bcaffo · erouirior · May 5, 2014 · May 5, 2014 · May 9, 2014 · May 21, 2014
diff --git a/02_RProgramming/ControlStructures/index.Rmd b/02_RProgramming/ControlStructures/index.Rmd
@@ -8,7 +8,7 @@ framework   : io2012        # {io2012, html5slides, shower, dzslides, ...}
 highlighter : highlight.js  # {highlight.js, prettify, highlight}
 hitheme     : tomorrow      # 
 url:
-  lib: ../../libraries
+  lib: ../../librariesNew
   assets: ../../assets
 widgets     : [mathjax]            # {mathjax, quiz, bootstrap}
 mode        : selfcontained # {standalone, draft}
@@ -243,4 +243,4 @@ Summary
 
 - Infinite loops should generally be avoided, even if they are theoretically correct.
 
-- Control structures mentiond here are primarily useful for writing programs; for command-line interactive work, the *apply functions are more useful.
+- Control structures mentiond here are primarily useful for writing programs; for command-line interactive work, the *apply functions are more useful.
diff --git a/02_RProgramming/ControlStructures/index.html b/02_RProgramming/ControlStructures/index.html
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+  <script data-main="../../librariesNew/frameworks/io2012/js/slides" 
+    src="../../librariesNew/frameworks/io2012/js/require-1.0.8.min.js">
   </script>
 
-    <link rel="stylesheet" href = "../../assets/css/custom.css">
-<link rel="stylesheet" href = "../../assets/css/ribbons.css">
+
 
 </head>
 <body style="opacity: 0">
   <slides class="layout-widescreen">
 
     <!-- LOGO SLIDE -->
-    <!-- END LOGO SLIDE -->
+        <slide class="title-slide segue nobackground">
+  <aside class="gdbar">
+    <img src="../../assets/img/bloomberg_shield.png">
+  </aside>
+  <hgroup class="auto-fadein">
+    <h1>Introduction to the R Language</h1>
+    <h2>Control Structures</h2>
+    <p>Roger Peng, Associate Professor<br/>Johns Hopkins Bloomberg School of Public Health</p>
+  </hgroup>
+  <article></article>  
+</slide>
 
 
-    <!-- TITLE SLIDE -->
-    <!-- Should I move this to a Local Layout File? -->
-    <slide class="title-slide segue nobackground">
-      <aside class="gdbar">
-        <img src="../../assets/img/bloomberg_shield.png">
-      </aside>
-      <hgroup class="auto-fadein">
-        <h1>Introduction to the R Language</h1>
-        <h2>Control Structures</h2>
-        <p>Roger Peng, Associate Professor<br/>Johns Hopkins Bloomberg School of Public Health</p>
-      </hgroup>
-          </slide>
-
     <!-- SLIDES -->
-      <slide class="" id="slide-1" style="background:;">
+    <slide class="" id="slide-1" style="background:;">
   <hgroup>
     <h2>Control Structures</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p>Control structures in R allow you to control the flow of execution of the program, depending on runtime conditions. Common structures are</p>
 
 <ul>
@@ -66,11 +66,11 @@ <h2>Control Structures</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-2" style="background:;">
+<slide class="" id="slide-2" style="background:;">
   <hgroup>
     <h2>Control Structures: if</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <pre><code class="r">if(&lt;condition&gt;) {
         ## do something
 } else {
@@ -89,11 +89,11 @@ <h2>Control Structures: if</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-3" style="background:;">
+<slide class="" id="slide-3" style="background:;">
   <hgroup>
     <h2>if</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p>This is a valid if/else structure.</p>
 
 <pre><code class="r">if(x &gt; 3) {
@@ -116,11 +116,11 @@ <h2>if</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-4" style="background:;">
+<slide class="" id="slide-4" style="background:;">
   <hgroup>
     <h2>if</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p>Of course, the else clause is not necessary. </p>
 
 <pre><code class="r">if(&lt;condition1&gt;) {
@@ -136,11 +136,11 @@ <h2>if</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-5" style="background:;">
+<slide class="" id="slide-5" style="background:;">
   <hgroup>
     <h2>for</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p><code>for</code> loops take an interator variable and assign it successive values from a sequence or vector. For loops are most commonly used for iterating over the elements of an object (list, vector, etc.)</p>
 
 <pre><code class="r">for(i in 1:10) {
@@ -154,11 +154,11 @@ <h2>for</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-6" style="background:;">
+<slide class="" id="slide-6" style="background:;">
   <hgroup>
     <h2>for</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p>These three loops have the same behavior.</p>
 
 <pre><code class="r">x &lt;- c(&quot;a&quot;, &quot;b&quot;, &quot;c&quot;, &quot;d&quot;)
@@ -182,11 +182,11 @@ <h2>for</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-7" style="background:;">
+<slide class="" id="slide-7" style="background:;">
   <hgroup>
     <h2>Nested for loops</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p><code>for</code> loops can be nested.</p>
 
 <pre><code class="r">x &lt;- matrix(1:6, 2, 3)
@@ -204,11 +204,11 @@ <h2>Nested for loops</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-8" style="background:;">
+<slide class="" id="slide-8" style="background:;">
   <hgroup>
     <h2>while</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p>While loops begin by testing a condition. If it is true, then they execute the loop body. Once the loop body is executed, the condition is tested again, and so forth.</p>
 
 <pre><code class="r">count &lt;- 0
@@ -224,11 +224,11 @@ <h2>while</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-9" style="background:;">
+<slide class="" id="slide-9" style="background:;">
   <hgroup>
     <h2>while</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p>Sometimes there will be more than one condition in the test.</p>
 
 <pre><code class="r">z &lt;- 5
@@ -251,11 +251,11 @@ <h2>while</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-10" style="background:;">
+<slide class="" id="slide-10" style="background:;">
   <hgroup>
     <h2>repeat</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p>Repeat initiates an infinite loop; these are not commonly used in statistical applications but they do have their uses. The only way to exit a <code>repeat</code> loop is to call <code>break</code>.</p>
 
 <pre><code class="r">x0 &lt;- 1
@@ -276,22 +276,22 @@ <h2>repeat</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-11" style="background:;">
+<slide class="" id="slide-11" style="background:;">
   <hgroup>
     <h2>repeat</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p>The loop in the previous slide is a bit dangerous because there’s no guarantee it will stop. Better to set a hard limit on the number of iterations (e.g. using a for loop) and then report whether convergence was achieved or not.</p>
 
   </article>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-12" style="background:;">
+<slide class="" id="slide-12" style="background:;">
   <hgroup>
     <h2>next, return</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p><code>next</code> is used to skip an iteration of a loop</p>
 
 <pre><code class="r">for(i in 1:100) {
@@ -309,11 +309,11 @@ <h2>next, return</h2>
   <!-- Presenter Notes -->
 </slide>
 
-      <slide class="" id="slide-13" style="background:;">
+<slide class="" id="slide-13" style="background:;">
   <hgroup>
     <h2>Control Structures</h2>
   </hgroup>
-  <article>
+  <article data-timings="">
     <p>Summary</p>
 
 <ul>
@@ -328,34 +328,113 @@ <h2>Control Structures</h2>
 
     <slide class="backdrop"></slide>
   </slides>
-
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+        data-slide=1 title='Control Structures'>
+         1
+      </a>
+    </li>
+    <li>
+      <a href="#" target="_self" rel='tooltip' 
+        data-slide=2 title='Control Structures: if'>
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+        data-slide=12 title='next, return'>
+         12
+      </a>
+    </li>
+    <li>
+      <a href="#" target="_self" rel='tooltip' 
+        data-slide=13 title='Control Structures'>
+         13
+      </a>
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