Academic programming

2024-02-05

Navigating R for specific analyses, like statistical or bioinformatics tasks, is a common quest for many users who don’t identify as professional programers. Drawing from my own journey, here are some suggestions:

  1. Scripting Smarts: Starting off, resist the urge to compile all your tasks into one colossal script. Trust me; it’s like trying to decipher a mystery novel written in code. Not only does it make things confusing, but saving that Rdata file becomes a puzzle too. To keep things clear and straightforward, break down your tasks into manageable scripts. And hey, if you’re into debugging (who isn’t?), the R terminal is your go-to spot. Just remember, what happens in the terminal stays in the terminal. So, script it out! Write your code and execute it with Rscript for results that are both dependable and reproducible. And when your calculations start dragging their feet, don’t forget to stash that Rdata file.

  2. Parameter Play: Ever find yourself juggling parameters like a circus act? It’s time for a more graceful solution. Say hello to the config YAML file. Instead of playing the manual game with script changes, stash your parameters there. It’s like having a control panel for your tasks. Plus, throw in Git, and you’ve got a neat record-keeping system for your parameter shenanigans.

  3. Plotting Prowess: Research demands results that dance to the tune of your expectations. But hold off on the glitter and polish for a sec. Resist the temptation to create the Mona Lisa of figures right away. Instead, let each task have its own script for plotting. Adding the sparkle directly to the main script? Nah, that’s like mixing oil and water. Keep the logic clean and separate. Save the original scripts’ Rdata file and let it moonlight in your figure plotting scripts. And here’s a golden nugget: don’t reshuffle variables meant for plotting; it’s like keeping your ingredients in order for a smooth recipe. Also, keep an eye on the colors – pre-define your palette (sequential, diverged, ordered) to keep things harmonized in your report.

  4. Quarto Chronicles: When it’s time to pen down the final chapter of your analytical escapade, make it a Quarto affair. It’s the ultimate tool to weave together code, storytelling, and visual flair. Your report becomes not just a summary but a captivating narrative, thanks to Quarto’s magic touch.

So there you have it – a roadmap to infuse some natural finesse into your R journey. Embrace these tips, and may your code be as smooth as jazz on a lazy Sunday afternoon.

Modified by chatGPT😎…*