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!! Work in progress !! #WIP

Motivation

  • Reproducability - for you and others
  • easier to understand and navigate -> standardized structure
  • standardized structure

Contents

  • code, raw data, results, analysis, metadata, (software) dependencies, documentation and workflow

Basic structure for an R project

bash yourProject ├── raw_data # folder contains all raw data (read-only) - modified data is in the outputs/ folder │ └── README # text file which describes what is to be stored in that folder ├── DESCRIPTION # file contains project metadata (author, date, dependencies, etc.) ├── figures # folder contains all the figures created during the workflow │ └── README ├── inst │ └── CITATION # text file with bibentry on how to cite this project ├── LICENSE.md # license file. No license implicitly means no-one is allowed to re-use your code ├── make.R # file contains the complete workflow (i.e. sources all scripts from the rscripts folder in the correct order) ├── man # folder contains documentation of the functions in the R folder ├── yourProject.Rproj # file with the RStudio project information ├── NAMESPACE # file ├── outputs # folder contains all results created by user (including modified raw data) │ └── README ├── paper # contains manuscript materials (biblio, templates, Rmd, etc.) │ └── README ├── R # R functions coded for the analysis ├── README.md # Project "homepage" ├── rscripts # folder contains all analyses of the project (i.e. the steps of the workflow) │ └── README ├── src # folder for other code (e.g. C++, Python, Fortran, ...) └── tests # unit tests for the R-functions ├── testthat │ └── aUnitTest.R └── testthat.R

This structure is recognized by RStudio as an R-Package. This allows to build and even install your project! Also you don't need to setup this structure by hand. Either simply create an R-Package, with R Studio or usethis::create_package()

Note: use "raw_data" if you do not want to include the data to the project as you cannot exclude 'data' from the package

Include your compute environment

  • use the renv R package to include all R packages with the respective versions in the compendium
  • or put everything in a container (e.g. Docker)

Include and manage your workflow

Hexstickers and Status badges

│ │ ├── hexsticker.png # always nice to have for R packages ;-) │ │ └── lifecycle # is used to show the state of this project, important for others to decided wether or not to trust and use your work │ │ ├── lifecycle-deprecated.svg │ │ ├── lifecycle-experimental.svg │ │ ├── lifecycle-stable.svg │ │ └── lifecycle-superseded.svg

References: Related: