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---
layout: workshop # DON'T CHANGE THIS.
root: . # DON'T CHANGE THIS EITHER. (THANK YOU.)
carpentry: "swc" # what kind of Carpentry (must be either "lc" or "dc" or "swc")
venue: "University of Chicago" # brief name of host site without address (e.g., "Euphoric State University")
address: "CLSC, 119 E 57th St, Chicago, IL 60637" # full street address of workshop (e.g., "Room A, 123 Forth Street, Blimingen, Euphoria")
country: "us" # lowercase two-letter ISO country code such as "fr" (see https://en.wikipedia.org/wiki/ISO_3166-1)
language: "en" # lowercase two-letter ISO language code such as "fr" (see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "41.791836,-87.602679" # decimal latitude and longitude of workshop venue (e.g., "41.7901128,-87.6007318" - use http://www.latlong.net/)
humandate: "January 12-13, 2019" # human-readable dates for the workshop (e.g., "Feb 17-18, 2020")
humantime: "8:00 am - 4:30 pm" # human-readable times for the workshop (e.g., "9:00 am - 4:30 pm")
startdate: 2019-01-20 # machine-readable start date for the workshop in YYYY-MM-DD format like 2015-01-01
enddate: 2019-01-21 # machine-readable end date for the workshop in YYYY-MM-DD format like 2015-01-02
instructor: ["Nick Knoblauch", "Arjun Biddanda", "Briana Mittleman", "Angela Li"] # boxed, comma-separated list of instructors' names as strings, like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Peter Carbonetto", "Maryn Carlson", "Ankeeta Shah", "Zach Miller", "Rahul Subramanian" ] # boxed, comma-separated list of helpers' names, like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: ["[email protected]", "[email protected]"] # boxed, comma-separated list of contact email addresses for the host, lead instructor, or whoever else is handling questions, like ["[email protected]", "[email protected]", "[email protected]"]
collaborative_notes: # optional: URL for the workshop collaborative notes, e.g. an Etherpad or Google Docs document
eventbrite: # optional: alphanumeric key for Eventbrite registration, e.g., "1234567890AB" (if Eventbrite is being used)
---
<!DOCTYPE html>
<html>
<head>
<meta charset='utf-8'>
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
<link href='https://fonts.googleapis.com/css?family=Architects+Daughter' rel='stylesheet' type='text/css'>
<link rel="stylesheet" type="text/css" href="stylesheets/stylesheet.css" media="screen">
<link rel="stylesheet" type="text/css" href="stylesheets/github-light.css" media="screen">
<link rel="stylesheet" type="text/css" href="stylesheets/print.css" media="print">
<link rel="stylesheet" type="text/css" href="/stylesheets/bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/stylesheets/bootstrap-theme.css" />
<!-- <link rel="stylesheet" type="text/css" href="/stylesheetsassets/lesson.css" /> -->
<title>2019-01-12-chicago</title>
</head>
<body>
<header>
<div class="inner">
<h1>Software Carpentry</h1>
<h2>An intermediate programming workshop for UChicago BSD researchers</h2>
<h2>Saturday-Sunday, January 12-13, 2019</h2>
</div>
</header>
<div id="content-wrapper">
<div class="inner clearfix">
<section id="main-content">
<ul>
<li><a href="#registration">Registration</a></li>
<li><a href="#links">Useful links</a></li>
<li><a href="#general">General Information</a></li>
<li><a href="#schedule">Schedule</a></li>
<li><a href="#syllabus">Syllabus</a></li>
<li><a href="#setup">Setup</a></li>
<li><a href="#acknowledgments">Acknowledgments</a></li>
</ul>
<h2 id ="registration">Registration</h2>
<p>
Registration is required and is limited to those affiliated with the
Biological Sciences Division. <br>
Please register at <a href="https://2019-01-12-chicago.eventbrite.com">2019-01-12-chicago.eventbrite.com</a>
</p>
<hr/>
<h2 id ="links">Useful links</h2>
<ul>
<!-- <li>Please complete <b>both</b> of the pre-workshop surveys. Your responses -->
<!-- are critical for us to improve our teaching and to request funding for future -->
<!-- workshops. -->
<!-- <ul> -->
<!-- <li> -->
<!-- <a href="https://goo.gl/forms/EZYgOH6zZ76x1YW83", target="_blank">UChicago post-workshop survey</a> -->
<!-- </li> -->
<!-- <li> -->
<!-- <a href="https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id=2019-01-12-chicago", target="_blank">Software Carpentry post-workshop survey</a> -->
<!-- </li> -->
<!-- </ul> -->
<!-- </li> -->
<!-- <li>The UChicago pre-workshop survey is closed.</li> -->
<!-- <li>The Software Carpentry pre-workshop survey is closed.</li> -->
<!--TODO : need to update these survey links-->
<!--<li>Please complete-->
<!--the <a href="https://goo.gl/forms/x1MDvB0B9jp1w3et1", target="_blank"> pre-workshop survey</a>.</li>-->
<li>The UChicago pre-workshop survey is closed.</li>
<li> Please complete the <a href="https://goo.gl/forms/NjAXl5MXEiss20Hd2", target="_blank"> post-workshop survey</a> </li>
<!--<li> Please complete the <a href="https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id=2019-01-12-chicago", target="_blank">Software Carpentry pre-workshop survey</a></li>-->
<!-- <li>R script <a href="session-01.R">session-01.R</a> from first session.</li> -->
<!-- <li>R script <a href="session-02.R">session-02.R</a> from second session.</li> -->
<!-- <li>R script <a href="session-03.R">session-03.R</a> from second session.</li> -->
<!-- <li>R script <a href="session-04.R">session-04.R</a> from second session.</li> -->
<!-- <li>Download this <a href="http://swcarpentry.github.io/r-novice-inflammation/files/r-novice-inflammation-data.zip">zip file</a> and save it in the folder "workshop" on your Desktop.</li> -->
<!--<li><a href="https://education.github.com/pack", target="_blank"> Click here to sign up for the Github Student Developer Pack</a></li>-->
<!-- <li>Click <a href="exercises.html">here</a> for the exercises.</li> -->
<!--<li><a href="https://github.com/CreRecombinase/intro-r-project-2019", target="_blank"> Github repo for the workshop</a></li>-->
</ul>
<h2 id="general">General Information</h2>
<p>
<!-- This interactive workshop will cover the basics of R, the Unix shell,-->
<!--and version control.-->
<!--<a href="http://www.r-project.org">R</a> is a computing environment-->
<!--that is especially powerful for data exploration, visualization, and-->
<!--statistical analysis.-->
This interactive workshop is for learners that are comfortable programming in R and want to learn some of R's powerful tools for analyzing and visualizing data. We will begin with a brief overview of R and the Unix Shell, and cover topics such as developing reproduceable reports in R Markdown, defensive programming, and data visualization in ggplot2.
</p>
<p>
<u>Coffee and lunch will be provided.</u>
</p>
<p>
<strong>When:</strong> 8:00 am - 4:30 pm, Saturday-Sunday (January 12-13), 2019
</p>
<p>
<strong>Who:</strong> The course is limited to graduate students and
other researchers in the Biological Sciences Division at the
University of Chicago.
</p>
<p>
<strong>Prerequisites:</strong>
Attendees are expected to have some previous programming experience.
</p>
<p>
<strong>Where:</strong>
CLSC 119, 924 E 57th St, Chicago, IL 60637.
Get directions with
<a href="//www.openstreetmap.org/?mlat=41.791836&mlon=-87.602679}}&zoom=16">OpenStreetMap</a>
or
<a href="//maps.google.com/maps?q=41.791836, -87.602679">Google Maps</a>.
</p>
<p id="requirements">
<strong>Requirements:</strong> 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
<a href="#setup">below</a>).
</p>
<p>
<strong>Instructors:</strong>
Arjun Biddanda, Nicholas Knoblauch, Briana Mittleman, Angela Li
</p>
<p>
<!-- <strong>Helpers:</strong>
Peter Carbonetto, Gao Wang, John Blischak, Sahar Mozaffari, Briana Mittleman, Yeonwoo Park, Maryn Carlson
</p>
-->
<p>
<strong>Faculty advisor:</strong>
Allan Drummond
</p>
<p>
<strong>Administrator:</strong>
Sue Levison
</p>
<p>
<strong>Funding:</strong> This workshop was made possible through
the generous sponsorship of
the <a href="http://gradprograms.bsd.uchicago.edu/our_office.html">Office
of Graduate and Postdoctoral Affairs</a>,
the <a href="http://genes.uchicago.edu/">Department of Human
Genetics</a>, and
the <a href="http://bmb.uchospitals.edu/">Department of Biochemistry
and Molecular Biology</a>.
</p>
<p>
<strong>Contact</strong>:
Please mail
<a href='mailto:[email protected]'>[email protected]</a> or
<a href='mailto:[email protected]'>[email protected]</a>
for more information.
</p>
<hr/>
<!--TODO : this schedule will need to change to more accurately reflect what we are teaching -->
<h2 id="schedule">Schedule</h2>
<h3>January 12</h3>
<table class="table table-striped">
<tr><td class="alignleft">08:00 am - 08:30 am - <a href="#setup">Installation help</a></td></tr>
<tr><td class="alignleft">08:30 am - 10:00 am - <a href="https://crerecombinase.github.io/r-intermediate-altmetrics/index.html#topics"> Review of Unix shell and R</a> </td></tr>
<tr><td class="alignleft">10:00 am - 10:30 am - Coffee break</td></tr>
<tr><td class="alignleft">10:30 am - 12:00 pm - <a href="https://crerecombinase.github.io/r-intermediate-altmetrics/index.html#topics">Writing reproducible reports</a></td></tr>
<tr><td class="alignleft" >12:00 pm - 01:00 pm - Lunch</td></tr>
<tr><td class="alignleft">01:00 pm - 02:30 pm - <a href="https://crerecombinase.github.io/r-intermediate-altmetrics/index.html#topics">Debugging</a></td></tr>
<tr><td class="alignleft">02:30 pm - 03:00 pm - Coffee break</td></tr>
<tr><td class="alignleft">03:00 pm - 04:30 pm - <a href="https://crerecombinase.github.io/r-intermediate-altmetrics/index.html#topics">Defensive programming</a></td></tr>
</table>
<h3>January 13</h3>
<table class="table table-striped">
<tr><td class="alignleft" >08:00 am - 08:30 am - <a href="#setup">Installation help</a></td></tr>
<tr><td class="alignleft">08:30 pm - 10:00 pm - <a href="https://crerecombinase.github.io/r-intermediate-altmetrics/index.html#topics"> Analyzing data with dplyr</a></td></tr>
<tr><td class="alignleft">10:00 pm - 10:30 pm - Coffee break</td></tr>
<tr><td class="alignleft">10:30 pm - 12:00 pm - <a href="https://crerecombinase.github.io/r-intermediate-altmetrics/index.html#topics"> Visualizing data with ggplot2</a></td></tr>
<tr><td class="alignleft" >12:00 pm - 01:00 pm - Lunch</td></tr>
<tr><td class="alignleft">01:00 am - 02:30 pm - <a href="https://crerecombinase.github.io/git-lessons/index.html#topics">Version control with Git</a></td></tr>
<tr><td class="alignleft">02:30 pm - 03:00 pm - Coffee break</td></tr>
<tr><td class="alignleft">03:00 pm - 04:30 pm - <a href="https://crerecombinase.github.io/git-lessons/index.html#topics">Version control with Git</a></td></tr>
</table>
<hr/>
<h2 id="syllabus">Syllabus</h2>
<h3>Review of the Unix shell and R programming</h3>
<p>
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.
</p>
<h3>Writing reproducible reports</h3>
<p>
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.
</p>
<h3>Exploring and visualizing data</h3>
<p>
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.
</p>
<h3>Tracking code development</h3>
<p>
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.
</p>
<h3>Debugging, defensive programming, and automated testing</h3>
<p>
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.
<p>
<hr/>
<!--
SETUP
Delete irrelevant sections from the setup instructions. Each
section is inside a 'div' without any classes to make the beginning
and end easier to find.
This is the other place where people frequently make mistakes, so
please preview your site before committing, and make sure to run
'tools/check' as well.
-->
<h2 id="setup">Setup</h2>
<p>
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.
</p>
<p>
We maintain a list of common issues that occur during installation as a reference for instructors
that may be useful on the
<a href = "https://github.com/swcarpentry/workshop-template/wiki/Configuration-Problems-and-Solutions">Configuration Problems and Solutions wiki page</a>.
</p>
<div id="shell"> <!-- Start of 'shell' section. -->
<h3>The Bash Shell</h3>
<p>
Bash is a commonly-used shell that gives you the power to do simple
tasks more quickly.
</p>
<div class="row">
<div class="col-md-4">
<h4 id="shell-windows"> Windows </h4>
<a href="https://www.youtube.com/watch?v=339AEqk9c-8">Video Tutorial</a>
<ol>
<li>Download the Git for Windows <a href="https://git-for-windows.github.io/">installer</a>.</li>
<li>Run the installer and follow the steps bellow:
<ol style="font-size:1em">
<!-- Git 2.8.2 Setup -->
<!-- Information -->
<li>Click on "Next".</li>
<!-- Select Components -->
<li>Click on "Next".</li>
<!-- Adjusting your PATH environment -->
<li>
<strong>
Keep "Use Git from the Windows Command Prompt" selected and click on "Next".
</strong>
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.
</li>
<!-- Choosing the SSH executable -->
<li>Click on "Next".</li>
<!-- Configuring the line ending conversions -->
<li>
<strong>
Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
</strong>
</li>
<!-- Configuring the terminal emulator to use with Git Bash -->
<li>
<strong>
Keep "Use Windows' default console window" selected and click on "Next".
</strong>
</li>
<!-- Configuring experimental performance tweaks -->
<li>Click on "Install".</li>
<!-- Installing -->
<!-- Completing the Git Setup Wizard -->
<li>Click on "Finish".</li>
</ol>
</li>
<li>
If your "HOME" environment variable is not set (or you don't know what this is):
<ol>
<li> Open command prompt (Open Start Menu then type <code>cmd</code> and press [Enter])</li>
<li>
Type the following line into the command prompt window exactly as shown:
<p><code>setx HOME "%USERPROFILE%"</code></p>
</li>
<li> Press [Enter], you should see <code>SUCCESS: Specified value was saved. </code></li>
<li> Quit command prompt by typing <code>exit</code> then pressing [Enter] </li>
</ol>
</li>
</ol>
<p>This will provide you with both Git and Bash in the Git Bash program.</p>
</div>
<div class="col-md-4">
<h4 id="shell-macosx">Mac OS X</h4>
<p>
The default shell in all versions of Mac OS X is Bash, so no
need to install anything. You access Bash from the Terminal
(found in
<code>/Applications/Utilities</code>).
See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
for an example on how to open the Terminal.
You may want to keep
Terminal in your dock for this workshop.
</p>
</div>
<div class="col-md-4">
<h4 id="shell-linux">Linux</h4>
<p>
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing <code>bash</code>. There is no need to
install anything.
</p>
</div>
</div>
</div> <!-- End of 'shell' section. -->
<div id="git"> <!-- Start of 'Git' section. GitHub browser compatability
is given at https://help.github.com/articles/supported-browsers/-->
<h3>Git</h3>
<p>
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 <a href="https://github.com/">github.com</a>. You will need a
<a href="https://help.github.com/articles/supported-browsers/">supported</a>
web browser (current versions of Chrome, Firefox or Safari,
or Internet Explorer version 9 or above).
</p>
<p>
You will need an account at <a href="https://github.com/">github.com</a>
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
<a href="https://help.github.com/articles/keeping-your-email-address-private/">instructions
for keeping your email address private</a> provided at GitHub.
</p>
<div class="row">
<div class="col-md-4">
<h4 id="git-windows">Windows</h4>
<p>
Git should be installed on your computer as part of your Bash
install (described above).
</p>
</div>
<div class="col-md-4">
<h4 id="git-macosx">Mac OS X</h4>
<a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">Video Tutorial</a>
<p>
<strong>For OS X 10.9 and higher</strong>, install Git for Mac
by downloading and running the most recent "mavericks" installer from
<a href="http://sourceforge.net/projects/git-osx-installer/files/">this list</a>.
After installing Git, there will not be anything in your <code>/Applications</code> folder,
as Git is a command line program.
<strong>For older versions of OS X (10.5-10.8)</strong> use the
most recent available installer labelled "snow-leopard"
<a href="http://sourceforge.net/projects/git-osx-installer/files/">available here</a>.
</p>
</div>
<div class="col-md-4">
<h4 id="git-linux">Linux</h4>
<p>
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
<code>sudo apt-get install git</code> and for Fedora run
<code>sudo yum install git</code>.
</p>
</div>
</div>
</div> <!-- End of 'Git' section. -->
<div id="editor"> <!-- Start of 'editor' section. -->
<h3>Text Editor</h3>
<p>
To create small files in this workshop, you will use the basic
text editor nano. It's a much different experience from the text
editor you are likely familiar with for creating documents,
e.g. Microsoft Word, but it is very convenient for writing short
scripts.
</p>
<p>
Warning: The default text editor on Mac OS X and Linux is usually
set to Vim, which is not famous for being intuitive. If you
accidentally find yourself stuck in it, try typing the escape key,
followed by <code>:q!</code> (colon, lower-case 'q', exclamation
mark), then hitting Return to return to the shell.
</p>
<div class="row">
<div class="col-md-4">
<h4 id="editor-windows">Windows</h4>
<a href="https://www.youtube.com/watch?v=339AEqk9c-8">Video Tutorial</a>
<p>
nano is a basic editor and the default that instructors use in the workshop.
To install it,
download the <a href="https://github.com/swcarpentry/windows-installer/releases/download/v0.3/SWCarpentryInstaller.exe">Software Carpentry Windows installer</a>
and double click on the file to run it.
<strong>This installer requires an active internet connection.</strong>
</p>
</div>
<div class="col-md-4">
<h4 id="editor-macosx">Mac OS X</h4>
<p>
nano is a basic editor and the default that instructors use in the workshop.
See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
for an example on how to open nano.
It should be pre-installed.
</p>
</div>
<div class="col-md-4">
<h4 id="editor-linux">Linux</h4>
<p>
nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.
</p>
</div>
</div>
</div> <!-- End of 'editor' section. -->
<div id="r"> <!-- Start of 'R' section. -->
<h3>R</h3>
<p>
<a href="http://www.r-project.org">R</a> is a programming language
that is especially powerful for data exploration, visualization, and
statistical analysis. To interact with R, we use
<a href="http://www.rstudio.com/">RStudio</a>.
</p>
<div class="row">
<div class="col-md-4">
<h4 id="r-windows">Windows</h4>
<a href="https://www.youtube.com/watch?v=q0PjTAylwoU">Video Tutorial</a>
<p>
Install R by downloading and running
<a href="http://cran.r-project.org/bin/windows/base/release.htm">this .exe file</a>
from <a href="http://cran.r-project.org/index.html">CRAN</a>.
Also, please install the
<a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
</p>
</div>
<div class="col-md-4">
<h4 id="r-macosx">Mac OS X</h4>
<a href="https://www.youtube.com/watch?v=5-ly3kyxwEg">Video Tutorial</a>
<p>
Install R by downloading and running
<a href="http://cran.r-project.org/bin/macosx/R-latest.pkg">this .pkg file</a>
from <a href="http://cran.r-project.org/index.html">CRAN</a>.
Also, please install the
<a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
</p>
</div>
<div class="col-md-4">
<h4 id="r-linux">Linux</h4>
<p>
You can download the binary files for your distribution
from <a href="http://cran.r-project.org/index.html">CRAN</a>. Or
you can use your package manager (e.g. for Debian/Ubuntu
run <code>sudo apt-get install r-base</code> and for Fedora run
<code>sudo yum install R</code>). Also, please install the
<a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
</p>
</div>
</div>
</div> <!-- End of 'R' section. -->
<div id="r-packages">
<h3>R packages</h3>
<p>
Please install the following R packages using <code>install.packages</code>:
<ul>
<li> <a href="https://cran.r-project.org/web/packages/tidyverse/index.html">tidyverse</a></li>
<li><a href="https://cran.r-project.org/web/packages/testit/index.html">testit</a></li>
<li><a href="https://cran.r-project.org/web/packages/rmarkdown/index.html">rmarkdown</a></li>
</ul>
</p>
</div>
<h2 id="acknowledgments">Acknowledgments</h2>
<p>
This workshop was made possible by the instructor training and
lesson development created by the Software Carpentry team and of
course our generous sponsors
(<a href="http://gradprograms.bsd.uchicago.edu/our_office.html">OGPA</a>,
<a href="http://genes.uchicago.edu/">HG</a>,
<a href="http://bmb.uchospitals.edu/">BMB</a>).
</p>
<p>
This page was generated by <a href="https://pages.github.com">GitHub
Pages</a> using the Architect theme
by <a href="https://twitter.com/jasonlong">Jason Long</a>.
</p>
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