Lund University

13-14 November 2019

09:00 - 17:00

Instructors: Joachim Hein, Hadrien Gourlé, Dmytro Perepolkin

Helpers: Ullrika Sahlin

Introduction to data handling using R tidyverse in a modern software environment

What: The aim of Software Carpentry is to teach researchers the fundamental skills that will help them be more productive while producing work of higher quality. During this two day workshop, students learn how to automate tasks using the Unix shell, how to track and share work using version control in Git, and data management and visualisation in R.

This is not a full Software Carpentry, but an R tidyverse workshop based on Software Carpentry material.

Who: PhD students as well as more senior researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Rooms V:O2, V:S2 and V:P2, V-huset, LTH, John Ericssons väg 1, 223 63 Lund, Sweden. Get directions with OpenStreetMap or Google Maps.

When: 13-14 November 2019. Add to your Google Calendar.

Participants must bring a laptop 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). The laptop needs to be able to access the internet via Eduroam. Internet access via Eduroam needs to be activated at the participant's home institution prior to attending the course. Participants are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide that.

Contact: Please email dmytro.perepolkin@cec.lu.se for more information.

Registration

Registration is open as October the 3rd 2019. Workshop is limited to 35 people.

Sponsors

This workshop is possible thanks to the collaboration of the following entities, which allow us to do this under our working schedule and contribute to the associated costs.

Schedule

Wednesday, 13 November 2019

Room V:O2 (before lunch) and Room V:S2 (after lunch), V-huset, LTH
09:00 Command-line efficiency
11:00 Coffee break
10:45 Understanding command line options
12:30 Lunch break
13:30 Introduction to Git
14:45 Coffee break
15:00 Git commands
16:00 Collaboration via Github
17:00 Wrap-up

Thursday, 14 November 2019

Room V:P2, V-huset, LTH
09:00 Introduction to RStudio and tidyverse
09:30 Elegant data visualisations with ggplot2
11:00 Coffee break
11:15 Elegant data visualisations with ggplot2 (continued)
12:30 Lunch break
13:30 Data manipulation with dplyr
14:45 Coffee break
15:00 Easily arrange data with tidyr
16:00 Pair excercises
17:00 Wrap-up

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

Setup

To participate in a Software Carpentry workshop, you will need access to the software 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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Video Tutorial
  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. Select "Use the nano editor by default" and click on "Next".
    3. Keep "Git from the command line and also from 3rd-party software" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Select "Use the native Windows Secure Channel library", and click "Next".
    6. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    7. Select "Use Windows' default console window" and click on "Next".
    8. Leave all three items selected, and click on "Next".
    9. Do not select the experimental option. Click "Install".
    10. Click on "Finish".
  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.

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

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 the Git lesson. Basic GitHub accounts are free. We encourage you to 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.

Git should be installed on your computer as part of your Bash install (described above).

Video Tutorial

For OS X 10.9 and higher, 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.

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.

R

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

Video Tutorial

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.

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.