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rUM

This is a collection of R things from your friends at UM (The University of Miami).

To see a tutorial video on rUM check out our presentation at R Medicine 2025{target="_blank"}.

rUM includes:

• A research project template. It creates a new RStudio project that has your choice of an analysis.qmd Quarto file or analysis.Rmd R markdown file that load the tidyverse and conflicted packages and set many useful default details. These files can also include example tables and figures.

• rUM streamlines creating a package that include a paper outline with the make_package() function.

• rUM helps with project documentation files (write_readme() and write_notes()), and Quarto styling files (write_scss()).

• 💥 NEW in Version 2.2.0 (rUM Runner) 💥

  • rUM can make documentation/manual pages for datasets with the write_man() function.
    
  • rUM now includes templates to produce slide decks with the write_slides() function. There are now functions (find_slides() and show_slides()) to find and render/show slides that are included with a package.
  • write_quarto() now accepts an example argument. If this is set to TRUE, then it will use the Quarto paper template with examples of a table and figure with cross-referencing. If this is FALSE, then it will use the Quarto paper template without examples for tables. The default value is NULL and will provide a minimal Quarto template. See ?write_quarto() for more documentation.

How do I add rUM?

Modern versions of the RStudio interface (v2022.07 or later) ships with Quarto; update to the most recent version of RStudio here. You can install the latest version of Quarto directly from here.

Then you should run this in the console of RStudio:

r if (!requireNamespace("remotes")) install.packages("remotes") remotes::install_cran("rUM")

If you would like the (unstable) development version, use the following code instead: r if (!requireNamespace("remotes")) install.packages("remotes") remotes::install_github("RaymondBalise/rUM")

Can I make a R package that includes my paper as a vignette?

Yes! When you use the make_project() function set vignette = TRUE. See the "Make a Package" vignette which ships with rUM. Run this line vignette("Make a Package", package = "rUM") to see it now.

Can I make a Quarto based vignette?

Yes! If you would like to write a Quarto vignette you need have Quarto version 1.4.549 or higher. You can check your version with quarto::quarto_version(). You can install the latest version of Quarto directly from here.

Where can I get rUM?

https://raymondbalise.github.io/rUM/

https://github.com/RaymondBalise/rUM

How do I make rUM research project?

1. Use File > New Project > New Directory
2. Scroll down and then click rUM Research Project Template
3. Specify where you want your research project to be saved.

How do change the reference style for my paper?

The default reference style is the New England Journal of Medicine. The style is set by the Citation Style Language (csl:) option near the top of the file. To use a different style, download a csl file from https://www.zotero.org/styles/ into the folder with your analysis file. Then change the-new-england-journal-of-medicine.csl to the name of the file you downloaded.

How do I control what files appear in my reference section?

The analysis file includes this code near the bottom:

c( .packages(), "rUM", "table1" ),

If you want to acknowledge a package that is not used directly in your analysis file, add its name inside of the c() function. The authors of the packages that you used for exploratory data analysis will thank you.

After you knit/render the analysis file once the packages will appear in the "packages.bib" file in the same directory/folder as your analysis file. If you are using the RStudio Visual Editor, put the cursor when you want to add the citation, then use the Insert Menu and choose @ Citation... and pick the article. If you are using the Visual Studio Source Editor, open the "packages.bib" file, find the manual reference for the package that you want to add and copy it. For example, if you needed to add a reference to the rUM package you would find this line:

@Manual{R-rUM

and copy the reference name. Here the name is R-rUM. Paste that where you want the citation like this [@R-rUM].

How do I use rUM for R Markdown headers?

1. Use File > New File > RMarkdown...
2. Click From Template
3. Choose a template
   • html2 with rUM
   • html2 Details with rUM
   • pdf2 showing LaTeX with rUM
   • bookdown_site with rUM

This will create a new subdirectory in your current working directory with the same name as the name of the .Rmd file you specified. Within this directory, you will find the analysis R Markdown file. For example, if you created an R Markdown file called wrangle_cytometry_data.Rmd with the steps above, then your current directory will now have a subdirectory called wrangle_cytometry_data/ which will contain the file wrangle_cytometry_data.Rmd and any subsequent files from the knitting process (such as .PDF, .html, or .docx files created by knitting the RMarkdown document).

What are the headers?

html2 with rUM

This is a basic web page

html2 Details with rUM

This shows a table of contents

pdf2 showing LaTeX with rUM

PDF report where table and figures don't float to other pages. Many thanks to https://stackoverflow.com/questions/16626462/figure-position-in-markdown-when-converting-to-pdf-with-knitr-and-pandoc

bookdown_site with rUM

A bookdown website with a good table of contents for a book