Resources

[annakrystalli]

Project Organisation

• Rstudio Projects documentation
• Rstudio IDE cheatsheets
• Project-oriented workflow - Jenny Bryan blogpost
• SWC R for Reproducible Scientific Analysis lesson.
  • Project Management With RStudio episode
  • Introduction to R and RStudio
  • Writing Good Software
• File & Workflow Management
  • NHM-stars
  • ACCE DTP
  • BES Guide to Reproducible Code

[annakrystalli]

Data Management

[annakrystalli]

Dependency Management:

• Packrat
  • BES Guide to Reproducible Code
  • Packrat Rstudio tutorial
  • Creating Reproducible Software Environments with Packrat
• pacman
• miniCRAN
  • blog
• session package versioning management:
  • unload & reload a (new version of a) package
• recording dependencies:
  • Writing R Extensions

[annakrystalli]

Workflow Management

• As a package

  • Analysis as package: pkgdown

• Project template hosted on GitHub:

  • analysis_framework
  • cboettig/template
  • knitr-jekyll
  • Pakillo/template
  • rddj-template
  • researchcompendium
  • rmd-notebook
  • rr-init

• Project template created via R package:

  • makeProject
  • manuscriptPackage
  • prodigenr
  • pRojects
  • ProjectTemplate
  • rrtools
  • workflowr

• Create websites from R Markdown files:

  • blogdown
  • blogR
  • bookdown
  • knowledge-repo
  • lnraw
  • pkgdown
  • poirot
  • rmarkdown
  • rsmith
  • samantha

• Guides for reproducible research with R:

  • CRAN Task View: Reproducible Research
  • rmflight: Analyses as Packages
    • how to
  • rOpenSci Guide to Reproducible Research

[annakrystalli]

Reproducible Research

• practice reproducible research