inst/shinyApp/ui/13_sensitivity.R

In presize: Precision Based Sample Size Calculation

# sensitivity
# UI ----
senspage <- tabItem(tabName = "sens",
        h2("Precision of sensitivity"),
        "Sensitivity is the proportion of positive test results that are identified as such. It is also known as the true positive rate, recall or probability of detection. It is actually a simple proportion, but as the total sample size, rather than the number of cases, is typically of interect this function requires an estimate of the prevalence of cases.",
        tags$br(),
        h4("Please enter the following"),
        sliderInput("sens_sens", "Sensitivity",
                    min = 0, max = 1, value = .5),
        # sliderInput("sens_prev", "Prevalence",
        #             min = 0, max = 1, value = .4),
        tags$br(),
        h4("Please enter one of the following"),
        uiOutput("sens_resetable_input"),
        actionButton("sens_reset_input",
                     "Reset 'Total sample size' or 'Confidence interval width'"),
        h4("Optional parameters"),
        selectInput("sens_method", label = "Confidence interval method",
                    choices = c("Wilson" = "wilson",
                                "Agresti-Coull" = "agresti-coull",
                                "Exact" = "exact",
                                "Wald" = "wald"),
                    selected = "wilson"),
        selectInput("sens_round", label = "When rounding the number of cases, round...",
                    choices = c("up" = "ceiling",
                                "down" = "floor"),
                    selected = "up"),
        "The number of cases is calculated as sample size * prev, which can result in fractions so rounding is necessary.",
        tags$hr(),
        verbatimTextOutput("sens_out"),
        tableOutput("sens_tab"),
        "Code to replicate in R:",
        verbatimTextOutput("sens_code"),
        h4("References"),
        "Brown LD, Cai TT, DasGupta A (2001) Interval Estimation for a Binomial Proportion, ", tags$i("Statistical Science"), ", 16:2, 101-117, ", tags$a(href="doi:10.1214/ss/1009213286","doi:10.1214/ss/1009213286")

)

# SERVER ----
sens_fn <- function(input, code = FALSE){
        if(is.na(input$sens_ntot) & is.na(input$sens_ciwidth)) {
                cat("Awaiting 'number of observations' or 'confidence interval width'")
        } else {
                z <- ifelse(is.na(input$sens_ntot),
                            paste0("conf.width = ", input$sens_ciwidth),
                            paste0("ntot = ", input$sens_ntot, ", prev = ", input$sens_prev))
                x <- paste0("prec_sens(sens = ", input$sens_sens,
                            ", ", z, ", conf.level = ", input$conflevel,
                            ", round = '", input$sens_round,
                            "', method = '", input$sens_method, "')")
                if(code){
                        cat(x)
                } else {
                        eval(parse(text = x))
                }
        }
}