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<!DOCTYPE html>
<html>
<head>
<title>Reading XML</title>
<meta charset="utf-8">
<meta name="description" content="Reading XML">
<meta name="author" content="Jeffrey Leek">
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<body style="opacity: 0">
<slides class="layout-widescreen">
<!-- LOGO SLIDE -->
<slide class="title-slide segue nobackground">
<aside class="gdbar">
<img src="../../assets/img/bloomberg_shield.png">
</aside>
<hgroup class="auto-fadein">
<h1>Reading XML</h1>
<h2></h2>
<p>Jeffrey Leek<br/>Johns Hopkins Bloomberg School of Public Health</p>
</hgroup>
<article></article>
</slide>
<!-- SLIDES -->
<slide class="" id="slide-1" style="background:;">
<hgroup>
<h2>XML</h2>
</hgroup>
<article data-timings="">
<ul>
<li>Extensible markup language</li>
<li>Frequently used to store structured data</li>
<li>Particularly widely used in internet applications</li>
<li>Extracting XML is the basis for most web scraping</li>
<li>Components
<ul>
<li>Markup - labels that give the text structure</li>
<li>Content - the actual text of the document</li>
</ul></li>
</ul>
<p><a href="http://en.wikipedia.org/wiki/XML">http://en.wikipedia.org/wiki/XML</a></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-2" style="background:;">
<hgroup>
<h2>Tags, elements and attributes</h2>
</hgroup>
<article data-timings="">
<ul>
<li>Tags correspond to general labels
<ul>
<li>Start tags <code><section></code></li>
<li>End tags <code></section></code></li>
<li>Empty tags <code><line-break /></code></li>
</ul></li>
<li>Elements are specific examples of tags
<ul>
<li><code><Greeting> Hello, world </Greeting></code></li>
</ul></li>
<li>Attributes are components of the label
<ul>
<li><code><img src="jeff.jpg" alt="instructor"/></code></li>
<li><code><step number="3"> Connect A to B. </step></code></li>
</ul></li>
</ul>
<p><a href="http://en.wikipedia.org/wiki/XML">http://en.wikipedia.org/wiki/XML</a></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-3" style="background:;">
<hgroup>
<h2>Example XML file</h2>
</hgroup>
<article data-timings="">
<p><img class=center src=../../assets/img/03_ObtainingData/xmlexample.png height=450></p>
<p><a href="http://www.w3schools.com/xml/simple.xml">http://www.w3schools.com/xml/simple.xml</a></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-4" style="background:;">
<hgroup>
<h2>Read the file into R</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">library(XML)
fileUrl <- "http://www.w3schools.com/xml/simple.xml"
doc <- xmlTreeParse(fileUrl,useInternal=TRUE)
rootNode <- xmlRoot(doc)
xmlName(rootNode)
</code></pre>
<pre><code>[1] "breakfast_menu"
</code></pre>
<pre><code class="r">names(rootNode)
</code></pre>
<pre><code> food food food food food
"food" "food" "food" "food" "food"
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-5" style="background:;">
<hgroup>
<h2>Directly access parts of the XML document</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">rootNode[[1]]
</code></pre>
<pre><code><food>
<name>Belgian Waffles</name>
<price>$5.95</price>
<description>Two of our famous Belgian Waffles with plenty of real maple syrup</description>
<calories>650</calories>
</food>
</code></pre>
<pre><code class="r">rootNode[[1]][[1]]
</code></pre>
<pre><code><name>Belgian Waffles</name>
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-6" style="background:;">
<hgroup>
<h2>Programatically extract parts of the file</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">xmlSApply(rootNode,xmlValue)
</code></pre>
<pre><code> food
"Belgian Waffles$5.95Two of our famous Belgian Waffles with plenty of real maple syrup650"
food
"Strawberry Belgian Waffles$7.95Light Belgian waffles covered with strawberries and whipped cream900"
food
"Berry-Berry Belgian Waffles$8.95Light Belgian waffles covered with an assortment of fresh berries and whipped cream900"
food
"French Toast$4.50Thick slices made from our homemade sourdough bread600"
food
"Homestyle Breakfast$6.95Two eggs, bacon or sausage, toast, and our ever-popular hash browns950"
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-7" style="background:;">
<hgroup>
<h2>XPath</h2>
</hgroup>
<article data-timings="">
<ul>
<li><em>/node</em> Top level node</li>
<li><em>//node</em> Node at any level</li>
<li><em>node[@attr-name]</em> Node with an attribute name</li>
<li><em>node[@attr-name='bob']</em> Node with attribute name attr-name='bob'</li>
</ul>
<p>Information from: <a href="http://www.stat.berkeley.edu/%7Estatcur/Workshop2/Presentations/XML.pdf">http://www.stat.berkeley.edu/~statcur/Workshop2/Presentations/XML.pdf</a></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-8" style="background:;">
<hgroup>
<h2>Get the items on the menu and prices</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">xpathSApply(rootNode,"//name",xmlValue)
</code></pre>
<pre><code>[1] "Belgian Waffles" "Strawberry Belgian Waffles" "Berry-Berry Belgian Waffles"
[4] "French Toast" "Homestyle Breakfast"
</code></pre>
<pre><code class="r">xpathSApply(rootNode,"//price",xmlValue)
</code></pre>
<pre><code>[1] "$5.95" "$7.95" "$8.95" "$4.50" "$6.95"
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-9" style="background:;">
<hgroup>
<h2>Another example</h2>
</hgroup>
<article data-timings="">
<p><img class=center src=../../assets/img/03_ObtainingData/ravens.png height=450></p>
<p><a href="http://espn.go.com/nfl/team/_/name/bal/baltimore-ravens">http://espn.go.com/nfl/team/_/name/bal/baltimore-ravens</a></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-10" style="background:;">
<hgroup>
<h2>Viewing the source</h2>
</hgroup>
<article data-timings="">
<p><img class=center src=../../assets/img/03_ObtainingData/ravenssource.png height=450></p>
<p><a href="http://espn.go.com/nfl/team/_/name/bal/baltimore-ravens">http://espn.go.com/nfl/team/_/name/bal/baltimore-ravens</a></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-11" style="background:;">
<hgroup>
<h2>Extract content by attributes</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">fileUrl <- "http://espn.go.com/nfl/team/_/name/bal/baltimore-ravens"
doc <- htmlTreeParse(fileUrl,useInternal=TRUE)
scores <- xpathSApply(doc,"//li[@class='score']",xmlValue)
teams <- xpathSApply(doc,"//li[@class='team-name']",xmlValue)
scores
</code></pre>
<pre><code> [1] "49-27" "14-6" "30-9" "23-20" "26-23" "19-17" "19-16" "24-18"
[9] "20-17 OT" "23-20 OT" "19-3" "22-20" "29-26" "18-16" "41-7" "34-17"
</code></pre>
<pre><code class="r">teams
</code></pre>
<pre><code> [1] "Denver" "Cleveland" "Houston" "Buffalo" "Miami" "Green Bay"
[7] "Pittsburgh" "Cleveland" "Cincinnati" "Chicago" "New York" "Pittsburgh"
[13] "Minnesota" "Detroit" "New England" "Cincinnati"
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-12" style="background:;">
<hgroup>
<h2>Notes and further resources</h2>
</hgroup>
<article data-timings="">
<ul>
<li>Official XML tutorials <a href="http://www.omegahat.org/RSXML/shortIntro.pdf">short</a>, <a href="http://www.omegahat.org/RSXML/Tour.pdf">long</a></li>
<li><a href="http://www.stat.berkeley.edu/%7Estatcur/Workshop2/Presentations/XML.pdf">An outstanding guide to the XML package</a></li>
</ul>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="backdrop"></slide>
</slides>
<div class="pagination pagination-small" id='io2012-ptoc' style="display:none;">
<ul>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=1 title='XML'>
1
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=2 title='Tags, elements and attributes'>
2
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=3 title='Example XML file'>
3
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=4 title='Read the file into R'>
4
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=5 title='Directly access parts of the XML document'>
5
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=6 title='Programatically extract parts of the file'>
6
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=7 title='XPath'>
7
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=8 title='Get the items on the menu and prices'>
8
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=9 title='Another example'>
9
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=10 title='Viewing the source'>
10
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=11 title='Extract content by attributes'>
11
</a>
</li>
<li>
<a href="#" target="_self" rel='tooltip'
data-slide=12 title='Notes and further resources'>
12
</a>
</li>
</ul>
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