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InstallationInstructions.md

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Installation Instructions

Installing Python Using Anaconda

Python is great for general-purpose programming and is a popular language for scientific computing as well. Installing all of the packages required for this lessons individually can be a bit difficult, however, so we recommend the all-in-one installer Anaconda.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., Python 3.6 version).

Windows - Video tutorial

  1. Open anaconda.com/download with your web browser.

  2. Download the Python 3 installer for Windows.

  3. Double-click the executable and install Python 3 using MOST of the default settings. The only exception is to check the Make Anaconda the default Python option.

macOS - Video tutorial

  1. Open anaconda.com/download with your web browser.

  2. Download the Python 3 installer for macOS.

  3. Install Python 3 using all of the defaults for installation.

Linux

Note that the following installation steps require you to work from the shell. If you run into any difficulties, please request help before the workshop begins.

  1. Open anaconda.com/download with your web browser.

  2. Download the Python 3 installer for Linux.

  3. Install Python 3 using all of the defaults for installation.

    a. Open a terminal window.

    b. Navigate to the folder where you downloaded the installer

    c. Type

    $ bash Anaconda3-

    {: .bash}

    and press tab. The name of the file you just downloaded should appear.

    d. Press enter.

    e. Follow the text-only prompts. When the license agreement appears (a colon will be present at the bottom of the screen) hold the down arrow until the bottom of the text. Type yes and press enter to approve the license. Press enter again to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

Starting Python

We will teach Python using Jupiter Notebook. If you installed Python using Anaconda, Jupyter Notebook should already be on your system. If you did not use Anaconda, use the Python package manager pip (see the Jupyter website for details.)

To start Jupyter Notebook Open the Anaconda Navigator and Launch Jupyter Notebook

Install R and RStudio

R and RStudio are two separate pieces of software:

  • R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis
  • RStudio is an integrated development environment (IDE) that makes using R easier. In this course we use RStudio to interact with R.

If you don't already have R and RStudio installed, follow the instructions for your operating system below. You have to install R before you install RStudio.

Windows

  • Download R from the CRAN website.
  • Run the .exe file that was just downloaded
  • Go to the RStudio download page
  • Under Installers select RStudio x.yy.zzz - Windows Vista/7/8/10 (where x, y, and z represent version numbers)
  • Double click the file to install it
  • Once it's installed, open RStudio to make sure it works and you don't get any error messages.

MacOS

  • Download R from the CRAN website.
  • Select the .pkg file for the latest R version
  • Double click on the downloaded file to install R
  • It is also a good idea to install XQuartz (needed by some packages)
  • Go to the RStudio download page
  • Under Installers select RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit) (where x, y, and z represent version numbers)
  • Double click the file to install RStudio
  • Once it's installed, open RStudio to make sure it works and you don't get any error messages.

Linux

  • Follow the instructions for your distribution from CRAN, they provide information to get the most recent version of R for common distributions. For most distributions, you could use your package manager (e.g., for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora sudo yum install R), but we don't recommend this approach as the versions provided by this are usually out of date. In any case, make sure you have at least R 3.3.1.
  • Go to the RStudio download page
  • Under Installers select the version that matches your distribution, and install it with your preferred method (e.g., with Debian/Ubuntu sudo dpkg -i rstudio-x.yy.zzz-amd64.deb at the terminal).
  • Once it's installed, open RStudio to make sure it works and you don't get any error messages.

Update R and RStudio

If you already have R and RStudio installed, check if your R and RStudio are up to date:

  • When you open RStudio your R version will be printed in the console on the bottom left. Alternatively, you can type sessionInfo() into the console. If your R version is 4.0.0 or later, you don't need to update R for this lesson. If your version of R is older than that, download and install the latest version of R from the R project website for Windows, for MacOS, or for Linux
  • To update RStudio to the latest version, open RStudio and click on Help > Check for updates. If a new version is available, quit RStudio, follow the instruction on screen.

Note: It is not necessary to remove old versions of R from your system, but if you wish to do so you can check here.

Credits