shine_coxph {shinyCox}

Generates a shiny app for predictions from Cox model(s)

Description

Writes a shiny app to visualize predicted survival curves from one or multiple Cox models. One feature of this function is that the shiny app, once created, will not contain any identifiable data, containing only information necessary for predictions.

Usage

shine_coxph(..., app.dir = NULL, theme = c("default", "dashboard"))

Arguments

...

Arbitrary number of Cox proportional hazard models, created by survival::coxph() or make_coxph(), which automatically ensures the models are appropriate for shine_coxph()

app.dir

Directory where shiny app is created. Specifically, a sub-folder will be made containing the app.R file as well as the .Rdata file within app.dir. If no directory is provided, execution will pause and the user will be asked to confirm whether this sub-folder may be created in the working directory or to stop the function and provide an input app.dir.

theme

Theme of shiny app.

• ⁠"default⁠: default theme, requires only shiny

• "dashboard": requires "shinydashboard" and "DT" packages

Value

A list containing Cox model information along with the shiny app code. The app is written to the directory while the function is operating.

Notes

There are some requirements in order for this function to run without error: in your original survival::coxph() function or functions, model = TRUE and x = TRUE are required arguments (used to create the simplified "coxph" object). Currently, this function does not support penalized models (e.g., as created by ridge() and pspline()). Multiple strata terms and strata by covariate interaction terms in the formula are also not currently supported, but workarounds are available by respectively using a new strata factor variable encompassing all combinations of desired stratum variable levels. Use of time-varying covariates (e.g. with tt()) and multi-state models is not supported in our function. The package is not intended to support Fine-gray models by survival::finegray() creating Cox models, but doing so will not result in an error.

Guidelines

This package is intended to visualize and present predicted survival functions for fitted Cox models. In regards to formula notation, the variable names used are ultimately what will be displayed in the application. Using functions in the formula will work, but with multiple nested functions it will fail. Using "." notation is not currently supported. The na.action is inherited from the Cox models, with omit being the only option with support at this time. For these reasons, we recommend creating all final variables (including suitable transformations) with meaningful names prior to using survival::coxph().

Examples

  library(survival)

  # Data used is from survival package, renamed for legibility
  names(leukemia)[names(leukemia) == "x"] <- "treatment"
  # Make Cox model, with x = TRUE and model = TRUE
  model1 <- coxph(Surv(time, status) ~ treatment,
  leukemia, x = TRUE, model = TRUE)

  # Use shine_coxph() to create shiny app in temporary directory
  shine_coxph("Model 1" = model1)

  # Get directory for shiny app (should be first, check file list if not)
  filedir <- list.files(tempdir())[1]

  # Run shiny app from temporary directory
  shiny::runApp(paste0(tempdir(), "/", filedir))
  # Remove app from directory once finished
  unlink(paste0(tempdir(),"/",filedir), recursive = TRUE)