vsoch / prostate

prostate cancer re-ocurrence and survival prediction app for shinyapps.io

RAPS

Risk After Prostate Surgery Shiny Web Application

We have developed a tool called RAPS (Risks After Prostate Surgery) that uses a man’s personal characteristics to estimate his probability of: a) prostate cancer recurrence, and b) dying without recurrence within 10 years of radical prostatectomy for his cancer.

Deployment Instructions

Clone the repo

You must clone the code base to work on it.

  git clone https://github.com/vsoch/prostate

or if you use ssh for github

  git clone [email protected]:vsoch/prostate.git

Note that the app is named on the server according to the folder name. The folder is called "prostate," so this would be deployed as http://predict.shinyapps.io/prostate. To fix this, and deploy as "raps," change the folder name:

  mv prostate raps 

Do not CD into the folder, you will work one level above it to deploy. It is most comfortable to work in the rstudio environment. If you have not installed it, do so, and run as so from the command line:

  rstudio

Once in R, you need to install devtools, shiny, and shiny apps.

  install.packages('devtools')
  install.packages('shiny')

  if (!require("devtools"))
    install.packages("devtools")
    devtools::install_github("rstudio/shinyapps")

If any installations don't work, it is recommended to find the source code on github, and install from source instead of a repository.

Setting up R

First, load the shinyapps, shiny, and devtools

  library('devtools')
  library('shiny')
  library('shinyapps')

You must first log into shinyapps.io to get the token and secret to use in R. Click on Account then Tokens and then Show. You will need to click show secret and copy to clipboard to copy the entire line of code and then copy paste into rstudio. Do that.

Make sure you are one folder above the app, you can check by doing "list.files()" and you should see "raps." When you are, the command to deploy is:

 deployApp("raps",account="predict")

The browser will open when it is finished.

Notes about the application

Shiny applications are usually required to have a server.R and ui.R. More advanced apps can roll their own html, meaning that we get rid of the ui.R and replace with an index.html file in the www folder. Note that it MUST be called this, and is expecting it. Thus, to make changes to the UI, you must change this file. Changes to the computation or the "R part" of the server should be changed in server.R.