_prevalence("sirconn"),
    slider_input_rate("sirconn", "Transmission probability", 0.1, input_label = "transmission_rate"),
    slider_input_rate("sirconn", "Recovery probability (daily)", 0.14, input_label = "recovery_rate"),
    slider_input_rate("sirconn", "Contact Rate", 4, maxval = 20),
    shiny::sliderInput(
      inputId = "sirconn_population_size",
      label   = "Population Size",
      min     = 0,
      max     = 100000,
      value   = 50000,
      step    = 1000,
      ticks   = FALSE
    ),
    numeric_input_ndays("sirconn"),
    seed_input("sirconn"),
    npis_input("sirconn")
  )
}