index.html

---
layout: workshop      # DON'T CHANGE THIS.
root: .               # DON'T CHANGE THIS.
venue: "University of Wisconsin, Madison"        # brief name of host site without address (e.g., "Euphoric State University")
address: "Wisconsin Institutes for Discovery, 3rd Floor Teaching Lab, 330 North Orchard St., Madison, WI 53715"      # street address of workshop (e.g., "123 Forth Street, Blimingen, Euphoria")
country: "us"      # country (lowercase two-letter ISO code such as "fr" - see https://en.wikipedia.org/wiki/ISO_3166-1)
language: "en"     # language (lowercase two-letter ISO code such as "fr" - see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "43.072834, -89.408136"       # fractional latitude and longitude (e.g., "41.7901128,-87.6007318"; you can use http://www.latlong.net/)
humandate: "August 23-24, 2016"    # human-readable date (e.g., "Feb 17-18, 2020")
humantime: "8:30am - 4pm"    # human-readable time (e.g., "9:00 am - 4:30 pm")
startdate: 2016-08-23      # use YYYY-MM-DD format like 2015-01-01
enddate: 2016-08-24        # use YYYY-MM-DD format like 2015-01-02
instructor: ["Trisha Adamus", "Karl Broman", "Christina Koch"] # list of names like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Cameron Cook", "Steve Goldstein", "Andy Pohl"]     # list of names like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: "ckoch5@wisc.edu"      # contact email address for workshop organizer, such as "grace@hopper.org"
etherpad: http://pad.software-carpentry.org/2016-08-23-uwmadison        # optional (insert the URL for your Etherpad if you're using one)
eventbrite: 26430778169      # optional (insert the alphanumeric key for Eventbrite registration, e.g., "1234567890AB")
day1_am: "Data organization in spreadsheets and OpenRefine"
day1_pm: "SQL for data management"
day2_am: "Introduction to R"
day2_pm: "Data analysis and visualization in R"
---
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  HEADER

  Edit the values in the block above to be appropriate for your
  workshop.  Run 'tools/check' *before* committing to make sure that
  changes are good.
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<p>
<b>Registration is required and will be available just below,
starting at 5:00pm on Tuesday, July 26.</b> Make sure to read
all details below before registering and to choose appropriately
between UW-Madison's Data Carpentry and Software Carpentry workshops.
</p>

{% if page.eventbrite %}
<iframe
  src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt"
  frameborder="0"
  width="100%"
  height="206px"
  scrolling="auto">
</iframe>
{% endif %}

<h2>General Information</h2>

<!--
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  the pitch.
-->

<a href=http://datacarpentry.org>Data Carpentry</a> 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. We will cover {{page.day1_am}}, {{page.day1_pm}}, {{page.day2_am}} and {{page.day2_pm}}.
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.
</br>
</br>
<p>
For researchers who have already been programming and seek to expand
their capabilities, our UW-Madison <a href="http://uw-madison-aci.github.io/2016-08-29-uwmadison">
<i>Software Carpentry</i> workshop (August 29-30)</a> will likely be
more appropriate. These two workshops are <b>NOT</b> intended to be taken back-to-back,
and you can learn about future workshops at UW-Madison by joining the
<a href="http://wisc.us9.list-manage.com/subscribe?u=c3aae71670855b66d79d170b8&id=6d65510fb6">
mailing list</a> of UW-Madison's <a href="http://aci.wisc.edu/">Advanced Computing Initiative</a>.
</p>

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<p id="who">
  <strong>Who:</strong>
  The course is aimed at UW-Madison-affiliated graduate students and other researchers.
  The <a href="http://www.datacarpentry.org/lessons/">curriculum and examples</a> are
  somewhat specific to Biology/Ecology data, but still teach generalizable practices.
</p>

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-->
{% if page.latlng %}
<p>
  <strong>Where:</strong>
  {{page.address}}.
  Get directions with
  <a href="//www.openstreetmap.org/?mlat={{page.latlng | replace:',','&mlon='}}&zoom=16">OpenStreetMap</a>
  or
  <a href="//maps.google.com/maps?q={{page.latlng}}">Google Maps</a>.
</p>
{% endif %}

<!--
  SPECIAL REQUIREMENTS

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-->
<p>
  <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>). An individual should only register if he/she is able
  to attend ALL days of the workshop. While coffee and tea will be provided, participants
  should eat a full breakfast and plan to bring or buy their own lunch nearby.
  Attendees are also required to abide by Data Carpentry's
  <a href="{{site.swc_site}}/conduct.html">Code of Conduct</a>.</br>
  <b>Registration is required, and will be available just above General
  Information, starting at 5:00pm on Tuesday, August 2.</b>
</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.
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<p>
  <strong>Contact</strong>:
  Please mail
  {% if page.contact %}
    <a href='mailto:{{page.contact}}'>{{page.contact}}</a>
  {% else %}
    <a href='mailto:{{site.contact}}'>{{site.contact}}</a>
  {% endif %}
  for more information.
</p>

<p id="accessibility">
  <strong>Accessibility:</strong> We are committed to making this workshop
  accessible to everybody.
  The workshop organisers have checked that:
</p>
<ul>
  <li>The room is wheelchair / scooter accessible.</li>
  <li>Accessible restrooms are available.</li>
  <li>Lactation facilities are available.</li>
</ul>
<p>
  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 please
  <a href="mailto:{{page.contact}}">get in touch</a> and we will
  attempt to provide them.
</p>


<hr/>

<!--
  SCHEDULE

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  to match your plans.  You may also want to change 'Day 1' and 'Day
  2' to be actual dates or days of the week.
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<h2>Preliminary Schedule</h2>

<!-- DO NOT EDIT SURVEY LINKS -->
<p><em>Surveys</em></p>
<p>Please be sure to complete these surveys before and after the workshop.</p>
<p><a href='{{ site.dc_pre_survey }}'>Pre-workshop Survey</a></p>
<p><a href='{{ site.dc_post_survey }}'>Post-workshop Survey</a></p>

<div class="row">
  <div class="col-md-6">

    <h3>Day 1</h3>
    <table class="table table-striped">
      <tr> <td>8:30 - 9:00</td>  <td>Installation Help</td> </tr>
      <tr> <td>9:00 - 9:10</td>  <td><a href="assets/DC_intro.pdf">Introduction</a></td> </tr>
      <tr><td>9:10 - 10:30</td> <td><a href="http://www.datacarpentry.org/spreadsheet-ecology-lesson/">Data Organization in Spreadsheets</a></td></tr>
      <tr><td>10:30 - 10:45</td> <td>Coffee</td></tr>
      <tr><td>10:45 - 12:00 </td> <td><a href="http://www.datacarpentry.org/OpenRefine-ecology-lesson/">Data Cleaning with OpenRefine</a></td></tr>
      <tr><td>12:00 - 1:00</td> <td>Lunch Break</td></tr>
      <tr><td>1:00 - 2:15</td> <td><a href="http://www.datacarpentry.org/sql-ecology-lesson/">Data Management with SQL</a></td></tr>
      <tr><td>2:15 - 2:30</td> <td>Coffee</td></tr>
      <tr><td>2:30 - 4:00</td> <td>Data Management with SQL</td></tr>
    </table>
 </div>
 <div class="col-md-6">
    <h3>Day 2</h3>
    <table class="table table-striped">
      <tr> <td>8:30 - 9:00</td>  <td>Installation Help</td> </tr>
      <tr><td>9:00 - 9:15</td> <td><a
    href="assets/DC_day2intro.html">Day 2 intro</a></td></tr>
      <tr><td>9:15 - 9:45</td> <td><a
    href="http://kbroman.org/datacarpentry_R_2016-08-23/01-intro-to-R.html">Intro
    to R</a> [<a
    href="http://kbroman.org/datacarpentry_R_2016-08-23/data_carpentry_2016-08-24.R">Script
    from the day</a>]</td></tr>
      <tr><td>9:45 - 10:30</td> <td><a
    href="http://kbroman.org/datacarpentry_R_2016-08-23/02-dplyr.html">Data
    manipulation with dplyr</a></td></tr>
      <tr><td>10:30 - 10:45</td> <td>Coffee</td></tr>
      <tr><td>10:45 - 12:00</td> <td><a href="http://kbroman.org/datacarpentry_R_2016-08-23/03-ggplot2.html">Data visualization with ggplot2</a></td></tr>
      <tr><td>12:00 - 1:00</td> <td>Lunch Break</td></tr>
      <tr><td>1:00 - 2:00</td> <td>More ggplot2</a></td></tr>
      <tr><td>2:00 - 2:30</td> <td><a href="http://kbroman.org/datacarpentry_R_2016-08-23/04-rmarkdown.html">Reproducible reports with R Markdown</a></td></tr>
      <tr><td>2:30 - 2:45</td> <td>Coffee</td></tr>
      <tr><td>2:45 - 4:00</td> <td><a
      href="http://kbroman.org/datacarpentry_R_2016-08-23/capstone.html">Capstone
        project</a> [Solution: <a
    href="http://kbroman.org/datacarpentry_R_2016-08-23/capstone_soln/capstone_soln.Rmd">Rmd</a>
    | <a href="http://kbroman.org/datacarpentry_R_2016-08-23/capstone_soln/capstone_soln.html">html</a>]
      </td></tr>
    </table>
 </div>
</div>


<!--
  ETHERPAD

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  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://etherpad.mozilla.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>
  <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 %}

<hr/>

<!--
  SYLLABUS

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  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>Syllabus</h2>

<div class="row">
  <div class="col-md-6">
    <h3>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_lessons}}/ref/01-shell.html">Reference...</a></li>
    </ul>
  </div>
  <div class="col-md-6">
    <h3>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_lessons}}/ref/03-python.html">Reference...</a></li>
    </ul>
  </div>

  <div class="col-md-6">
    <h3>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_lessons}}/ref/06-R.html">Reference...</a></li>
    </ul>
  </div>

</div>

<div class="row">
  <div class="col-md-6">
    <h3>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_lessons}}/ref/02-git.html">Reference...</a></li>
    </ul>
  </div>
  <div class="col-md-6">
    <h3>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_lessons}}/ref/04-sql.html">Reference...</a></li>
    </ul>
  </div>
</div>


<hr/>
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<h2 id="setup">Setup</h2>

<p>
To participate in a Data Carpentry workshop, you will need working copies of the
described software. Please make sure to install everything (or at least to download
the installers) before the start of your workshop. Participants should bring and use
their own laptops to insure the proper setup of tools for an efficient workflow
once you leave the workshop.
<p>
Please follow these <a href=install.html>Setup Instructions</a>.

<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>