Before we start

  • Use the GitHub Discussions as our communication forum for the workshop.
  • Use the Code of Conduct to report unacceptable behaviour.

Introduction

  • Our vision is to increase the awareness of tools to improve the reproducibility of data analysis.
  • Our strategy is to incorporate good practices in scientific computing gradually.
  • We plan to share specific tools to create a research compendium, make a reproducible analysis, and write READMEs.

Research compendium

  • Use rcompendium templates to reuse all the files and folders a research project needs.
  • Use usethis to add complementary community files to a research project.
  • Version control, Research compendium, and Community files are features related to Sustainable software.

Reproducible analysis

  • A dependency is a package that your project needs to run.

  • Use the DESCRIPTION file to register your project dependencies.

  • Use renv to isolate and create package-specific reproducible environments for your dependencies.

  • Use the folder template to differentiate your raw-data/ and derived-data/.

  • Save analysis and generated files in isolated folders like analyses/, figures/, and outputs/.

  • Use the make.R to list your analysis scripts and facilitate the regeneration of all your outputs.

  • Reproducible environments and Make files are features related to Reproducible research.

README files

  • Complement the README template with Installation steps, Citations, Licenses and Contributing guides.
  • Use different types of licenses of text and figures, software code, and data.
  • Licenses is a feature related to Open Science.

Wrap up

  • Use the JOSS review checklist to self-assess your progress.
  • Use the GitHub Discussions as our communication forum after the workshop.
  • Use the feedback form to share your constructive comments.

Appendix

  • Write your functions documentation following the R/fun-demo.R template.
  • Run your project functions with devtools::load_all().
  • Update your functions documentation with devtools::document().
  • Read your functions documentation with the ?function notation in the R console.
  • Create a website for the project with usethis::use_pkgdown_github_pages().
  • Use a manuscript template with rrtools::use_analysis(location = "inst", data_in_git = FALSE).
  • Documentation strings and Manuscripts using literate programming are features related to Reproducible research.

Definitions

  • The definitions of Open science, Reproducible research, and Sustainable software help us identify their specific software features.

  • Differentiating these concepts helps us to differentiate the characteristics of a project.