The Road to Progress

November 14, 2022 ยท View on GitHub

Step-by-step guide for vectorizing/parallelizing your R code

Open in Gitpod

You can best follow this tutorial the following way: checkout the individual commits and look at the diffs. This way you'll be able to observe how the code evolved. The evolution shows the typical workflow.

Watch the video

What you'll need

install.packages(c("pbapply", "mgcv"))

Steps

These steps demonstrate the usual workflow of how to interactively develop code and encapsulate it into a loop, then a function. This all sets us up for using vectorized functions that are well suited for parallel computing as well.

Locally with Git

Clone the repository:

git clone https://github.com/psolymos/the-road-to-progress.git

Open the repository as an R project in RStudio Desktop, VSCode, or R GUI. Check out revisions using git tags to follow the steps:

  • Step 1: git checkout 45d5a67 or git checkout step-1
  • Step 2: git checkout 59eacb9 or git checkout step-2
  • Step 3: git checkout da685ae or git checkout step-3
  • Step 4: git checkout 8321cdc or git checkout step-4
  • Step 5: git checkout 9fc2c61 or git checkout step-5
  • Step 6: git checkout c0e1973 or git checkout step-6
  • Step 7: git checkout 370432f or git checkout step-7
  • Step 8: git checkout 8ea4cd9 or git checkout step-8
  • Step 9a: git checkout b6c7729 or git checkout step-9b
  • Step 9b: git checkout db7c892 or git checkout step-9b

The example.R code will change along the steps, introducing new tricks.

Tags

Locally without Git

Download the zip file for this release: https://github.com/psolymos/the-road-to-progress/releases/tag/start.

Then follow along this commit history: https://github.com/psolymos/the-road-to-progress/commits/master/example.R.

Diffs

In your browser with Gitpod

This link will open up a preinstalled Gitpod environment where you can run the scripts from each step by launching R and copy-pasting the contents from the step-*.R files.

Open in Gitpod

Gitpod

Exercise

Check out Step 4 (git checkout 8321cdc) while creating a new branch from it: git checkout -b <new-branch-name> 8321cdc, or dowload this release: https://github.com/psolymos/the-road-to-progress/releases/tag/middle, then

  1. Develop modular code by splitting the function into 2 pieces: (1) data processing + model training, and (2) prediction.
  2. Use lapply/sapply to run the code in a vectorized fashion.
  3. Adapt the vectorized format to show the progress and do it in parallel.

Additional topics