R programming tips

💻 Set up

• How to set up a Positron IDE

🎨 Data visualisation

• An introduction to ggplot2 using volcano plots (Updated)
• Using DiagrammeR to draw flow charts (Updated)

📚 Data cleaning

• Data cleaning using data.table or tidyverse (or Python Pandas) (Updated)
• Cleaning strings using regular expressions with base R or stringr (Updated)

🔨 Productionisation

• Creating SQL <> R workflows - Part 1 (Updated)
• Creating SQL <> R workflows - Part 2 (Updated)
• Automating R Markdown report generation - Part 1 (Updated)
• Automating R Markdown report generation - Part 2 (updated)

🔢 Statistical modelling

• TBC

🔮 Machine learning

• TBC

Other resources

The resources below also cover a comprehensive range of practical R tutorials.

• Statistical Computing by Alex Reinhart and Christopher Genovese
• Data Science Toolkit by David Benkeser
• What They Forgot to Teach You About R by Jennifer Bryan and Jim Hester

Tutorial style guide

This repository now contains the following file naming and code style rules.

• Folders are not ordered with a numerical prefix and names are not case sensitive e.g r_tips\tutorials\... and r_tips\figures\...
• Tutorial subtopics share the same prefix e.g. r_tips\tutorials\dv-... for data visualisation tutorials and r_tips\tutorials\sm-... for statistical modelling tutorials
• File names use - to separate tutorial topics and _ instead of other white space e.g. r_tips\figures\dv-using_diagrammer-simple_flowchart.svg
• Comments are styled according to the tidyverse style guide:
  • The first comment explains the purpose of the code chunk and is styled differently for enhanced readability e.g. # Code as header --------
  • Comments are written in sentence case and only end with a full stop if they contain at least two sentences
  • Short comments explaining a function argument do not have to be written on a new line
  • Comments should not be followed by a blank line, unless the comment is a stand-alone paragraph containing in-depth rationale or an alternative solution
• To render github documents:
  • Results are generally suppressed using results='hide' and manually entered in a new line beneath the code
  • Figures are generally outputed using fig.show='markdown' and individual figure outputs can then be suppressed using fig.show='hide' in a code chunk
• Set a margin of 80 characters length in RStudio through Tools\Global options --> Code --> Display --> Show margin and use this margin as the cut-off for code and comments length

Acknowledgements

Many kudos to Dr Chuanxin Liu, my former PhD student and code editor, for teaching me how to code in R in my past life as an immunologist.