University of Mpumalanga,Mbombela Campus, Building 4

Oct 22-23, 2019

8:30am-16:30pm

Instructors: Zine Sapula, Dr Caroline Ajilogba, Isak Van der Walt

Helpers: Mafuza Maya, Sinazo Matyila, Zizipho Madibi

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers 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.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: , Building 4, Rm 103/104,Cnr R40 and D725 Roads, Nelspruit, 1200. Get directions with OpenStreetMap or Google Maps.

When: Oct 22-23, 2019. Add to your Google Calendar.

Requirements: 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).

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.

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

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. 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 them.

Contact: Please email zine.sapula@ump.ac.za for more information.

REGISTRATION: Please complete the registration form available at https://forms.gle/GxyYQv7KB1qXVi817. Only 30 spaces are available.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1

08:00 -08:30 Morning Coffee/Tea
08:30-09:30 Installation of software
Data organization in spreadsheets
10:00-10:15 Introduction
10:15-11:00 Formatting data tables in Spreadsheets
11:00-11:20 Formatting problems
11:20-11:40 Tea Break
11:40-11:50 Dates as data
11:50-12:00 Quality control
12:00-12:15 Exporting data
12:15-13:00 Lunch Break
OpenRefine for data cleaning
13:00-13:10 Introduction
13:10-13:55 Working with OpenRefine
13:55-14:15 Filtering and Sorting with OpenRefine
14:15-14:35 Examining Numbers in OpenRefine
14:35-14:50 Scripts from OpenRefine
14:50:15:10 Exporting and Saving Data from OpenRefine
15:10-15:30 Other Resources in OpenRefine
15:30-16:00 Introduction to R

Day 2

08:00-08:30 Morning Coffee/Tea
08:30-10:00Starting with data in R
10:00-12:15Manipulating and analyzing data with dplyr; Exporting data
12:15-13:00 Lunch Break
13:00-14:30Data visualization with ggplot2
14:30-16:00databases and R

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


Syllabus


Setup

To participate in a Data 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.

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.

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.

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.

Download software from http://openrefine.org/

Create a new directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...".

Go to your newly created OpenRefine directory.

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).

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.

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.

Download software from http://openrefine.org/.

Create a new directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory by double-clicking it.

Go to your newly created OpenRefine directory.

Launch OpenRefine by dragging the icon into the Applications folder.

Use Ctrl-click/Open ... to launch it.

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.

Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser.

Download software from http://openrefine.org/.

Make a directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory.

Go to your newly created OpenRefine directory.

Launch OpenRefine by entering ./refine into the terminal within the OpenRefine directory.

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.