index.html

---
layout: workshop
root: .
venue: "Intro to R - School of Global Policy and Strategy"      # brief name of host site without address (e.g., "Euphoric State University")
address: "School of Global Policy and Strategy, 9500 Gilman Drive, #0519, La Jolla, CA"    # 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: "32.885125,-117.241173"     # fractional latitude and longitude (e.g., "41.7901128,-87.6007318"; you can use http://www.latlong.net/)
humandate: "Jan 4 - Jan 21, 2021"  # human-readable date (e.g., "Feb 17-18, 2020")
humantime: "12:30 pm -1:50 pm"  # human-readable time (e.g., "9:00 am - 4:30 pm")
startdate: "2021-01-04"  # use YYYY-MM-DD format like "2015-01-01"
enddate: "2021-01-21"  # use YYYY-MM-DD format like" 2015-01-02"
days: "Zoom Tuesday, Thursday"
instructor: ["Rick Mccosh (OBGYN-Repro Sci)", "Stephanie Labou (Library)"] # list of names like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Chi Gao (TA-GPS)", "Reid Otsuji (Library)", "Kimberly Thomas(Research IT)", "Harry Zhao(Research IT)"]     # list of names like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: "rotsuji@ucsd.edu"    # contact email address for workshop organizer, such as "grace@hopper.org"
etherpad: "https://hackmd.io/3JeMSRvbRJ-ySHqvl_wS1A" # optional (insert the URL for your Etherpad if you're using one)
eventbrite:       # optional (insert the alphanumeric key for Eventbrite registration, e.g., "1234567890AB")
---
<!--
  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.
-->
<p>
  This is the website for the <a href="{{site.gps_site}}">School of Global Policy and Strategy</a> skills course in the R programming language.  This course will introduce you the R programming language and how to use R to work with data from GapMinder.  In order to earn a certificate of proficiency, you must attend all of the class meetings for the course, do the short coding assignments, and pass the short, in-class quiz at the end of the course.
</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 GPS graduate students.
  <strong>You don't need to have any previous knowledge of programming or the tools presented in the course to attend.  A laptop is required for the class.</strong>
</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>
  {{page.address}}.
  <strong>Zoom - link and access information in Canvas<strong>
</p>
{% endif %}

<!--
  SPECIAL REQUIREMENTS

  Modify the block below if there are any special requirements.
-->
<p id="requirements">
  <strong>Requirements:</strong> Participants must bring a laptop with
  a few specific software packages installed (listed
  <a href="#setup">below</a>).
</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 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="certificate">
<strong>Assessment</strong>:
A certificate of proficiency will be given to the student who:
</p>

<ul>
<li>20% Attends and participates in classes</li>
<li>40% Passes all in-course quizzes</li>
<li>40% Satisfactorily completes the weekly homework assignments</li>
</ul>

<p id="help">
{% if site.lib_appt %}
  <strong>Need help?</strong>:
  <ul>
    <li> Reid Otsuji: Email <a href='mailto:{{page.contact}}'>{{page.contact}}</a></li>
{% endif %}
  <li>TA Chi Gao <a href='mailto:chg043@ucsd.edu'>chg043@ucsd.edu</a>, Office Hours: Zoom: Wednesday 4-5pm, Friday 5-6pm<!-- <a href="{{site.lib_data_lab}}">Library Data/GIS Lab</a> --> </li>
  <li><a href="{{site.lib_data_lab}}">Library Data/GIS Lab</a> has R specialists</li>
</ul>
</p>
<p id = "data">
<strong>Data:</strong> We will be using the 5 year <a href="http://www.gapminder.org/data/">gapminder data</a>. You can go ahead and set up a RStudio project and download the data following these <a href="newproject.html">instructions</a>. The CSV can be downloaded from <a href="https://raw.githubusercontent.com/resbaz/r-novice-gapminder-files/master/data/gapminder-FiveYearData.csv">here</a>.

</p>

<strong>Lecture notes & command histories:</strong>

{% capture notes %}{% include notes.md %}{% endcapture %}
{{ notes  | markdownify }}

<p>
<strong>Credits:</strong>  The course materials are adpated from the Software Carpentry <a href="http://software-carpentry.org/lessons/">lessons</a>. Many thanks to the authors of those lessons.
</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>

{% capture schedule %}{% include schedule.md %}{% endcapture %}
{{ schedule  | markdownify }}
<!--
{% include schedule.html %}
-->
<!--
  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>HackMD:</strong> <a href="{{page.etherpad}}">{{page.etherpad}}</a>.
  <br/>
  We will use this HackMD for taking notes, and sharing URLs and bits of code.
</p>
{% endif %}


<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><a href="http://swcarpentry.github.io/r-novice-gapminder/reference/">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>
  To participate in this course, you will need
  access to the software described below. In addition, you will
  need an up-to-date web browser.
</p>

<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>.
        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.
      </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. -->
<!-- hiding SQL Lite insrtuctions
<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_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>

</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>
-->