2. Create a Research Project with R Markdown and rUM

Introduction

This is a collection of document templates, available through R, from your friends at the University of Miami (UM). \(R+UM=rUM\)

The rUM package will help you create research manuscripts by removing the configuration hassles commonly encountered when learning to write papers using R. rUM will initialize a new RStudio project and a Markdown file that includes the outline for a research paper. The Markdown file comes preconfigured with a YAML header (don’t worry if you don’t know what that means yet) with code chunks to load the tidyverse and conflicted packages. Manuscript sections have been created for Introduction, Methods, Results, Conclusion, and References. The project also includes a .gitignore file which is designed to help protect against accidentally leaking data when using git with websites like www.github.com.

rUM’s documentation can be found here:

How do I get `RMarkdown` and `rUM`? (Add a “quart o’ `rUM`”!)

Modern version RStudio (v2022.07 or later) ships with R Markdown integrated into the RStudio IDE.
Add rUM to your computer by:
- using RStudio: click on the Packages tab in the bottom right windowpane, click the Install button, type rUM, and click Install.
- downloading rUM from CRAN and installing it by running this code in R console:
```
install.packages("rUM")
```
- downloading the latest version of rUM from GitHub by running commands into the R console:
```
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("RaymondBalise/rUM")
```
Use rUM by running this in the console of RStudio:

library(rUM)

Ordering `rUM` from the Menu

To create a research project that uses rUM, follow these steps. This will initialize a new RStudio project that has an analysis.Rmd R Markdown file using the tidyverse and conflicted packages and some other useful files which are described below.

Using the RStudio menus, choose: File > New Project > New Directory
Scroll down and then select rUM Research Project Template
Specify the location of where your research project will be saved

Add `rUM` into an existing folder/directory that does not have an RStudio project.

What if you have already created a folder containing the important files for your project? Create a new project in your existing folder! This will now be your project directory (complete with a .Rproj file).

Navigate to File > New Project > Existing Directory
Specify the location of where your research project will be saved
Run the following script in your console:

# Change the text inside the quotes on the next line to indicate the path to your folder/directory.
PATH <- "~/Documents/blah"   

make_project(PATH, type = "R Markdown (analysis.Rmd)")

After your `rUM` has been served

A new project directory has been created and it will be populated with these files:

An aggressive .gitignore to help prevent the unintended sharing of sensitive study information or protected health information (PHI).
analysis.Rmd is a Markdown template for writing your research project. It has a preconfigured YAML header; Introduction, Methods, Results, Conclusion, and Reference sections; and a code chunk to construct your bibliography using knitr::write_bib().
An empty folder named data. This folder is listed within the .gitignore. That means that git should not track these files. This should help prevent data leakage but be sure to talk to a data security expert before sharing any biomedical projects on websites like GitHub.
A .Rproj file with the same name as your project folder.
Two text files, packages.bib and references.bib, which are used to hold details for your paper’s bibliography. Refer to the Methods and References sections, respectively, within the analysis.Rmd file for initial examples of how to add/use references.
the-new-england-journal-of-medicine.csl is the citation style language (CSL) based on the New England Journal of Medicine requirements.

Newly created files:

analysis.Rmd:

`rUM` infused Markdown headers

Navigate to File > New File > R Markdown
Select From Template
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.Rmd 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 R Markdown document).

What are the headers

html2 with rUM

This is a basic web page

html2 Details with rUM

This is a basic web page with 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

Session

If you are new to R, ignore this.

sessionInfo()
#> R version 4.4.0 (2024-04-24)
#> Platform: x86_64-apple-darwin20
#> Running under: macOS Monterey 12.7.5
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> time zone: America/New_York
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] vctrs_0.6.5       cli_3.6.2         knitr_1.46        rlang_1.1.3      
#>  [5] xfun_0.43         purrr_1.0.2       textshaping_0.3.7 jsonlite_1.8.8   
#>  [9] htmltools_0.5.8.1 ragg_1.3.0        sass_0.4.9        rmarkdown_2.26   
#> [13] evaluate_0.23     jquerylib_0.1.4   fastmap_1.1.1     yaml_2.3.8       
#> [17] lifecycle_1.0.4   memoise_2.0.1     compiler_4.4.0    fs_1.6.4         
#> [21] htmlwidgets_1.6.4 rstudioapi_0.16.0 systemfonts_1.0.6 digest_0.6.35    
#> [25] R6_2.5.1          magrittr_2.0.3    bslib_0.7.0       tools_4.4.0      
#> [29] pkgdown_2.0.9     cachem_1.0.8      desc_1.4.3