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rcompendiumtest5

Research Compendium of the project on Open, Reproducible and Sustainable code for epidemic analysis with R packages.

How to cite

Please cite this compendium as in Citing rcompendiumtest5.

utils::readCitationFile(file = "inst/CITATION",
                        meta = packageDescription("cffr"))
#> 
#> To cite package 'cffr' in publications use:
#> 
#>   Valle-Campos A (????). "rcompendiumtest5: Research Compendium for
#>   Epidemic Analysis." <https://avallecam.github.io/rcompendiumtest5/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Misc{vallecampos,
#>     title = {rcompendiumtest5: Research Compendium for Epidemic Analysis},
#>     author = {Andree Valle-Campos},
#>     url = {https://avallecam.github.io/rcompendiumtest5/},
#>     abstract = {A paragraph providing a full description of the project on Open, Reproducible and Sustainable code for epidemic analysis with R packages},
#>     version = {0.0.0.9000},
#>   }

Content

This repository is structured as follow:

  • data/: contains all raw data required to perform analyses

  • analyses/: contains R scripts to run each step of the workflow

  • outputs/: contains all the results created during the workflow

  • figures/: contains all the figures created during the workflow

  • R/: contains R functions developed especially for this project

  • man/: contains help files of R functions

  • DESCRIPTION: contains project metadata (author, date, dependencies, etc.)

  • make.R: main R script to run the entire project by calling each R script stored in the analyses/ folder

Usage

First, clone the repository. Then, to reproduce all the outputs, open R/RStudio and run:

source("make.R")

Notes

  • All required packages, listed in the DESCRIPTION file, will be installed (if necessary)
  • All required packages and R functions will be loaded
  • Some analyses listed in the make.R might take time