Open Science Workflow with RStudio

University of Kansas

Online

April 27, 2022

12:00 - 4:00 pm CDT (UTC-5)

Instructors: Samantha Thomas, Sam Zipper, PhD, Nate Jones, PhD

Helpers: Jamene Brooks-Kieffer, Paul Trana, Chris Wheeler, Caroline Kisielinski, Elizabeth Everman, Terry Loecke, Rob Ramos

General Information

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of open science workflows to attend this workshop. However, you do need to have some knowledge of R. This workshop assumes that you are able to:

If you’re unsure whether you have enough experience to participate in this workshop, please review sections 1-3 of this introductory R lesson material. If most of these concepts are familiar to you, you should be able to participate fully in this 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: April 27, 2022. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. 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 jamenebk@ku.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.

Collaborative Notes

We will use this collaborative document, called an Etherpad, 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

Wednesday, April 27, 2021

Before Pre-workshop survey
12:00 - 12:10 pm Introductions and hellos
12:10 - 1:00 pm Intro to Markdown and Read Me documentation; create a GitHub repository and build a Markdown cheatsheet
1:00 - 1:45 pm Bring an existing GitHub repository into RStudio; create an RMarkdown document
1:45 - 2:00 pm Break
2:00 - 2:40 pm Download, quality check, and report on streamflow data using RMarkdown
2:40 - 3:55 pm Revise report and share results via GitHub; if time, create dygraphs
3:55 pm Wrap-up
4:00 pm Post-workshop Survey

Setup

To participate in this 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.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

In this workshop we will use some specific R packages, including rmarkdown, knitr, dataRetrieval, dplyr, zoo, lubridate, ggplot2, and dygraphs. If you have these packages installed, please make sure they are updated before the workshop. If you need to install these packages and need assistance, please contact the organizers.

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

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at <https://cran.r-project.org/bin/linux/>. These will instruct you to use your package manager (e.g. for Fedora run sudo dnf install R and for Debian/Ubuntu, add a ppa repository and then run sudo apt-get install r-base). Also, please install the RStudio IDE.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of this workshop. Basic GitHub accounts are free. Please create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
    3. On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
    4. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    5. Select "Use bundled OpenSSH".
    6. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    7. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    8. Ensure that "Use Windows' default console window" is selected and click on "Next".
    9. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    10. Ensure that "Git Credential Manager" is selected and click on "Next".
    11. Ensure that "Enable file system caching" is selected and click on "Next".
    12. Click on "Install".
    13. Click on "Finish" or "Next".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press Enter)
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press Enter, you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing Enter

This will provide you with both Git and Bash in the Git Bash program.

Video Tutorial

For macOS, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Video Tutorial

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.