Files

1 File types and structure (folders)

1.1 The root

1.1.1 One root folder for each project

Should contain

• RStudio project (*.RProj)
• README.md
• sessionInfo.txt
• Your main R scripts
• Your RMarkdown and quarto scripts
• Relevant subfolders (/custom_functions, /gfx, /data, etc)

1.2 Files and folders

1.2.1 Make and use your own folder/sub-folder template for new projects

1.3 File types

• Text always preferable to binary files
• Markup files (HTML, XML, etc) are human readable, but can be complex
• Application files (.odt, .docx) are often either binary files or very complex markup files

gfx/prefer_text_files.pdf

gfx/prefer_text_files.pdf

gfx/prefer_text_files.xml

1.4 File types

Stick to simple, human-readable files like R-scripts, markdown, csv files, etc, as far into the process as you can and only generate pdf, word, tiff, jpeg etc files as the final step.

If any characters look weird in a simple txt file (it does happen) – it’s probably the character encoding – just stick to UTF8/UTF16

• By the way, what do you think the first thing the typesetters at Springer does with your manuscript once accepted?

1.5 Files and folders

Main points

• Use a strict folder structure you can handle – make a template!
• Use relational folder paths if possible
• Use human-readable files only if possible (txt, md, Rmd, csv, etc)
• Only use non-human readable files for ‘final output’ (pdf, docx, xlsx, etc)