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Installation
These are notes on installation for the various tools and packages we'll use throughout the course.
Before you arrive, you should install three things: a command-line terminal, R, and RStudio.
If you are bringing a Mac or Linux computer to work on, this is already taken care of for you. If you are bringing a Windows computer, you will need to set up a working command-line environment.
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If your operating system is Windows 10 or later, the operating system includes a way to run a command-line environment. You can follow the helpful steps outlined here to get set up.
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If you have an older Windows operating system, you can set up a command-line working environment relatively easily through Git for Windows by following these steps.
- Download the "Git-2.18.0-32-bit.exe" file from the Git for Windows download page
- After it is finished downloading, run the installer by opening the file and proceed through the installation:
- installing in the default folder location is fine
- for "Which components should be installed?", make sure the following boxes are checked: "On the Desktop"; "Git Bash Here"; "Git GUI Here"; "Associate .git* configuration files with the default text editor"; and "Associate .sh files to be run with Bash"
- the shortcuts default location is fine
- change the default Git editor to "Nano"
- on the "Adjusting your PATH environment" screen, select "Use Git from Git Bash only"
- just click "Next" on the remaining configuration windows, and "Install" at the final one
- When the installation is finished, you should be able to open a terminal window by launching Git Bash from your desktop.
R is a programming language that is extremely useful for statistical analysis and generating figures. Follow the instructions at the following pages to download and install the appropriate version for your operating system:
Mac – https://cran.r-project.org/bin/macosx/ (download the latest release "R-3.5.1.pkg")
Windows – https://cran.r-project.org/bin/windows/base/
Linux – https://cran.r-project.org/bin/linux/
Rstudio is an interface for R that not only makes everything you will do in R easier and more organized, but it’s also invaluable for reproducibility of your analyses as it makes it second-nature to generate and save log files (R scripts) of everything you’re doing.
Download and install the appropriate version of RStudio for your system from here: https://www.rstudio.com/products/rstudio/download/#download
On your badge, you have a username and password. That will be your account for the course.
To connect, we'll use ssh. At the command line type
ssh class.mbl.edu
When prompted type in your login username and password.
The first time you log in you will get a message about security. Say 'yes'.
This will take you to a prompt. This is called the 'gateway'. We won't work here. On your badge you have something that says e.g. 'class-03'. That's where you'll be working for the course, so we don't overload the computing resources. Type:
ssh class-0* where * is whatever number you have
Now you're at the command linee prompt that you'll use for much of the course.