index.html

---
layout: workshop 
root: .
venue: University of Melbourne
address1: Room 5.71, Melbourne Brain Centre, Royal Parade, University of Melbourne, Parkville
address2: Room G-10, Old Quad, University of Melbourne, Parkville
country: Australia
language: en
latlng: -37.798305, 144.958370
humandate: March 24 and 27, 2017
humantime: 9:00 am - 5:00 pm
startdate: 2017-03-24
enddate: 2017-03-27
instructor: ["Brendan Ansell"]
helper: ["Michael Silk", "Thomas Teoh"]
contact: nicole.unimelb@gmail.com
contact2: 
etherpad: https://public.etherpad-mozilla.org/p/Intro_to_R_March24
eventbrite: 40127013979
survey1: http://goo.gl/forms/kG0Ma5FR37
survey2: http://goo.gl/forms/AQdU9I3Z3l
wifiUsername: introductoryrrstudioworkshop
wifiPassword: TBC
---



<!-- See instructions in the comments below for how to edit specific sections of this workshop template. 
Main things to edit include:
  The Header (if there are not 2 venues or 2 contacts, just delete the second one above)
  The Schedule and Training Material links
  The containers and passwords in the dit4c document
  The wifi username and password for guest access (delete this above if you don't want it)
  -->



<!--
  HEADER
  Edit the values in the block above to be appropriate for your workshop.
  If the value is not 'true', 'false', 'null', or a number, please use
  double quotation marks around the value, unless specified otherwise.
  And run 'tools/check' *before* committing to make sure that changes are good.
-->

<!--
  EVENTBRITE
  This block includes the Eventbrite registration widget if
  'eventbrite' has been set in the header.  You can delete it if you
  are not using Eventbrite, or leave it in, since it will not be
  displayed if the 'eventbrite' field in the header is not set.
-->
{% if page.eventbrite %}
<iframe
  src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt"
  frameborder="0"
  width="100%"
  height="248px"
  scrolling="auto">
</iframe>
{% endif %}



<h2 id="general">General Information</h2>

<!--
  INTRODUCTION
  Edit the general explanatory paragraph below if you want to change
  the pitch.
-->

  <b>Introduction to R for non-programmers.</b>
<p>
The goal of this lesson is to teach novice programmers to write modular code and best practices for using R for data analysis. 
R is commonly used in many scientific disciplines for statistical analysis and its array of third-party packages. 
The emphasis of these materials is to give attendees a strong foundation in the fundamentals of R, 
and to teach best practices for scientific computing: breaking down analyses into modular units, task automation, and encapsulation.
</p>

<p>
Note that this workshop will focus on teaching the fundamentals of the programming language R, and will <b><u>not</u></b> teach statistical analysis. If you would like help with your statistical analysis, you can contact the <a href="http://www.scc.ms.unimelb.edu.au/">Statistical Consulting Centre</a> for one-on-one consultations or see their <a href="SCS_2016 leaflet_PG_R17.pdf">flyer</a> for details of statistical training courses.</p>
<p>
A variety of third party packages are used throughout this workshop. These are not necessarily the best, nor are they comprehensive, 
but they are packages we find useful, and have been chosen primarily for their usability.

These materials are a modified version of those used by Software Carpentry for their "R for reproducible scientific analysis" workshop:
Greg Wilson: "Software Carpentry: Lessons Learned". F1000Research, 2016, 3:62 (doi: 10.12688/f1000research.3-62.v2).
</p>

<!--
  AUDIENCE
  Explain who your audience is.  (In particular, tell readers if the
  workshop is only open to people from a particular institution.
-->
<p id="who">
  <strong>Who:</strong>
  The course is aimed at graduate students and other researchers. 
  <strong>You don't need to have any previous knowledge of the tools that will
    be presented at the workshop.</strong> However, if you have no previous programming experience, we recommend that you
    consult the course materials for 
  <a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-programming-concepts/content/content/welcome-to-coding.html">introduction to programming concepts</a> prior to attending the current workshop.
</p>

<!--
  LOCATION
  This block displays the address and links to maps showing directions
  if the latitude and longitude of the workshop have been set.  You
  can use http://itouchmap.com/latlong.html to find the lat/long of an
  address.
-->
{% if page.latlng %}
<p id="where">
  <strong>Where:</strong>
  {% if page.address2 %}
  Day One ({{page.startdate}}) - {{page.address1}}; Day Two ({{page.enddate}}) - {{page.address2}}.
  {% else %}
  {{page.address1}}.
   {% endif %}
  Get directions with
  <a href="//maps.google.com/maps?q={{page.latlng}}">Google Maps</a>.
</p>
{% endif %}


<!--
  SPECIAL REQUIREMENTS
  Modify the block below if there are any special requirements.
-->
<p id="requirements">
  <strong>Requirements:</strong> <strong>**Participants must bring a laptop**</strong> with a 
  Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges
  on. Participants are also asked to install R, and the RStudio IDE prior to the workshop (details below).
</p>

<!--
  CONTACT EMAIL ADDRESS
  Display the contact email address set in the header.  If an address
  isn't set in the header, the Software Carpentry admin address is
  used.
-->
<p id="contact">
  <strong>Contact</strong>:
  Please email
  {% if page.contact %}
    <a href='mailto:{{page.contact}}'>{{page.contact}}</a>
  {% else %}
    <a href='mailto:{{site.contact}}'>{{site.contact}}</a>
  {% endif %}
  {% if page.contact2 %}
    or <a href='mailto:{{page.contact2}}'>{{page.contact2}}</a>
  {% endif %}
  for more information.
</p>


<hr/>

<!--
  SCHEDULE
  Show the workshop's schedule.  Edit the items and times in the table
  to match your plans.  You may also want to change 'Day 1' and 'Day
  2' to be actual dates or days of the week.
-->
<h2 id="schedule">Schedule</h2> 

<!-- DO NOT EDIT SURVEY LINKS -->
 <p><em>Surveys</em></p>
<p>Please be sure to complete these surveys at the end of each day of the workshop.</p>
<p><a href="{{page.survey1}}">End of first day survey</a></p>
<p><a href="{{page.survey2}}">End of second day survey</a></p>
<!--<p><a href='{{ site.





_pre_survey }}{{ site.github.project_title }}'>Pre-workshop Survey</a></p>
<p><a href='{{ site.swc_post_survey }}{{ site.github.project_title }}'>Post-workshop Survey</a></p>-->

<div class="row">
  <div class="col-md-6">
    <h3>Friday 24th March</h3>
    <table class="table table-striped">
      <tr> <td>09:00</td>  <td>Introduction</td> </tr>
      <tr> <td>10:00</td> <td>Intro to R and how to find help</td> </tr>
      <tr> <td>11:00</td>  <td>Data structures</td> </tr>
      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:00</td>  <td>Reading and subsetting data</td> </tr>
      <tr> <td>14:30</td>  <td>Functions</td> </tr>
      <tr> <td>16:00</td>  <td>Plotting data using ggplot2</td> </tr>
      <tr> <td>16:45</td>  <td>Wrap up</td> </tr>
    </table>
  </div>
  <div class="col-md-6">
    <h3>Monday 27th March</h3>
    <table class="table table-striped">
      <tr> <td>09:00</td>  <td>Setup</td> </tr>
      <tr> <td>09:30</td>  <td>Vectorisation</td> </tr>
      <tr> <td>10:30</td>  <td>Control flow ("if" and "for" statements)</td> </tr>
      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:00</td>  <td>Writing data and figures</td> </tr>
      <!--<tr> <td>13:30</td>  <td>Split-apply-combine</td> </tr> -->
      <tr> <td>13:30</td>  <td>Dataframe manipulation using dplyr</td> </tr>
      <tr> <td>15:00</td>  <td>Discussion</td></tr>
      <!--<tr> <td>16:00</td>  <td>Github</td></tr> -->
      <tr> <td>16:45</td>  <td>Wrap up</td> </tr>
    </table>
  </div>
</div>

<h2 id="topics">Topics</h2>
<ol style="list-style-type: decimal">
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/01-rstudio-intro.html">Introduction to R and RStudio</a></li>
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/02-seeking-help.html">Seeking help</a></li>
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/03-data-structures-part1.html">Data structures</a></li>
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/04-data-structures-part2.html">Data frames and reading in data</a></li>
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/05-data-subsetting.html">Subsetting data</a></li>
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/06-functions.html">Creating functions</a></li>
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/07-plot-ggplot2.html">Creating publication quality graphics</a></li>
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/08-vectorisation.html">Vectorisation</a></li>
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/09-control-flow.html">Control flow</a></li>
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/10-writing-data.html">Writing data</a></li>
<!--<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/11-plyr.html">Split-apply-combine</a></li>-->
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/11-dplyr.html">Dataframe manipulation with dplyr</a></li>
<!-- <li><a href="12-tidyr.html">Dataframe manipulation with tidyr</a></li>-->
<!--<li><a href=" 02-project-intro.html">Project management with RStudio</a></li>-->
<li><a href="https://nikkirubinstein.gitbooks.io/resguides-introductory-r-workshop/content/content/12-wrap-up.html">Wrapping up</a></li>
</ol>
<h2 id="other-resources">Other Resources</h2>
<ul>
<li><a href="reference.html">Reference</a></li>
<li><a href="instructors.html">Instructor’s Guide</a></li>
</ul>



<!--
  ETHERPAD
  At `_misc/etherpad.txt` you will find a template for the etherpad.
  Display the Etherpad for the workshop.  You can set this up in
  advance or on the first day; either way, make sure you push changes
  to GitHub after you have its URL.  To create an Etherpad, go to
      http://pad.software-carpentry.org/YYYY-MM-DD-site
  where 'YYYY-MM-DD-site' is the identifier for your workshop,
  e.g., '2015-06-10-esu'.
-->
{% if page.etherpad %}
<p id="etherpad">
  <strong>Etherpad:</strong> <a href="{{page.etherpad}}">{{page.etherpad}}</a>.
  <br/>
  We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.</p>
{% endif %}
The etherpad log is also available in this (more stable) <a href="https://go.unimelb.edu.au/3ua6">google doc<a/>
<hr/>

<!--
  SYLLABUS
  Show what topics will be covered.
  1. If your workshop is R rather than Python, remove the comment
     around that section and put a comment around the Python section.
  2. Some workshops will delete SQL.
  3. Please make sure the list of topics is synchronized with what you
     intend to teach.
  4. You may need to move the div's with class="col-md-6" around inside
     the div's with class="row" to balance the multi-column layout.
  This is one of the places where people frequently make mistakes, so
  please preview your site before committing, and make sure to run
  'tools/check' as well.
-->
<!-- <h2 id="syllabus">Syllabus</h2>

<div class="row">
  <div class="col-md-6">
    <h3 id="syllabus-shell">The Unix Shell</h3>
    <ul>
      <li>Files and directories</li>
      <li>History and tab completion</li>
      <li>Pipes and redirection</li>
      <li>Looping over files</li>
      <li>Creating and running shell scripts</li>
      <li>Finding things</li>
      <li><a href="{{site.swc_githubio}}/shell-novice/reference.html">Reference...</a></li>
    </ul>
  </div>
  <div class="col-md-6">
    <h3 id="syllabus-python">Programming in Python</h3>
    <ul>
      <li>Using libraries</li>
      <li>Working with arrays</li>
      <li>Reading and plotting data</li>
      <li>Creating and using functions</li>
      <li>Loops and conditionals</li>
      <li>Defensive programming</li>
      <li>Using Python from the command line</li>
      <li><a href="{{site.swc_githubio}}/python-novice-inflammation/reference.html">Reference...</a></li>
    </ul>
  </div> -->
  <!--
  <div class="col-md-6">
    <h3 id="syllabus-r">Programming in R</h3>
    <ul>
      <li>Working with vectors and data frames</li>
      <li>Reading and plotting data</li>
      <li>Creating and using functions</li>
      <li>Loops and conditionals</li>
      <li>Using R from the command line</li>
      <li><a href="{{site.swc_githubio}}/r-novice-inflammation/reference.html">Reference...</a></li>
    </ul>
  </div>
  -->
  <!--
  <div class="col-md-6">
    <h3 id="syllabus-matlab">Programming in MATLAB</h3>
    <ul>
      <li>Working with arrays</li>
      <li>Reading and plotting data</li>
      <li>Creating and using functions</li>
      <li>Loops and conditionals</li>
      <li>Defensive programming</li>
      <li><a href="{{site.swc_githubio}}/matlab-novice-inflammation/reference.html">Reference...</a></li>
     </ul>
   </div>
   -->
<!--</div>

<div class="row">
  <div class="col-md-6">
    <h3 id="syllabus-git">Version Control with Git</h3>
    <ul>
      <li>Creating a repository</li>
      <li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
      <li>Viewing changes: <code>status</code>, <code>diff</code>, ...</li>
      <li>Ignoring files</li>
      <li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
      <li>Resolving conflicts</li>
      <li>Open licenses</li>
      <li>Where to host work, and why</li>
      <li><a href="{{site.swc_githubio}}/git-novice/reference.html">Reference...</a></li>
    </ul>
  </div>-->
  <!--
  <div class="col-md-6">
    <h3 id="syllabus-sql">Managing Data with SQL</h3>
    <ul>
      <li>Reading and sorting data</li>
      <li>Filtering with <code>where</code></li>
      <li>Calculating new values on the fly</li>
      <li>Handling missing values</li>
      <li>Combining values using aggregation</li>
      <li>Combining information from multiple tables using <code>join</code></li>
      <li>Creating, modifying, and deleting data</li>
      <li>Programming with databases</li>
      <li><a href="{{site.swc_githubio}}/sql-novice-survey/reference.html">Reference...</a></li>
    </ul>
  </div>
  -->
<!--</div>

<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>
  <strong>Requirements:</strong>
  <strong>**Participants will be required to bring their own laptop**</strong> and charger.
<!--  from which they will logon to the
  <a href="http://resbaz.cloud.edu.au/ ">Data Intensive Tools for the Cloud</a>
  (DIT4C) environment on the
  <a href="http://cloud.nectar.org.au/">NeCTAR Research Cloud</a>.
  This environment has all the required software pre-installed,
  so there's nothing participants need to do in preparation for the workshop.
  Instructions for connecting to DIT4C can be found <a href="dit4c_access.html">here.</a>
  <!--Having said that, there are software installation instructions <a href="#software_install">below</a>
  for participants who'd like to install the software on their own computer before or after the workshop.-->
</p>

<p>
  <strong>Wifi:</strong>
  If you're bringing a wifi device to the workshop,
  access to the wifi network will depend on whether you're affiliated with the Univerity of Melbourne.
  University of Melbourne staff/students can connect to the UniWireless network;
  instructions on how to do this and where to get assistance can be found
  <a href="https://its.unimelb.edu.au/help/networks-access/networks-internet/connect-wireless/unimelb">here</a>.
  </p> 
{% if page.wifiPassword%}
For visitors who are not from a tertiary institution, the visitor login details for the Visitor network are: <ul>
<li>network: {{page.wifiUsername}}  </li>
<li>password: {{page.wifiPassword}}  </li>
</ul>
{% endif %}

<!--<p>
<strong>software_install</strong>
  Installing the following software on your computer is highly recomended. During the workshop you will have access to 
  experienced Python users who can help you if things go wrong. You will also have a working environment immediately 
  after the workshop to apply what you've learnt to your own reserach questions.
</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>
      <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>
            <!-- Git 2.6.1 Setup -->
            <!-- Welcome to the Git Setup Wizard -->
<!--            <li>Click on "Next".</li>
            <!-- Information -->
<!--            <li>Click on "Next".</li>
            <!-- Select Destination Location -->
<!--            <li>Click on "Next".</li>
            <!-- Select Components -->
<!--            <li>Click on "Next".</li>
            <!-- Select Start Menu Folder -->
<!--            <li>Click on "Next".</li>
            <!-- Adjusting your PATH environment -->
<!--            <li>
<!--              <strong>
                Select "Use Git from the Windows Command Prompt" 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>
            <!-- Configuring the line ending conversions -->
<!--            <li>
<!--              Click on "Next".
              <strong>
                Keep "Checkout Windows-style, commit Unix-style line endings" selected.
              </strong>
            </li>
            <!-- Configuring the terminal emulator to use with Git Bash -->
<!--            <li>
              <strong>
                Select "Use Windows' default console window" and click on "Next".
              </strong>
            </li>
            <!-- Configuring experimental performance tweaks -->
<!--            <li>Click on "Next".</li>
            <!-- Installing -->
            <!-- Completing the Git Setup Wizard -->
<!--            <li>Click on "Finish".</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>). 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>

  <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>
      <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>
    When you're writing code, it's nice to have a text editor that is
    optimized for writing code, with features like automatic
    color-coding of key words.  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>
      <p>
        nano is a basic editor and the default that instructors use in the workshop.
        To install it,
        download the <a href="{{site.swc_installer}}">Software Carpentry Windows installer</a>
        and double click on the file to run it.
        <strong>This installer requires an active internet connection.</strong>
      </p>
      <p>
        Others editors that you can use are
        <a href="http://notepad-plus-plus.org/">Notepad++</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
        <strong>Be aware that you must
          add its installation directory to your system path.</strong>
        Please ask your instructor to help you do this.
      </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.
        It should be pre-installed.
      </p>
      <p>
        Others editors that you can use are
        <a href="http://www.barebones.com/products/textwrangler/">Text Wrangler</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
      </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>
      <p>
        Others editors that you can use are
        <a href="https://wiki.gnome.org/Apps/Gedit">Gedit</a>,
        <a href="http://kate-editor.org/">Kate</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
      </p>
    </div>
  </div>
</div> <!-- End of 'editor' section. -->

<!--<div id="python"> <!-- Start of 'Python' section. Remove the third paragraph if
           the workshop will teach Python using something other than
           the IPython notebook.
           Details at http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility -->
<!--  <h3>Python</h3>

  <p>
    <a href="http://python.org">Python</a> is a popular language for
    scientific computing, and great for general-purpose programming as
    well.  Installing all of its scientific packages individually can be
    a bit difficult, so we recommend
    <a href="https://www.continuum.io/anaconda">Anaconda</a>,
    an all-in-one installer.
  </p>

    <p>
      Regardless of how you choose to install it,
      <strong>please make sure you install Python version 3.x</strong>
      (e.g., 3.4 is fine).
    </p>

    <p>
      We will teach Python using the IPython notebook, a programming environment
      that runs in a web browser. For this to work you will need a reasonably
      up-to-date browser. The current versions of the Chrome, Safari and
      Firefox browsers are all <a
      href='http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility'>supported</a>
      (some older browsers, including Internet Explorer version 9
      and below, are not).
    </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="python-windows">Windows</h4>
      <ol>
        <li>Open <a href="http://continuum.io/downloads">http://continuum.io/downloads</a> with your web browser.</li>
        <li>Download the Python 3 installer for Windows.</li>
        <li>Install Python 3 using all of the defaults for installation <em>except</em> make sure to check <strong>Make Anaconda the default Python</strong>.</li>
      </ol>
    </div>
    <div class="col-md-4">
      <h4 id="python-macosx">Mac OS X</h4>
      <ol>
        <li>Open <a href="http://continuum.io/downloads">http://continuum.io/downloads</a> with your web browser.</li>
        <li>Download the Python 3 installer for OS X.</li>
        <li>Install Python 3 using all of the defaults for installation.</li>
      </ol>
    </div>
    <div class="col-md-4">
      <h4 id="python-linux">Linux</h4>
      <ol>
        <li>Open <a href="http://continuum.io/downloads">http://continuum.io/downloads</a> with your web browser.</li>
        <li>Download the Python 3 installer for Linux.</li>
        <li>Install Python 3 using all of the defaults for installation.
        (Installation requires using the shell. If you aren't
        comfortable doing the installation yourself
        stop here and request help at the workshop.)</li>
        <li>
          Open a terminal window.
        </li>
        <li>
          Type <pre>bash Anaconda-</pre> and then press
          tab. The name of the file you just downloaded should
          appear.
        </li>
        <li>
          Press enter. You will follow the text-only prompts.  When
          there is a colon at the bottom of the screen press the down
          arrow to move down through the text. Type <code>yes</code> and
          press enter to approve the license. Press enter to approve the
          default location for the files. Type <code>yes</code> and
          press enter to prepend Anaconda to your <code>PATH</code>
          (this makes the Anaconda distribution the default Python).
        </li>
      </ol>
    </div>
  </div>
<!--
  <p>
  Once you are done installing the software listed above,
  please go to <a href="setup/index.html">this page</a>,
  which has instructions on how to test that everything was installed correctly.
  </p>
-->
<!--</div> <!-- End of 'Python' 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>
      <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>
      <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="sql"> <!-- Start of 'SQLite' section. -->
<!--
  <h3>SQLite</h3>
  <p>
    SQL is a specialized programming language used with databases.  We
    use a simple database manager called
    <a href="http://www.sqlite.org/">SQLite</a> in our lessons.
  </p>
  <div class="row">
    <div class="col-md-4">
      <h4 id="sql-windows">Windows</h4>
      <p>
        The <a href="{{site.swc_github}}/windows-installer">Software Carpentry Windows Installer</a>
        installs SQLite for Windows.
        If you used the installer to configure nano, you don't need to run it again.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="sql-macosx">Mac OS X</h4>
      <p>
        SQLite comes pre-installed on Mac OS X.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="sql-linux">Linux</h4>
      <p>
        SQLite comes pre-installed on Linux.
      </p>
    </div>
  </div>
  <p><strong>If you installed Anaconda, it also has a copy of SQLite
    <a href="https://github.com/ContinuumIO/anaconda-issues/issues/307">without support to <code>readline</code></a>.
    Instructors will provide a workaround for it if needed.</strong></p>
</div> <!-- End of 'SQLite' section. -->

<!--
  Uncomment this section if you are using our virtual machine.
<div id="vm">
  <h3>Virtual Machine</h3>
  <p>
    Some instructors prefer to have learners use a virtual machine (VM)
    rather than install software on their own computers.  If your
    instructors have chosen to do this, please:
  </p>
  <ol>
    <li>
      Install <a href="https://www.virtualbox.org/">VirtualBox</a>.
    </li>
    <li>
      Download our <a href="{{site.swc_vm}}">VM image</a>.
      <strong>Warning:</strong> this file is 1.7 GByte, so please
      download it <em>before</em> coming to your workshop.
    </li>
    <li>
      Load the VM into VirtualBox by selecting "Import Appliance" and
      loading the <code>.ova</code> file.
    </li>
  </ol>
</div>
-->