Reproducible workflows in R

(A new draft started on 4.5.2023 after the old one in Hedgedoc disappeared.)

data management
- R scripts
- data storage and accessibility
R version
R package versions
- tip: define R version when loading the r-env moduleon Puhti: r-env/432 etc.
operating system, its version and other underlying parts

R Markdown and Quarto
projects in R
- help organizing multiple projects
- make version control easier
- https://r4ds.had.co.nz/workflow-projects.html
- https://support.posit.co/hc/en-us/articles/200526207-Using-RStudio-Projects
don't save workspace (save objects and scripts instead)
keep original data - modified data separate should be a separate copy
R script reproducibility
- commenting
- file paths
- general readability
- functions for repeating sections of code
- set.seed()
- aim for scripts that can produce the output again at any time (instead of relying on storage of output)
version control
- Git
- Linking RStudio with Github
- https://happygitwithr.com/
renv
- the ultimate tool for reprodubility
- BUT be careful when using on Puhti
containers
package versions
- packages on Puhti tied to a specific date
- sessionInfo()
- Posit Public Package manager snapshots

R versions on Puhti
R package versions on Puhti
minimum information to record for reproducibility
light-weight tools and tips for R reproducibility
- stand-alone script principle
- version control
- general script tips
heavy-weight tools for R reproducibility
- renv
- containers