TTEMapping: Time to event mapping module

In Novartis/subpat: Subpopulation and subgroups shiny modules

Description

Aids in the mapping of variables in a data set to common time-to-event (TTE) analysis variables. Input is any data set (data frame, tibble, etc.)

Format

R6 class

Input

data

A data set (data frame, tibble, etc.) for the TTE variable mapping

Output

mapping

a reactive list with values

population

time

event

strata

treatment

parameter

parameter_value

Super class

tidymodules::TidyModule -> TTEMapping

Methods

Public methods

• TTEMapping$new()

• TTEMapping$ui()

• TTEMapping$server()

• TTEMapping$clone()

Inherited methods

• tidymodules::TidyModule$addInputPort()

• tidymodules::TidyModule$addOutputPort()

• tidymodules::TidyModule$assignPort()

• tidymodules::TidyModule$callModule()

• tidymodules::TidyModule$countInputPort()

• tidymodules::TidyModule$countOutputPort()

• tidymodules::TidyModule$deepClone()

• tidymodules::TidyModule$definePort()

• tidymodules::TidyModule$doServer()

• tidymodules::TidyModule$execInput()

• tidymodules::TidyModule$execOutput()

• tidymodules::TidyModule$getGlobalSession()

• tidymodules::TidyModule$getInput()

• tidymodules::TidyModule$getInputPort()

• tidymodules::TidyModule$getInputPorts()

• tidymodules::TidyModule$getOutput()

• tidymodules::TidyModule$getOutputPort()

• tidymodules::TidyModule$getOutputPorts()

• tidymodules::TidyModule$getPortDef()

• tidymodules::TidyModule$getPortName()

• tidymodules::TidyModule$getSession()

• tidymodules::TidyModule$getSessionId()

• tidymodules::TidyModule$getShinyInput()

• tidymodules::TidyModule$getShinyOutput()

• tidymodules::TidyModule$getShinySession()

• tidymodules::TidyModule$getStore()

• tidymodules::TidyModule$iport()

• tidymodules::TidyModule$isGlobal()

• tidymodules::TidyModule$isStored()

• tidymodules::TidyModule$ns()

• tidymodules::TidyModule$oport()

• tidymodules::TidyModule$print()

• tidymodules::TidyModule$render()

• tidymodules::TidyModule$reset()

• tidymodules::TidyModule$updateInputPort()

• tidymodules::TidyModule$updateInputPorts()

• tidymodules::TidyModule$updateOutputPort()

• tidymodules::TidyModule$updateOutputPorts()

• tidymodules::TidyModule$use()

---

Method new()

Usage

TTEMapping$new(...)

---

Method ui()

Usage

TTEMapping$ui()

---

Method server()

Usage

TTEMapping$server(input, output, session)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

TTEMapping$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

See Also

Other tidymodules: Filter, SubgroupManager, Subgroup, SubpopulationManager, Subpopulation, TTE, TableListing, VariableSelection

Examples

## Not run: 
library(shiny)
library(subpat)
library(tidymodules)

tteMappingModule <- TTEMapping$new()
tteModule <- TTE$new()

ui <- fluidPage(
  titlePanel("TTE Analysis"),
  
  sidebarLayout(
    sidebarPanel(
      selectInput('dataset', 'survival dataset', choices = data(package = "survival")$results[, "Item"], selected = "lung"),
      tteMappingModule$ui()
    ),
    mainPanel(
      # Use the base shiny UI
      tteModule$standardUi()
    )
  )
)

server <- function(input, output, session) {
  
  options <- reactiveValues(
    makePlotly = FALSE,
    conftype = "log-log"
  )
  
  optionsMapping <- reactiveValues(
    population = FALSE,
    parameter = FALSE,
    parameter_value = FALSE,
    adam = FALSE
  )
  
  tteMappingModule$callModule()
  tteModule$callModule()
  
  # Load the data set from the survival package
  data_reactive <- reactive({
    req(input$dataset)
    ds <- trimws(gsub("\\(.*\\)", "", input$dataset))
    data(list = ds, package = "survival")
    
    # Reset the modules
    tteMappingModule <- TTEMapping$new()
    tteModule <- TTE$new()
    tteMappingModule$callModule()
    tteModule$callModule()
    
    
    get(ds)
  })
  
  observe({
    options %>4% tteModule
    optionsMapping %>2% tteMappingModule
    data_reactive %>1% tteModule
    # Get the mapping and pass into the TTE module
    data_reactive %>1% tteMappingModule %1>2% tteModule
  })
}

# Run the application
shinyApp(ui = ui, server = server)

## End(Not run)

Novartis/subpat documentation built on April 11, 2020, 3:11 p.m.