CBW Infectious Disease Epidemiology 2023 Module 5 Lab Setup

Module 5 Lab

The lab assignment is written in Rmarkdown (.Rmd) which means that the lab is intended to be run in RStudio IDE.

Set up

Before connecting to your RStudio instance, please perform the following steps:

  1. Log into your remote instance using ssh
# replace xx with your student number
ssh -i CBW.pem xx.uhn-hpc.ca
  1. Copy the lab materials from CourseData to workspace/
cp -r  ~/CourseData/IDE_data/module5/ ~/workspace/
  1. You should now find a directory called module5 under ~/workspace/. Use ls to list the file content in ~/workspace/module5 to verify that you have successfully copied all of the required files.
ls ~/workspace/module5

Expected output:

Launching RStudio

  1. Open a browser tab and navigate to http://xx.uhn-hpc.ca:8080 (Remember to replace xx with your student number!)

  2. Log in using the following credentials:

    • Username: ubuntu
    • Password will be provided in class

    If logged in successfully, you should see the following graphical interface in your browser:

  1. Load up Module_5_Lab.Rmd by clicking [File] -> [Open File] -> [Select the .Rmd file in module5 directory]

    If you have successfully opened the .Rmd file, you will see the following screen: