inst/app/ui.R

In multigroup.vaccine: Analyze Outbreak Models of Multi-Group Populations with Vaccination

## dependencies
require(deSolve)
require(shiny)
## dependent functions
library(shiny)
library(bslib)
library(shinya11y)


#' @import shiny

library(bslib)

myToolTip <- function(tipText = NULL, id = NULL) {
  if (!is.null(tipText)) {
    return(tooltip(img(
      src = "figs/tooltip.png",
      height = 20,
      width = 20,
      alt = tipText
    ),
    tags$label(tipText)
    ))


  }
}

double_input_row <- function(input_ida,
                             input_idb,
                             label,
                             valuea,
                             valueb,
                             tip = NULL) {
  tags$tr(
    tags$td(myToolTip(tip), label),
    tags$td(
      numericInput(
        inputId = input_ida,
        value = valuea,
        label = NULL,
        width = "100px"
      )
    ),
    tags$td(
      numericInput(
        inputId = input_idb,
        value = valueb,
        label = NULL,
        width = "100px"
      )
    )
  )
}

single_input_row <- function(input_id, label, value, tip = NULL) {
  tags$tr(tags$td(myToolTip(tip), label), tags$td(
    numericInput(
      inputId = input_id,
      value = value,
      label = NULL,
      width = "100px"
    )
  ))
}

ui <- page_fluid(
  use_tota11y(),
  gap = 0,
  tags$head(
    tags$style(
      "table {font-size: 8pt;
                       border-collapse: collapse;
                       compact; nowrap;}
                       th, tr, td {padding: 0px;
                               border-spacing: 0px;
                               margin: 0px;
                       }
                       shiny-input-number{
                          padding-block: 0px;
                          padding-inline: 0px;
                       }"
    )
  ),
  theme = bslib::bs_theme(version = 5, bootswatch = "pulse"),
  titlePanel("Vaccine Strategies in Disparate Populations"),
  navset_tab(
    nav_panel(
      "Model",
      layout_column_wrap(
        width = "250px",
        card(
          card_title("Population Setup"),
          tags$table(
            tags$tr(tags$td(""), tags$th("Group A"), tags$th("Group B")),
            double_input_row("popsize_a", "popsize_b", "Population Size", 80000, 20000, tip = "Size of each population"),
            double_input_row(
              "vacPortion_a",
              "vacPortion_b",
              "Fraction vaccinated",
              0.3,
              0.2,
              tip = "Fraction of each population that is vaccinated, all at once, at the
              vaccination time."
            ),
            double_input_row(
              "contactWithinGroup_a",
              "contactWithinGroup_b",
              "Fraction of contacts exclusively within-group",
              0.4,
              0.4,
              tip = "Propotion of contacts made by individuals in each population that are
              exclusively within their own group. The remaining contacts will be
              distributed proportionally between both groups."
            ),
            double_input_row(
              "hospProb_a",
              "hospProb_b",
              "Hospitilization probability",
              0.017,
              0.032,
              tip = "The fraction of infected individuals who are hospitilized due to the infection."
            ),
            double_input_row(
              "hospDeathProb_a",
              "hospDeathProb_b",
              "Death probability among hospitalized",
              0.25,
              0.25,
              tip = "The fraction of infected, hospitalilized individuals who die from the infection."
            ),
            double_input_row(
              "nonHospDeathProb_a",
              "nonHospDeathProb_b",
              "Death probability among non-hospitalized",
              0.00055,
              0.00055,
              tip = "The fraction of infected, non-hospitalilized individuals who die from the infection."
            )
          )
        ),
        card(
          card_title("Parameters"),
          tags$table(
            single_input_row("vacTime", "Vaccination start time (days)", 0,
                             tip = "Time when vaccine will be started"),
            single_input_row("recoveryRate", "Recovery rate (per day)", 0.1,
                             tip = "Rate per day of an infected individual recovering"),
            single_input_row("R0", "R0", 2, tip = "Basic reproduction number"),
            single_input_row("contactRatio", "Contact ratio", 1.1,
                             tip = "The ratio of the contact rate of the second group to the first group"),
            single_input_row("suscRatio", "Susceptibility ratio", 1.2,
                             tip = "The ratio of the susceptibility of the second group to the first group"
            ),
            single_input_row("transmRatio", "Transmissibility ratio", 1.05,
                             tip = "The ratio of the transmissibility of the second group to the first group"
            )
          )
        ),
        card(
          card_title("Output"),
          tableOutput("table"),
        )
      ),
    ),
    nav_panel(
      "About",
      br(),
      p(
        "This application allows exploration of the health effects of disparities in transmission
        epidemiology and vaccine uptake in a two group population outbreak model. The model has
        been used to assess the cost effectiveness of targeted outreach programs aiming to
        compare the overall and distributional health and cost outcomes of different vaccination
        programs, as described in the following publications:"
      ),
      tags$i("Nguyen et al. (2024)"),
      a("https://doi.org/10.1016/j.jval.2024.03.039", href = "https://doi.org/10.1016/j.jval.2024.03.039", class = "link-class", id = "paper_link"),
      br(),
      tags$i("Duong et al. (2026)"),
      a("https://doi.org/10.1093/ofid/ofaf695.217", href = "https://doi.org/10.1093/ofid/ofaf695.217", class = "link-class", id = "paper_link"),
      br(), br(),
      p("This project was made possible by cooperative agreement CDC-RFA-FT-23-0069 from the CDC’s Center for Forecasting and Outbreak Analytics. Its contents are solely the responsibility of
        the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention.")
    )
  ),
  absolutePanel(
    bottom = 0,
    left = 0,
    right = 0,
    fixed = TRUE,
    img(
      src = "figs/logo.jpg",
      align = "left",
      height = 100,
      width = 100
    )
  )
)