Cox模型在闪亮应用程序中的打印结果

Question

我正试图将Cox模型的结果添加到一个R闪亮的应用程序中。不幸的是，结果没有用下面的代码行打印出来：

 textOutput('modelSummary')

另外，我想通过复选框添加可选的协变量。例如，我有兴趣在最后一个‘selectInput’下面添加如下内容：

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

然后将所选变量添加到Cox模型中。

完整的闪亮应用程序如下：

#
# 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

要从复选框中添加协变量，可以这样做：

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