Intro to R for Bio and Enviro Sciences

Project Setup

Notes

R Studio Projects

  • Way of organizing related scripts, data, etc.

  • Think of it as a giant folder which will contain everything for this course

    • Other courses would be other projects

    • Gradschool: Each chapter or experiment might be it’s own projects

    • Professional: i.e., if you work for the Forest Service, might have a project for wildlife data, one for water quality monitoring, one for timber sales, etc.

  • Projects are self-contained and self-referential

    • Make project stored on your desktop, then move it to your Documents folder: project will still work

Create Project

  1. Create an ENVS396 folder somewhere on your computer
    • Could be on Desktop, in your Documents, etc.
    • Doesn’t matter, as long as you know where it is.
  2. Open RStudio
  3. Click on File –> New Project –> Existing Directory then Browse and select your “ENVS396” Folder.
  4. Check that you can see “ENVS396” in the top right corner of RStudio
  • When you are taking notes in class, working on homework assignments, etc., ALWAYS MAKE SURE YOU ARE IN THE CORRECT PROJECT! i.e., check that is says “ENVS396” in top right corner

Worskpace save option: Never

  • Never save your work space image
  • Click on Tools –> Global Options and select the General tab
  • Under the “Save workspace to .Rdata on exit:” option, select Never

Saving scripts

  • Always manually save the script you’re working on by clicking on the floppy disk icon or pressin Ctrl + S on a laptop or Cmd + S on a Mac

Open project

  • Always make sure to open up the project (icon is a little blue box with R inside of it, and file extension is .Rproj) at the beginning of class or when you’re working on it at home
  • If you try to just open up a script, it will open it in “project-none” directory
    • When you save, it will go to whatever default directory is set up
    • In other words, it may be hard to find, and you would then need to copy/paste your updated document back into your project
    • Avoid this by always opening up the project

Organize Project with Subfolders

  • In the “Files” pane, press the New Folder button and create the following folders (make sure spelling/capitalization matches exactly):
    • Scripts
    • Data
    • Assignments
    • Other_Resources

Filenames

  • R doesn’t always do well with spaces in file names
  • avoid potential issues by using “_” or “-“ in file names instead of spaces
  • Don’t use any other special characters like ., ,, @, !

  • Don’t begin a file name with a number

  • Do:
    • “Other_resources”
    • “last-name_homework-1”
    • “data-table-notes”
  • Do NOT:
    • “Other resources”
    • “2nd week home work, lastname”
    • “data-table-notes”

Scripts

  • Take notes and write code live demo’d in class
  • Make a new script by clicking the New File button or using the Ctrl-Shift-N keyboard shortcut (Cmd-Shift-N) on Mac
    • Add the following code to your script:
# my first script
2+2
x = 5
x
  • save your script by clicking on the floppy disk icon or pressing Ctrl + S on a laptop or Cmd + S on a Mac
  • name the file “my-first-script.R’ and make sure to save it in your “Scripts” folder

Data

  • Save all necessary data files here
  • We will be working with lots of data files in this class
    • Most files will be comma-separated-value files or plain text files (.csvor .txt file extensions, respectively)
  • Go to the Datasets section of the website and download the “Portal Surveys csv” file
  • Make sure to save the file in the “Data” folder and that the name is “surveys.csv”
  • Go to the “Files” pane in Rstudio and make sure you can see the surveys.csv file in the Data folder

Assignments

  • Folder to store all of your homework assignment scripts
  • Make a new script in the same way as above
  • Make sure to save it in your “ASsignments” folder and name it accordingly
    • i.e., “Pomeranz_HW1.R”

Other Resources

  • Optional folder
  • Good place to save RStudio cheat sheets and other references
  • Click on Help –> Cheat Sheets –> Data Transformation with dplyr
    • Should automatically prompt you to save the file
    • Make sure to save it in your “Other_resources” folder