Research Project Directory Generator

Create a project directory structure, along with typical files for that project. This allows projects to be quickly and easily created, as well as for them to be standardized. Designed specifically with scientists in mind (mainly bio-medical researchers, but likely applies to other fields).


This is a project directory generator (prodigenr) that will create a project directory structure with template files necessary for managing and analyzing data for a variety of projects. This allows for a standardized approach to having a modular research project, while also taking advantage of existing well-developed and maintained infrastructures and processes (Rstudio and devtools).

How to install

Install via CRAN or using devtools for the development version:

install.packages('prodigenr')

# Development version
devtools::install_github('lwjohnst86/prodigenr')

Usage

The main function is the prodigen command. So, for instance, if you want a manuscript project, type out:

library(prodigenr)
prodigen(type = 'manuscript', name = 'cancerToxins',
    path = '/path/to/new/project')

This then creates a directory tree, with template files for starting your analysis! The main secondary function is the template_list command, which lists the available template projects and files (submit a PR if you want another template included!):

template_list

For a more detailed tutorial, see the vignette:

vignette('introduction', 'prodigenr')

Or to directly preview it here.

Related packages or projects

There are several ways of creating projects, each of which has it's pros and cons.

prodigenr tries to use ideas from R packages/devtools while still being as simple as possible and be more specific to academic researchers primarily in biomedical/non-computer science fields. However, it can always improve! I welcome any suggestions, just submit a GitHub issue!

News

prodigenr 0.3.0

  • prodigen() now creates a new project structure that mimics R package development more, specifically devtools (since it is well documented and actively maintained) (#18, #15, #14). The old style has been removed.
  • Added a function to include a STROBE checklist for reporting guidelines (#21).
  • Added function to include an rfigshare script to send to figshare (#19).
  • Added function to include a more complete MIT license (#20).

prodigenr 0.2.7

  • Added a NEWS.md file to track changes to the package.
  • Fixed a bug that prevented an Rproj file and the Rprofile files from being installed and created.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("prodigenr")

0.3.0 by Luke Johnston, 10 months ago


https://github.com/lwjohnst86/prodigenr


Report a bug at https://github.com/lwjohnst86/prodigenr/issues


Browse source code at https://github.com/cran/prodigenr


Authors: Luke Johnston [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports devtools, stats, utils

Suggests rmarkdown, knitr, testthat, rvest, xml2, rfigshare


See at CRAN