R04: Reproducibility, File Organization, and Projects

Nicky Wakim

2024-10-09

Where are we?

Using OneDrive

• We all have free access to OneDrive to store files

• Let’s login into our online accounts

• You can also download OneDrive for your desktop

  • Allows you to access the OneDrive from your computer’s interface instead of the browser

  • Creates a link between your computer and the cloud!

• Let me show you mine

  • I can access all the files through RStudio as well!

• Let’s take a couple minutes to log into OneDrive

05:00

Folder organization

• Make a folder for our class!

  • I suggest naming it something like EPI_525_F24 to indicate the class and the term

• Make these folders in your computer

  • Only make them in OneDrive if you have a desktop connection

• For a project, I have the following folders

  • Background
  • Code
  • Data_Raw
  • Data_Processed
  • Dissemination
  • Reports
  • Meetings

• For our class, I suggest making one folder for the course with the following folders in it:

  • Data
  • Homework
  • Lessons
  • R_activities
  • And other folders if you want

• Take a few minutes to create these folders

05:00

Aside: folder and file naming

There are a few good practices for naming files and folders for easy tracking:

1. Keep the name short and relevant
2. Use leading numbers to help organize sequential items
   • I can show you my lessons folders as an example
3. Use dates in the format “YYYY-MM-DD” so that files are in chronological order
4. You can label different versions if you would like to
5. Use “_” to separate sections of the name
   • I also use this to separate words, but some people say you should use “-” to separate words

Let’s go into R_activities

• Make a folder called something like R04_work

• We are going to stay in the R_activities folder

• Now that we have some folders in order, we can start creating a project

Creating project in RStudio

• Way to designate a working directory: basically your home base when working in R

  • We have to tell R exactly where we are in our folders and where to find other things

  • A project makes it easier to tell R where we are

• Basic steps to create a project

  • Go into RStudio

  • Create new project for this class (under File or top right corner)

    • I would chose “Existing Directory” since we have already set up our folders
    • Make the new project in the EPI_525_F24 folder

• Once we have projects, we can open one and R will automatically know that its location is the start of our working directory

The nice thing about R projects

• 5 minute video explaining some of the nice features of R projects

https://rfortherestofus.com/2022/10/rstudio-projects

Reproducibility

• Research data and code can reach the same results regardless of who is running the code

  • This can also refer to future or past you!

• We want to set up our work so the entire folder can be moved around and work in its new location

Nicky’s process for R projects

• Let me show you my process

  • I will create one in my Sample_folder

  • I will show you how I switch between classes

• Make a project file in your class folder!

05:00

If time, we will move to R05: Intro to Quarto!