Useful Links

The following links will be useful during the workshop:

• Please complete the pre-workshop survey if you haven't already.
• Here is a link to the R lesson material
• Here is a link to the git lesson material
• Here are two datasets (raw) and (normalized) that we will use in the R section. Right click to save as and save in the altmetrics/data folder.
• Please complete the post-workshop survey after the workshop is complete.
• R code from first day: swc_bsd_day1_7_24_17.zip
• R code for debugging: loops.R

Registration

Registration is required and is limited to those affiliated with the Biological Sciences Division. Please register at 2017-07-24-chicago.eventbrite.com

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General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop is aimed at intermediate programmers that know the basics of R and want to learn more. It is ideal for past attendees of our novice Software Carpentry workshops (e.g. 2014), incoming graduate students that attended the MBL bootcamp, and graduate students or postdocs that currently use R for their research.

Coffee and lunch will be provided both days.

This workshop will cover material similar to last year's workshop.

Who: The course is limited to graduate students and other researchers in the Biological Sciences Division at the University of Chicago.

Prerequisites: Attendees should be familiar with the basics of navigating a filesystem in a Unix-like shell and writing functions and loops in R. If you are new to programming, you should consider attending our Introduction to R workshop later in the year (we'll cover the same material as last year's workshop)

Where: Stuart 105, 5835 South Greenwood Avenue Chicago, IL 60637. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Funding: This workshop was made possible through the generous sponsorship of the Office of Graduate and Postdoctoral Affairs, the Department of Human Genetics, and the Department of Biochemistry and Molecular Biology. Additional support provided by the University of Chicago Research and Computing Center.

Faculty advisors: Allan Drummond, Matthew Stephens, Mark Abney

Administrators: Lisa Anderson, Candice Lewis

Contact: Please mail abiddanda@uchicago.edu for more information.

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Schedule

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Syllabus

Review of the Unix shell and R programming

We will start with a refresher on the Unix shell and R programming. Specifically, we will quickly review how to manage files with the Unix shell and write loops and functions in R. This will ensure that everyone is reminded of the relevant syntax needed for the rest of the workshop.

Writing reproducible reports

We will introduce the concept of literate programming, in which code, plots, and text are combined into one document. This makes it easier to organize a research project and share the results. Specifically, we will use knitr/rmarkdown/pandoc to convert R code into html, pdf, and Word documents.

Exploring and visualizing data

We will teach how to subset, summarize, and clean a data set using the R package dplyr. Furthermore, we will demonstrate how to visualize multivariate data using the popular graphics package ggplot2.

Tracking code development

We will cover how to track code development using the version control software Git. This facilitates both experimenting with new ideas and the ability to reproduce past results with a specific version of the code. Furthermore, we will teach how to share their code online and collaborate using the website GitHub.

Debugging, defensive programming, and automated testing

We will cover multiple aspects of ensuring that code is working correctly. This will include how to debug functions, programming defensively by including assertion statements to check code behavior, and writing tests that can be run automatically.

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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.

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