Data Carpentry with R

Smithsonian Institution

Online

October 18/19 and 25/26, 2022

1 PM ET to 4 PM ET

Instructors: Mike Trizna, Luis Villanueva, Richie Hodel, Matt Kweskin

Helpers: Jen Hammock, Michael O'Mahoney

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers and others who create, manage, and use data who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

The Smithsonian Institution has been a member organization of the Carpentries organization since 2017, and a Platinum Member since 2021. Smithsonian Carpentries workshops are taught by a volunteer team of Smithsonian staff and fellows who have all been trained and certified by the Carpentries organization in the principles of effective teaching of computational skills. You can learn about the Smithsonian Carpentries organization at our website: https://datascience.si.edu/carpentries

Who: The course is aimed at Smithsonian researchers and others who create, manage, and use data. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: October 18/19 and 25/26, 2022, from 1 PM ET to 4 PM ET each day.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email carpentries@si.edu for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Registration

We encourage learners to sign up for all 3 lessons (GitHub, OpenRefine, and R), but we are splitting up registration so that learners can sign up for the lessons that fit into their busy schedules.

Registration for all 3 lessons will open to the Smithsonian community on Tuesday, October 11, at 10AM. Here is an Outlook calendar invite to remind you of that date and time: registration_reminder.ics





Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Detailed schedule coming soon!

Day 1 (Tuesday, October 18)

Day 2 (Wednesday, October 19)

Day 3 (Tuesday, October 25)

Day 4 (Wednesday, October 26)

Setup

To participate in a Data Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

GitHub

For this lesson you will need a GitHub account and GitHub Desktop installed on your machine.

To sign up for a GitHub account:

  1. Go to https://github.com/signup and enter your email address (preferably your @si.edu or @cfa.harvard.edu address), choose a secure password, and then choose a username.
  2. Complete the "puzzle" to prove you are not a robot, click Create Account, and then confirm your email address with the code provided.
  1. Open Software Center, click on GitHub Desktop, and then click Install.
  2. Check the Desktop for a GitHub Desktop icon. If it is not there, you may need to restart your computer.
  3. Open GitHub Desktop, click on File > Options, and then click the Sign In button on the Accounts tab. This will direct you to a browser, where you will sign in to the account you created previously.
  1. Open the Self Service app, click on the Scientific category, and then click Install under the GitHub Desktop icon.
  2. Check the Desktop for a GitHub Desktop icon. If it is not there, you may need to restart your computer.
  3. Open GitHub Desktop, in the top menu click on GitHub Desktop > Preferences, and then click the Sign In button on the Accounts tab. This will direct you to a browser, where you will sign in to the account you created previously.
  1. Go to https://desktop.github.com/ and click on the big Download for Windows button.
  2. Follow the prompts to install the software.
  3. Open GitHub Desktop, click on File > Options, and then click the Sign In button on the Accounts tab. This will direct you to a browser, where you will sign in to the account you created previously.
  1. Go to https://desktop.github.com/ and click on the big Download for macOS button.
  2. Follow the prompts to install the software.
  3. Open GitHub Desktop, in the top menu click on GitHub Desktop > Preferences, and then click the Sign In button on the Accounts tab. This will direct you to a browser, where you will sign in to the account you created previously.

OpenRefine

For this lesson you will need OpenRefine and a web browser. Note: this is a Java program that runs on your machine (not in the cloud). It runs inside a web browser, but no web connection is needed.

  1. Open Software Center, click on OpenRefine, and then click Install.
  2. Check the Desktop for an OpenRefine icon. If it is not there, you may need to restart your computer.
  3. If you get a Windows Defender warning about running the software, select 'More Info', then select 'Run Anyway'.
  • Open the Self Service app, click on the Utilities category, and then click Install under the OpenRefine icon.
  • Check the Desktop for an OpenRefine icon. If it is not there, you may need to restart your computer.
    1. Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It will not run correctly in Internet Explorer.
    2. Download software from http://openrefine.org/
    3. Create a new directory called OpenRefine.
    4. Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...".
    5. Go to your newly created OpenRefine directory.
    6. Launch OpenRefine by clicking openrefine.exe (this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser).
    7. If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
    1. Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It may not run correctly in Safari.
    2. Download software from http://openrefine.org/.
    3. Create a new directory called OpenRefine.
    4. Unzip the downloaded file into the OpenRefine directory by double-clicking it.
    5. Go to your newly created OpenRefine directory.
    6. Launch OpenRefine by dragging the icon into the Applications folder.
    7. Use Ctrl-click/Open ... to launch it.
    8. If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
    1. Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser.
    2. Download software from http://openrefine.org/.
    3. Make a directory called OpenRefine.
    4. Unzip the downloaded file into the OpenRefine directory.
    5. Go to your newly created OpenRefine directory.
    6. Launch OpenRefine by entering ./refine into the terminal within the OpenRefine directory.
    7. If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

    If you ran into any difficulty installing OpenRefine on your machine, we have a browser-based back-up solution that will run at this link: Binder

    R

    R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio. R and RStudio are separate downloads and installations. R is the underlying statistical computing environment, but using R alone is no fun. RStudio is a graphical integrated development environment (IDE) that makes using R much easier and more interactive. You need to install R before you install RStudio. After installing both programs, you will need to install some specific R packages within RStudio. Follow the instructions below for your operating system, and then follow the instructions to install tidyverse.

    1. Open Software Center, click on R, and then click Install.
    2. After R is installed via the Software Center, click on the RStudio icon, and install RStudio.
  • Open the Self Service app, click on the Utilities category, and then click Install under the OpenRefine icon.
  • Check the Desktop for an OpenRefine icon. If it is not there, you may need to restart your computer.

    • Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

    Video Tutorial

    If you ran into any difficulty installing R or RStudio on your machine, we have a browser-based back-up solution that will run at this link: Binder