R programming tips

🎨 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

• Introduction to expectation and variance
• Beyond expectations: centrality measures in statistics

🔮 Machine learning

• Working with dummy variables and factors

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 no longer ordered with a numerical prefix and names are no longer case sensitive e.g r_tips\tutorials\... and r_tips\figures\...
• Tutorial subtopics share the same prefix e.g. r_tips\tutorials\dv-... and r_tips\tutorials\st-...
• File names contain - to separate file name prefixes 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
• R code chunks are styled as follows:
  • Each R chunk should be named with a short unique description written in the active voice e.g. create basic plot and modify plot labels
  • Arguments inside code chunks should not contain white space and boolean argument options should be written in capitals e.g. {r load libraries, message=FALSE, warning=FALSE}
  • To render the github document, results are generally suppressed using results='hide' and manually entered in a new line beneath the code.
  • To render the github document, figures are generally outputed using fig.show='markdown' and figure outputs can then be suppressed at the local chunk level using fig.show='hide'
• 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

Citations

Citing packages is a good practice when you are publishing research papers. To do this, use citations("package") to print the relevant package publication. A non-exhaustive list of R packages used in this repository is found below.

• R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
• Wickham et al., (2019). Welcome to the tidyverse. Journal of Open Source Software, 4(43), 1686, https://doi.org/10.21105/joss.01686
• H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
• Matt Dowle and Arun Srinivasan (2021). data.table: Extension of data.frame. R package version 1.14.2. https://CRAN.R-project.org/package=data.table

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.