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https://github.com/rostools/prodigenr

Project directory generator R package
https://github.com/rostools/prodigenr

cran devtools open-science open-source project-management reproducibility reproducible-research reproducible-science rstats rstudio usethis

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Project directory generator R package

Awesome Lists containing this project

README 

        
---

output: github_document

---



```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```



# Create projects with prodigenr 



[![CRAN Status

Badge](http://www.r-pkg.org/badges/version/prodigenr)](https://cran.r-project.org/package=prodigenr)

[![R-CMD-check](https://github.com/rostools/prodigenr/workflows/R-CMD-check/badge.svg)](https://github.com/rostools/prodigenr/actions)

[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)

[![CRAN RStudio mirror

downloads](http://cranlogs.r-pkg.org/badges/prodigenr)](https://www.r-pkg.org:443/pkg/prodigenr)



This package has a simple aim of being a project directory generator

(prodigenr), with a simple focus on:



1.  Creating a standardized project folder structure with a few template

    files needed for beginning a data analysis project.

2.  Following a "one project, one (main) output" principle, such as a

    report/manuscript in the case of scientific output or a book or

    website for things like courses or workshops.

3.  Adhering to established best practices that make it easier for the

    project to be reproducible and open.



This standardized approach to how a scientific project is structured

helps ensure that the final code and documents are fairly modular,

self-contained, easy to share and make public, and be as reproducible as

possible. The structure also makes use of the existing and established

applications and workflows ([RStudio](https://posit.co/),

[devtools](https://CRAN.R-project.org/package=devtools), and

[usethis](https://CRAN.R-project.org/package=usethis)).



## Installation



You can install the released version of prodigenr from

[CRAN](https://cran.r-project.org) with:



``` r

install.packages("prodigenr")

```



And the development version from [GitHub](https://github.com/) with:



``` r

# install.packages("pak")

pak::pak("rostools/prodigenr")

```



## Usage



There are two ways of creating a new project: using the R console or

using the RStudio "New Project" menu option.



Through the console, use the `setup_project()` command. So, for

instance, if you want a manuscript project, type out:



``` r

library(prodigenr)

setup_project("~/Desktop/DiseaseDiet")

```



This then creates a directory tree, with template files for starting

your analysis! Open the newly created project via the `.Rproj` file. For

the RStudio approach, go to "File -\> New Project", then "New directory"

and find the prodigenr project in the list.



Once in the project, you can add a manuscript/report

[Quarto](https://quarto.org/) file using:



``` r

create_report() 

```



The main secondary function is the `template_list` command, which lists

the available template files:



```{r, include=FALSE}

library(prodigenr)

```



```{r}

template_list

```



For a more detailed tutorial, see the introduction vignette:



``` r

vignette('prodigenr', 'prodigenr')

```



## Related packages or projects



There are several existing packages for creating projects, each of which

has it's own pros and cons. Check out the last section of the

`vignette("prodigenr")` for more details. Try them out and see which you

like!



prodigenr tries to use ideas from R

packages/[devtools](https://CRAN.R-project.org/package=devtools) while

still being as simple as possible and to 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](https://github.com/rostools/prodigenr/issues).



## Interested in contributing?



See the [contributing

documentation](https://rostools.github.io/prodigenr/CONTRIBUTING.html)

for information on how to contribute. Please note that this project is

released with a [Contributor Code of

Conduct](https://rostools.github.io/prodigenr/CODE_OF_CONDUCT.html). By

participating in this project you agree to abide by its terms.



Special thanks to Zhila Semnani for creating the logo!