Data Carpentry Zurich

August 19 - 22, 2015 · Faido Instructors: Karthik Ram, François Michonneau, Matthias Haeni.
Organizers: Frank Pennekamp, Philippe Saner, Owen Petchey

1. Introduction
2. Workshop schedule
3. Installation instructions
4. Useful links

Data Carpentry workshops are for any researcher who has data they want to analyze , and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.

The focus of this workshop will be on working with ecological data and data management and analysis for ecological research. We will cover metadata organization in spreadsheets, the command line, version control with Git, and R for data analysis and visualization. We will teaching foundational skills that will allow you to conduct any analysis and analyze the output of your research pipeline.

Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.

Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain.

Updates will be posted to this website as they become available.

Workshop Schedule

All morning/afternoon sessions include a 30 minute coffee break.

Time Topic
Wednesday 9-12
Spreadsheet basics
Introduction to R
(1, 2, 3, 4)
Wednesday 1-5
R (continued)
Manipulating data with dplyr
Introduction to data vizualization

Thursday 9-12 Introduction to SQL
Using SQL from R
Shell basics
Thursday 1-5 Interacting with APIs from R
Introduction to knitr (Rmarkdown file template)

Friday 9-12 Introduction to version control with Git
Friday afternoon
(open to ad-hoc topics)

Installation Instructions (all participants)


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 that makes using R much easier. You need R installed before you install RStudio.

1. Install R
You’ll need R version 3.2.0 or higher. Download and install R for Windows or Mac OS X (download the latest R-3.x.x.pkg file for your appropriate version of OS X).

2. Install RStudio Download and install the latest stable version of RStudio Desktop.

3. Install R packages Launch RStudio (RStudio, not R itself). Ensure that you have internet access, then enter the following commands into the Console panel (usually the lower-left panel, by default). Note that these commands are case-sensitive. At any point, R may ask you if you want to update any old packages by asking Update all/some/none? [a/s/n]:. If you see this, type a at the prompt and hit Enter to update any old packages. If you are using a Windows machine you might get some errors about not having permission to modify the existing libraries – don’t worry about this message. You can avoid this error altogether by running RStudio as an administrator.

Also be sure to install a few packages if you don't have them already.

             # Install the following packages with

4. Download a text editor. We will likely edit plain text files outside of RStudio. To do this, let’s use a better alternative to the built-in Notepad (Windows) or TextEdit (Mac).
Download and install Sublime Text (works on all platforms, with an unlimited free trial). There will be additional packages to install during the workshop.


For this workshop we're going to use the Firefox SQLite Plugin. It works through the web browser Firefox. If you don't already have Firefox installed install Firefox:

• Start Firefox
• Go to the plugin homepage.
• Click the "Add Now" button.
• Click "Install Now" on the dialog that appears after the download completes.
• Restart Firefox when prompted.
• Select "SQLite Manager" from the "Tools" menu and it will open within Firefox

Shell Instructions (Windows users only)


Linux and OSX users are already have a built in shell. You're all set Install git-bash. Download and run the installer. This will install a command line on a Windows machine.

Install the Software Carpentry Installer. After installing git-bash, download and install the software carpentry installer.

If you have trouble installing software, please speak with any of the instructors or helpers upon your arrival in Faido.

Useful links

Github repository for workshop
Etherpad for notes