Removed page breaks from HTML documents

Author: sux13

2_RPROG/R Programming Course Notes.Rmd

@@ -2,13 +2,13 @@
 title: "R Programming Course Notes"
 author: "Xing Su"
 output:
+  pdf_document:
+    toc: yes
+    toc_depth: 3
   html_document:
     highlight: pygments
     theme: spacelab
     toc: yes
-  pdf_document:
-    toc: yes
-    toc_depth: 3
 ---
 $\pagebreak$
 
@@ -901,9 +901,6 @@ system.time({
 * ***Note**: R must be compiled with profiles support (generally the case)*
 * ***Note**: should NOT be used with system.time()*
 
-
-
-
-`ylim=range(unlist(rss))`
-
-`ls("package:elasticnet")`
+### Miscellaneous
+* `unlist(rss)` = converts a list object into data frame/vector
+* `ls("package:elasticnet")` = list methods in package

2_RPROG/R_Programming_Course_Notes.html

@@ -133,11 +133,13 @@ <h4 class="author"><em>Xing Su</em></h4>
 <li><a href="#optimization">Optimization</a></li>
 </ul></li>
 <li><a href="#debugging">Debugging</a></li>
-<li><a href="#r-profiler">R Profiler</a></li>
+<li><a href="#r-profiler">R Profiler</a><ul>
+<li><a href="#miscellaneous">Miscellaneous</a></li>
+</ul></li>
 </ul>
 </div>
 
-<p><span class="math">\(\pagebreak\)</span></p>
+
 <div id="overview-and-history-of-r" class="section level2">
 <h2>Overview and History of R</h2>
 <ul>
@@ -194,7 +196,7 @@ <h2>Overview and History of R</h2>
 <li>5000+ packages available</li>
 </ul></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 <div id="coding-standards" class="section level2">
 <h2>Coding Standards</h2>
@@ -239,7 +241,7 @@ <h2>R Console and Evaluation</h2>
 </ul></li>
 <li><code>[1]</code> at the beginning of the output = which element of the vector is being shown</li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 <div id="r-objects-and-data-structures" class="section level2">
 <h2>R Objects and Data Structures</h2>
@@ -445,7 +447,7 @@ <h3>Factors</h3>
 <li><code>table(factorVar)</code> = how many of each are in the factor</li>
 </ul></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="missing-values" class="section level2">
@@ -481,7 +483,7 @@ <h2>Missing Values</h2>
 </ul></li>
 <li><p><strong>Imputing Missing Values</strong> = replacing missing values with estimates (can be averages from all other data with the similar conditions)</p></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 <div id="sequence-of-numbers" class="section level2">
 <h2>Sequence of Numbers</h2>
@@ -579,7 +581,7 @@ <h3>Partial Matching</h3>
 <li>x[[“a”, exact = false]]</li>
 </ul></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="logic" class="section level2">
@@ -628,7 +630,7 @@ <h2>Understanding Data</h2>
 </ul></li>
 <li><code>View(data.frame)</code> = opens and view the content of the data frame</li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 <div id="split-apply-combine-funtions" class="section level2">
 <h2>Split-Apply-Combine Funtions</h2>
@@ -786,7 +788,7 @@ <h3><code>aggregate()</code></h3>
 <li><code>na.rm = TRUE</code> –&gt; removes NA values</li>
 </ul></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="simulation" class="section level2">
@@ -880,7 +882,7 @@ <h3>Generate Numbers for a Linear Model</h3>
 <pre class="sourceCode r"><code class="sourceCode r">x &lt;-<span class="st"> </span><span class="kw">rnorm</span>(<span class="dv">100</span>)
 log.mu &lt;-<span class="st"> </span><span class="fl">0.5</span> +<span class="st"> </span><span class="fl">0.3</span>*<span class="st"> </span>x
 y &lt;-<span class="st"> </span><span class="kw">rpois</span>(<span class="dv">100</span>, <span class="kw">exp</span>(log.mu))</code></pre>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="dates-and-times" class="section level2">
@@ -921,7 +923,7 @@ <h2>Base Graphics</h2>
 <li><code>break = 100</code> = split data into 100 bins</li>
 </ul></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 <div id="reading-tabular-data" class="section level2">
 <h2>Reading Tabular Data</h2>
@@ -1009,7 +1011,7 @@ <h3>Interfaces to the Outside World</h3>
 </ul></li>
 </ul></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="control-structures" class="section level2">
@@ -1116,7 +1118,7 @@ <h3><code>next</code> and <code>return</code></h3>
     }
     ## Do something here
 }</code></pre>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="functions" class="section level2">
@@ -1171,7 +1173,7 @@ <h2>Functions</h2>
 <li><em><strong>Note</strong>: arguments coming after … must be explicitly matched and cannot be partially matched</em></li>
 </ul></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 <div id="scoping" class="section level2">
 <h2>Scoping</h2>
@@ -1309,7 +1311,7 @@ <h3>Optimization</h3>
 ##          b &lt;- -0.5*sum((data-mu)^2) / (sigma^2)
 ##          -(a + b)
 ##     }
-## &lt;environment: 0x7fb869178030&gt;</code></pre>
+## &lt;environment: 0x7fc51d30b668&gt;</code></pre>
 <pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Estimating Prameters</span>
 <span class="kw">optim</span>(<span class="kw">c</span>(<span class="dt">mu =</span> <span class="dv">0</span>, <span class="dt">sigma =</span> <span class="dv">1</span>), nLL)$par</code></pre>
 <pre><code>##       mu    sigma 
@@ -1322,7 +1324,7 @@ <h3>Optimization</h3>
 nLL &lt;-<span class="st"> </span><span class="kw">make.NegLogLik</span>(normals, <span class="kw">c</span>(<span class="dv">1</span>, <span class="ot">FALSE</span>))
 <span class="kw">optimize</span>(nLL, <span class="kw">c</span>(<span class="fl">1e-6</span>, <span class="dv">10</span>))$minimum</code></pre>
 <pre><code>## [1] 1.800596</code></pre>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="debugging" class="section level2">
@@ -1377,7 +1379,7 @@ <h2>R Profiler</h2>
     }
 })</code></pre>
 <pre><code>##    user  system elapsed 
-##   0.143   0.003   0.150</code></pre>
+##   0.150   0.005   0.170</code></pre>
 <ul>
 <li><code>system.time(expression)</code>
 <ul>
@@ -1426,8 +1428,13 @@ <h2>R Profiler</h2>
 <li><em><strong>Note</strong>: R must be compiled with profiles support (generally the case)</em></li>
 <li><em><strong>Note</strong>: should NOT be used with system.time()</em></li>
 </ul>
-<p><code>ylim=range(unlist(rss))</code></p>
-<p><code>ls(&quot;package:elasticnet&quot;)</code></p>
+<div id="miscellaneous" class="section level3">
+<h3>Miscellaneous</h3>
+<ul>
+<li><code>unlist(rss)</code> = converts a list object into data frame/vector</li>
+<li><code>ls(&quot;package:elasticnet&quot;)</code> = list methods in package</li>
+</ul>
+</div>
 </div>
 
 

2_RPROG/R_Programming_Course_Notes.pdf

@@ -80,7 +80,7 @@ <h4 class="author"><em>Xing Su</em></h4>
 </ul>
 </div>
 
-<p><span class="math">\(\pagebreak\)</span></p>
+
 <div id="overview" class="section level2">
 <h2>Overview</h2>
 <ul>

3_GETDATA/Getting_and_Cleaning_Data_Course_Notes.html

@@ -125,7 +125,7 @@ <h4 class="author"><em>Xing Su</em></h4>
 </ul>
 </div>
 
-<p><span class="math">\(\pagebreak\)</span></p>
+
 <div id="replication" class="section level2">
 <h2>Replication</h2>
 <ul>
@@ -433,7 +433,7 @@ <h3>Create Reproducible Code</h3>
 </ul></li>
 <li>ensure all analysis is reproducible (standard that most data analysis are judged on)</li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="organizing-data-analysis" class="section level2">
@@ -653,7 +653,7 @@ <h2>R Markdown</h2>
 <li><em><strong>Note</strong>: author should NOT edit/save the .md or .mtml document until you are done with the document </em></li>
 </ul></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 <div id="communicating-results" class="section level2">
 <h2>Communicating Results</h2>
@@ -691,7 +691,7 @@ <h3><a href="http://rpubs.com/">RPubs</a></h3>
 <li>after kniting the R Markdown file in HTML, you can click on <strong>Publish</strong> to publish the HTML document on RPubs</li>
 <li><em><strong>Note</strong>: all publications to RPups are publicly available immediately</em></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="reproducible-research-checklist" class="section level2">
@@ -820,7 +820,7 @@ <h3>Don’ts</h3>
 <li>should save the <strong>data/code</strong> instead of the output</li>
 </ul></li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="replication-vs-reproducibility" class="section level2">
@@ -916,7 +916,7 @@ <h3>Evidence-based Data Analysis</h3>
 <li>gives reviewers an important tool without dramatically increasing the burden on them</li>
 <li>allows more effort to be focused on improving the quality of “upstream” aspects of scientific research</li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="caching-computations" class="section level2">
@@ -1068,7 +1068,7 @@ <h3><code>cacher</code> Package</h3>
 <span class="co"># output:</span>
 <span class="co"># / transferring cache db file 81b6dc23736f3d72c6...</span>
 <span class="co"># [1] 0.000052457</span></code></pre>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="case-study-air-pollution" class="section level2">
@@ -1109,7 +1109,7 @@ <h3>Analysis: Does Nickel Make PM Toxic?</h3>
 <li>reproducibility of NMMAPS allowed for a secondary analysis (and linking with PM chemical constituent data) investigating a novel hypothesis (Lippmann <em>et al.</em>), as well as a critique of that analysis and new findings (Dominici <em>et al.</em>)</li>
 <li>original hypothesis not necessarily invalidated, but evidence not as strong as originally suggested (more work should be done)</li>
 </ul>
-<p><span class="math">\(\pagebreak\)</span></p>
+
 </div>
 </div>
 <div id="case-study-high-throughput-biology" class="section level2">