create_turing: Create executable research compendium according to the Turing...

In rang: Reconstructing Reproducible R Computational Environments

Create executable research compendium according to the Turing Way

Description

This usethis-style function creates an executable research compendium according to the Turing Way.

Usage

create_turing(
  path,
  add_rang = TRUE,
  add_makefile = TRUE,
  add_here = TRUE,
  verbose = TRUE,
  force = FALSE,
  apptainer = FALSE
)

Arguments

path	character, path to the project root
add_rang	logical, whether to run use_rang() to path
add_makefile	logical, whether to insert a barebone Makefile in the project root.
add_here	logical, whether to insert a hidden .here file in the project root
verbose	logical, whether to print out messages
force	logical, whether to overwrite files (inst/rang/update.R, Makefile, .here) if they exist.
apptainer	logical, whether to use apptainer. FALSE indicates using Docker

Details

According to the Turing Way, an executable research compendium should have the following properties

1. Files should be organized in a conventional folder structure;

2. Data, methods, and output should be clearly separated;

3. The computational environment should be specified.

We use the structure suggested by the Turing Way:

• data_raw: a directory to hold the raw data

• data_clean: a directory to hold the processed data

• code: a directory to hold computer code

• CITATION: a file holding citation information

• paper.Rmd: a manuscript This function provides the a clearly separated organizational structure. Components can be changed. For example, the manuscript can be in another format (e.g. quarto, sweave) or even optional. With add_rang, the computational environment can be recorded and reconstructed later.

Value

path, invisibly

References

The Turing Way: Research Compendia Gorman, KB, Williams TD. and Fraser WR (2014). Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis). PLoS ONE 9(3):e90081. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1371/journal.pone.0090081")}

See Also

use_rang()

rang documentation built on Oct. 8, 2023, 5:06 p.m.