The document presents a comprehensive guide on R scripting styles, emphasizing the importance of following established coding standards and naming conventions. It outlines key components for structuring R scripts, such as including program headers, commenting practices, and section headers for code chunks. Additionally, it refers to various style guides and the potential negative impacts of poorly organized code.

1. R scripting styles
SPEAKER: LUN-HSIEN CHANG
AFFILIATION: GENETIC EPIDEMIOLOGY, QIMR BERGHOFER MEDICAL
RESEARCH INSTITUTE
MEETING: R USER GROUP 20181003, HERSTON CAMPUS, UQ, BRISBANE

2. Why should you
care about
scripting style?

3. What people think of my script files

4. What they may look like

5. ?

6. • Follow an established coding standard, naming
conventions
• Respect advise from senior programmers

7. Recommended components in a R
script file
 Start with a program header documenting
 Program file name
 Directory of input files
 Directory of output files
 Names of external functions
 Names of functions created in this file
 Time and major changes to the script file
 Each code chunk has
 A section header describing the purpose
 Code written following Google’s R scripting guide
 End the file with a “end of this program” header

8. Program header
What is the file name?
Who created it and when?
What is the main purpose of the file?
Does it depend on another file or function?

9. Program header
Location of input, output files

10. Program header
Revision history

11. Program Header at PhUSE
https://www.phusewiki.org/wiki/index.php?title=Program_Header

12. Code chunk
section header

13. Code chunk
commenting your code
 What to comment?
 Above every function. This is called the function header and
provides information about the purpose of this "sub-component" of
the program. When and if there is only one function in a file, the
function header and file header comments should be merged into
a single comment. (See Function Header below)
 In line. Any "tricky" code where it is not immediately obvious what
you are trying to accomplish, should have comments right above it
or on the same line with it.

14. Code chunk
commenting your code
 How not to comment
 Comments should be useful high level descriptions
of what the program is doing. They should not
restate something that is "obvious".
 By using appropriate variable names, much of a
program can be (almost) as easy to read as English.

15. Code chunk
Google’s R scripting style
 Bioconductor’s coding standards http://wiki.fhcrc.org/bioc/Coding_
Standards
 Hadley Wickham’s style guide http://stat405.had.co.nz/r-style.html
 Google’s R style guide http://google-styleguide.googlecode.com/
svn/trunk/google-r-style.html
 Colin Gillespie’s R style guide http://csgillespie.wordpress.com/2010/
11/23/r-style-guide/
https://journal.r-project.org/archive/2012-2/RJournal_2012-2_Baaaath.pdf

17. Explicitly end a file with a header

18. The Human Cost of Messy Code

19. How will my script files look like