1. What is R?
2. Install Git
3. Installing and using R and RStudio

Short URL: bit.ly/biostats218

This is the GitHub repository for Biol/Math 218 Instructor: Matthew Lundquist, Ph.D.

If you are new to GitHub, you should check out this blog post by Lauren Orsini. However, you only need to know how to download content from the repo using RStudio (so keep reading!).

We will utilize the built-in capabilities of RStudio to interface directly with this GitHub repository using the git version control software.

All lessons, examples, and assignments will be under labeled sub-directories in the repository. For each folder, there will be a .rmd file with all the information you need as well as any data or supplementary material.

R is a statical software environment for the analysis of data and the production of graphics (R-project.org). Using R can be daunting for the uninitiated because it is entirely command-line based. However, this is the greatest strength that R has because it is extremely flexible, customizable, and (for most things) fast. R is also free and open-source, meaning that there are a lot of people out there that maintain the project and write specific statistical packages. There are plenty of other programs (SAS, SPSS, MATLAB, Excel) that you can use to do data analysis but they are expensive and less customizable. There are other software environments out there too (Python, Julia) for those who need a little more speed and flexibility. R brings to the table some very powerful analysis and graphics production tools in a package that is pretty easy to use, once you get the hang of it. It is an attractive program for students and professionals alike and is continuing to grow in interest and complexity. Skills in data analysis with R is now becoming a must for many looking for graduate or professional positions and is a great addition to a resumé.

Tutorial Videos

Whether you are using MacOS, Windows, or Linux, you will need to download Git.

MacOS:

Download Git for MacOS and just follow the prompts.

Windows:

Download Git for Windows and follow the prompts. The default settings should work fine.

Ubuntu:

Open Terminal and type:

sudo apt-get update
sudo apt-get install git

That's it, now you have Git!

These are the instructions for Linux, but they should be similar to what you need to do in Windows or MacOS

CLICK ON IMAGES FOR LARGER VERSIONS

1. Download latest version of R from cran.r-project.org
2. Download the latest version of RStudio from www.RStudio.org
3. Open RStudio.app (or your RStudio Server instance on campus Link)
4. Navigate to File > New Project...
5. Choose Version Control
6. Choose Git
7. Set Repository URL: https://github.com/lundquist-ecology-lab/biostats and set the Project directory name: biostatistics and set the project subdirectory as ~/Documents/biostatistics (or whatever directory you want to use) then select Create Project
8. At this point RStudio should download everything from this GitHub repository into your project directory (bottom right).
9. You can now navigate folders directly in RStudio. For example: Open porfolios and it will open the portfolios folder
10. You can also open .r and .rmd files, including the portfolios and other assignments. RStudio will open an Editor window on the Top Left panel
11. These files can be edited, tested with the -> Run command and saved within your project directory
12. Once you are done editing and testing your portfolios, the .Rmd files can be uploaded to Brightspace.

When in doubt, you can also get the files off of GitHub by downloading them manually. To do this:

1. Click on the folder that contains the file you are interested in.
2. Click on the file you are interested in downloading.
3. On the top right corner you will see a button that reads Raw.
4. Right click on Raw and select "Save Linked File"
5. Depending on your browser, it will either download automatically or you can choose where to download it on to your machine.
6. You should now be able to read and edit the file.