reproducR

The reproducr package allows users without any prior knowledge of R Markdown to implement reproducible research practices in their scientific workflows. The reproducr package offers an integrated-file solution that guides researchers from draft to final paper submission.

⭐ In the stage of explorative analysis and when focusing on content only, researchers may rely on the ‘draft mode’ of the template that knits to HTML and allows them to interactively explore their data and include interactive research output.

⭐ In the stage of research dissemination and when focusing on the presentation of results, in contrast, researchers may rely on the ‘manuscript mode’ that knits to PDF and allows them to circulate a publication-ready version of their working paper or submit it (blinded) for review.

Installation

# Get the development version from GitHub:

# install.packages("devtools")

devtools::install_github("jschultecloos/reproducr")

Usage

To start working with reproducr, simply change the output_format parameter in your YAML header to specify the two output formats of reproducr:

  1. reproducr::reproducr_manuscript
  2. reproducr::reproducr_draft
---
output: 
  reproducr::reproducr_manuscript: 
    blinded: false
  reproducr::reproducr_draft
---

You can also click on the ‘Knit’ button in the RStudio IDE or in PyCharm (with the R Markdown Plugin installed). In this case R Markdown will compile your document to the first output format that you specify in the YAML header.

💡 If you prefer to start working with reproducr by relying on a template, you can load the package template from within your RStudio IDE by navigating to: File > New File > RMarkdown.. > From Template > reproducr.

💡 Read more about how to use reproducr.

Optimisation for scientific writing

The reproducr package comes with extended functionality for scholarly writing. It helps you to…

✨ integrate scholarly information about authors, their (multiple) affiliations, their contributions, and the corresponding author in the title page of your manuscript

✨ blind your manuscript before submitting it for review

✨ include two separate bibliographies for the main article and the appendix

✨ generate documents that contain a date stamp in their file name while keeping a clean .Rmd for tracking changes with version control

✨ harmonise the fonts in your graphs with the fonts used in the respective output format

✨ create high-resolution graphs

✨ include your code with code-folding for HTML output and hide all of your code in PDF output

Flexible output formats

Thereproducr package offers you full flexibility to knit your document to a polished and well-formatted HTML that includes all your explorative analysis and dynamic research output. This feature is particularly useful while drafting a research paper or when writing up blog posts to communicate your results to a wider audience. At the same time, the reproducr package allows you to knit your document to a polished and submission-ready PDF manuscript which is optimised for scholarly use and can optionally be blinded for review.

When writing your paper and your code, simply wrap the parts of the paper that are exclusive to one output format in three colons ::: {.not-in-format .latex} closed by three more colons :::. The respective part of the document wrapped in the not-in-format div structure will not be included in LaTeX output.

You can also make the code evaluation conditional on the output format by asking knitr to conditionally evaluate your code only when the output is HTML: eval=knitr::is_html_output().

::: {.not-in-format .latex}

This interactive `DT` table and this text will not be included in our document 
when we knit to PDF manuscript mode with `reproducr::reproducr_manuscript`. 

```{r interactive-table-datatable, eval=knitr::is_html_output()}
pacman::p_load(DT, palmerpenguins)
DT::datatable(penguins)
```
:::

Integration into the R Markdown framework

The reproducr package does not simply offer yet another custom .Rmd template.

The existing templates by rmarkdown::pdf_document, bookdown::pdf_document2, and distill::distill_article are extremely well-maintained.

The reproducr package makes minimal changes to these existing templates. Instead, it advances the functionality of bookdown::pdf_document2 and distill::distill_article by feeding Lua Filters for Pandoc to the Pandoc command line just after R Markdown has evaluated the code and knitted the document based on the respective base format.

Citation:

Schulte-Cloos, Julia (2021). ReproducR: Drafting and publishing reproducible scientific articles with R Markdown. R package version 0.1.0, https://github.com/jschultecloos/reproducr.