Printing results of Cox Model in Shiny App

Question

I am attempting to add the results of a Cox model to an R Shiny app. Unfortunately the results aren't printing out with the following line of code:

 textOutput('modelSummary')

Also, I would like to add optional covariates via check-boxes. For example, I'm interested in adding something like the following below the last 'selectInput':

  checkboxGroupInput("variable", "Covariates:",
                     c("Covariate 1" = "cov1",
                       "Covariate 2" = "cov2",
                       "Covariate 3" = "cov3"))

and then adding the selected variables to the Cox model.

The full Shiny App is below:

#
# This is a Shiny web application. You can run the application by clicking
# the 'Run App' button above.
#
# Find out more about building applications with Shiny here:
#
#    http://shiny.rstudio.com/
#
library(shiny)
library(survival)
library(survminer)
library(ggplot2)

ui <- fluidPage(
  sidebarLayout(
    sidebarPanel(
      fileInput("file","File input"),

      selectInput("Survival",
                  label = "Length of Survival",
                  choices =  c('survival1',
                               'survival2'),
                  selected = 'survival1'),

      selectInput("Treatment",
                  "Treatment",
                  choices = c("treatment1", "treatmentt2"),
                  selected = "treatment1"),

      selectInput("Endpoint",
                  "Endpoint",
                  choices = c("endpoint1", "endpoint2"),
                  selected = "endpoint1")

    ),
    mainPanel(
      plotOutput("KM"), 
      textOutput('modelSummary')
    )
  )
)

server <- function(input, output) {
  options(shiny.maxRequestSize=40*1024^2)
  raw_surv_data <- reactive({
    req(input$file)
    read.csv(input$file$datapath)
  })

  surv_data <- reactive({
    raw_surv <- raw_surv_data()
    data.frame(
      Time = raw_surv[[input$Survival]],
      Treatment    = raw_surv[[input$Treatment]],
      Endpoint  = raw_surv[[input$Endpoint]]
    )
  })


  surv_fit <- reactive({

    survfit(Surv(Time , Endpoint) ~ Treatment, data = surv_data())
  })

  output$KM <- renderPlot({  
    ggsurvplot(surv_fit(), risk.table = TRUE, data = surv_data())
  })

  cox_fit <- reactive({
  coxph(Surv(Time, Endpoint) ~ Treatment, data = surv_data())
  })


  output$modelSummary <- renderPrint({
  summary(cox_fit)
  })


}

shinyApp(ui = ui, server = server)

Answer 1

To add the covariates from the checkboxes, you can do:

cox_fit <- reactive({
  model <- as.formula(paste0("Surv(Time, Endpoint) ~", 
                             paste0(input$variable, collapse = "+")))
  coxph(model, data = surv_data())
})