---
title: "3. Create a Research Project with R Markdown and rUM"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{3. Create a Research Project with R Markdown and rUM}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
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 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](https://github.com/).
rUM's documentation can be found here:
- <https://raymondbalise.github.io/rUM/>
- <https://github.com/RaymondBalise/rUM>
## How do I get `RMarkdown` and `rUM`? (Add a "quart o' `rUM`"!)
1. Modern version RStudio (v2022.07 or later) ships with R Markdown integrated into the RStudio IDE.
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.Rmd`](#fig:analysis_Rmd_file) R Markdown 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
{width=70%}
## 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
{width=70%}
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 = "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](#fig:created_rUM_markdown_files):
- An aggressive `.gitignore` to help prevent the unintended sharing of sensitive study information or protected health information (PHI).
- [`analysis.Rmd`](#fig:analysis_Rmd_file) 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`](#fig:analysis_Rmd_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.
Newly created files:
```{=html}
<br>
<p id="fig:created_rUM_markdown_files" >
</p>
```
{width=70%}
`analysis.Rmd`:
```{=html}
<br>
<p id="fig:analysis_Rmd_file" >
</p>
```
{width=80%}
## `rUM` infused Markdown headers
1. Navigate to File > New File > R Markdown
{width=70%}
1. Select **From Template**
{width=70%}
1. 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.
```{r}
sessionInfo()
```