---
title: "2. Create a Research Project with Quarto and rUM"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{2. Create a Research Project with Quarto and rUM}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 6,
fig.height = 4
)
options(rmarkdown.html_vignette.check_title = FALSE)
```
```{css, echo=FALSE}
body > h1 > img {
position: relative;
bottom: -30px;
border: 0px solid rgba(0, 0, 0, 0.1);
}
```
## 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 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 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](https://github.com/).
rUM's documentation can be found here:
- <https://raymondbalise.github.io/rUM/>
- <https://github.com/RaymondBalise/rUM>
## How do I get `quarto` and `rUM`? (Add a "quart o' `rUM`"!)
1. Modern version RStudio (v2022.07 or later) ships with Quarto but you can install the latest version of Quarto from [here](https://quarto.org/docs/get-started/).
2. 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:
``` r
install.packages("rUM")
```
- downloading the latest version of rUM from GitHub by running commands into the R console:
``` r
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("RaymondBalise/rUM")
```
3. Use `rUM` by running this in the console of RStudio:
``` r
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.qmd`](#fig:analysis_quarto_file) Quarto file using the `tidyverse` and `conflicted` packages and some other useful files which are described [below](#stuff).
1. Using the RStudio menus, choose: File \> New Project \> New Directory
2. Scroll down and then select **`rUM` Research Project Template**
{width="70%"}
3. Specify the location of where your research project will be saved
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## 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).
1. Navigate to File \> New Project \> Existing Directory
2. Specify the location of where your research project will be saved
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3. Run the following script in your console:
``` r
# 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 = "Quarto (analysis.qmd)")
```
## What is in the project? (What is served with your `rUM`?) {#stuff}
A new project directory is created and it will be populated with [these files](#fig:created_rUM_files):
- An aggressive `.gitignore` to help prevent the unintended sharing of sensitive study information or protected health information (PHI).
- [`analysis.qmd`](#fig:analysis_quarto_file) is 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 `knitr::write_bib()`.
- A `README.md` template containing structured sections for comprehensive project documentation, including study details, setup instructions, and file descriptions.
- A `dated_progress_notes.md` file that automatically tracks project milestones, starting with the project creation date.
- 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.qmd`](#fig:analysis_quarto_file) file for initial examples of how to add/use references.
- [`the-new-england-journal-of-medicine.csl`](https://www.zotero.org/styles?q=id%3Athe-new-england-journal-of-medicine) is the citation style language (CSL) based on the *New England Journal of Medicine* requirements.
- [`apa.csl`](https://www.zotero.org/styles?q=id%3Aapa) is the citation style language (CSL) based on the *American Psychological Association 7th edition* requirements.
- **Quarto only**: `custom.scss` provides styling customization options for your Quarto document. Additional style sheets can be added using `write_scss()`.
Newly created files:
```{=html}
<br>
<p id="fig:created_rUM_files" >
</p>
```
{width="80%"}
`analysis.qmd`:
```{=html}
<br>
<p id="fig:analysis_quarto_file" >
</p>
```
{width="80%"}
### Session
If you are new to R, ignore this.
```{r}
sessionInfo()
```