This is a collection of document templates, available through R, from your friends at the University of Miami (UM). \(R+UM=rUM\)
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 Quarto file that includes the outline for a
research paper. The Quarto file comes preconfigured with a YAML header
(don’t worry if you don’t know what that means yet) with code chunks to
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:
rUM? (Add a “quart o’
Modern version RStudio (v2022.07 or later) ships with Quarto but you can install the latest version of Quarto from here.
rUM to your computer by:
if (!requireNamespace("remotes")) install.packages("remotes") ::install_github("RaymondBalise/rUM")remotes
rUM by running this in the console of
rUMinto 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
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. <- "~/Documents/blah" PATH make_project(PATH, type = "Quarto (analysis.qmd)")
A new project directory is created and it will be populated with these files:
.gitignoreto help prevent the unintended sharing of sensitive study information or protected health information (PHI).
analysis.qmdis a Quarto 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
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.
.Rprojfile with the same name as your project folder.
references.bib, which are used to hold details for your paper’s bibliography. Refer to the Methods and References sections, respectively, within the
analysis.qmdfile for initial examples of how to add/use references.
the-new-england-journal-of-medicine.cslis the citation style language (CSL) based on the New England Journal of Medicine requirements.
Newly created files:
If you are new to R, ignore this.
sessionInfo() #> R version 4.2.2 (2022-10-31) #> Platform: x86_64-apple-darwin17.0 (64-bit) #> Running under: macOS Big Sur ... 10.16 #> #> Matrix products: default #> BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib #> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib #> #> locale: #>  C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 #> #> attached base packages: #>  stats graphics grDevices utils datasets methods base #> #> loaded via a namespace (and not attached): #>  digest_0.6.31 R6_2.5.1 jsonlite_1.8.4 evaluate_0.20 #>  cachem_1.0.6 rlang_1.0.6 cli_3.6.0 rstudioapi_0.14 #>  jquerylib_0.1.4 bslib_0.4.2 rmarkdown_2.20 tools_4.2.2 #>  xfun_0.37 yaml_2.3.7 fastmap_1.1.0 compiler_4.2.2 #>  htmltools_0.5.4 knitr_1.42 sass_0.4.5