Converts the Keynote slides to HTML5 ioslides

02-literate-programming-slides.Rmd

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+---
+title: "Literate Programming"
+author: "Reproducible Science Curriculum Participants"
+output:
+  ioslides_presentation:
+    highlight: pygments
+    widescreen: yes
+    css: slides.css
+---
+
+# Motivating literate programming
+
+## Issues
+
+How to
+
+* organize your work?
+* make work more pleasant for yourself? (less tedium, less manual, less ...) 
+* reduce friction for collaboration?
+* reduce friction for communication?
+* make your work navigable, interpretable, and repeatable by others?
+
+A lot of this can be built into the normal coding and analysis process by using specific tools and habits.
+
+## Getting the analysis right is only one link
+
+Process, packaging, and presentation are often the weak links in the chain.
+
+![The weakest link in the chain](media/brokenChain.jpg)
+
+# Markdown
+
+## What is Markdown?
+
+* Markdown is a particular type of markup language. Markup languages are designed to produce documents from plain text.
+    * You may be familiar with _LaTeX_, another (though less human friendly) text markup language.
+* Tools render markdown to different formats (for example, HTML/pdf/Word). 
+    * The main tool for rendering markdown is [pandoc](http://johnmacfarlane.net/pandoc/)).
+
+<p style="font-size: smaller;">Adapted from [Carson Sievert's markdown slides](http://cpsievert.github.io/slides/markdown/#/2).</p>
+
+## Why Markdown?
+
+* Easy to learn and use. Focus on _content_, rather than _coding_ and debugging _errors_.
+* Easy to edit yet very flexible. Can add HTML, CSS, and JavaScript.
+* The rendering process is through tools and is thus an automatable and repeatable process.
+* Lends itself well to version control, collaboration, sharing, and reuse.
+
+<p style="font-size: smaller;">Adapted from [Carson Sievert's markdown slides](http://cpsievert.github.io/slides/markdown/#/1).</p>
+
+## Markdown enables fast publishing to the web
+
+**Markdown**: Easy to write and read in an editor
+
+**HTML**: Easy to publish and read on the web
+
+## Markdown versus HTML code {.code-columns}
+
+<pre class="codesample" style="width: 49%; margin-right: 0;">
+This is a Markdown document.
+
+## Medium header &lt;!-- header 2, actually --&gt;
+
+It's easy to do *italics* or __make things bold__.
+
+> All models are wrong, but some are useful. An approximate answer to the right problem is worth a good deal more than an exact answer to an approximate problem. 
+
+Code block below. Just affects formatting here.
+
+```
+x <- 3 * 4
+```
+
+I can haz equations. Inline equations, such as the average is computed as $\frac{1}{n} \sum_{i=1}^{n} x_{i}$. Or display equations like this:
+
+$$
+\begin{equation*}
+|x|= 
+\begin{cases} x & \text{if $x\ge 0$,} \\\\
+-x &\text{if $x\lt 0$.}
+\end{cases}
+\end{equation*}
+$$
+</pre>
+
+<pre class="codesample" style="width: 49%; margin-left: 0.3em;">
+&lt;!DOCTYPE html&gt;
+&lt;html&gt;
+&lt;head&gt;
+&lt;meta http-equiv="Content-Type" content="text/html; charset=utf-8"/&gt;
+&lt;title&gt;Title&lt;/title&gt;
+&lt;!-- MathJax scripts --&gt;
+&lt;script type="text/javascript" src="..."&gt;&lt;/script&gt;
+&lt;style type="text/css"&gt;
+body {
+   font-family: Helvetica, arial, sans-serif;
+   font-size: 14px;
+...
+&lt;/style&gt;
+&lt;/head&gt;
+&lt;body&gt;
+&lt;p&gt;This is a Markdown document.&lt;/p&gt;
+
+&lt;h2&gt;Medium header&lt;/h2&gt;
+
+&lt;p&gt;It&#39;s easy to do &lt;em&gt;italics&lt;/em&gt; or &lt;strong&gt;make things bold&lt;/strong&gt;.&lt;/p&gt;
+
+&lt;blockquote&gt;&lt;p&gt;All models are wrong, but some are...&lt;/p&gt;&lt;/blockquote&gt;
+&lt;p&gt;Code block below. Just affects formatting here.&lt;/p&gt;
+
+&lt;pre&gt;&lt;code&gt;x &lt;- 3 * 4
+&lt;/code&gt;&lt;/pre&gt;
+</pre>
+<img style="max-width: 80px; position: absolute; left: 50%; top: 4.1em; margin-left: -85px;" src="media/smiley-face-clipart.png"/>
+<img style="max-width: 80px; position: absolute; left: 95%; top: 4.1em; margin-left: -80px;" src="media/frowny-face-clipart.png"/>
+
+## Markdown versus rendered HTML {.code-columns}
+
+<pre class="codesample" style="width: 49%; margin-right: 0;">
+This is a Markdown document.
+
+## Medium header &lt;!-- header 2, actually --&gt;
+
+It's easy to do *italics* or __make things bold__.
+
+> All models are wrong, but some are useful. An approximate answer to the right problem is worth a good deal more than an exact answer to an approximate problem. 
+
+Code block below. Just affects formatting here.
+
+```
+x <- 3 * 4
+```
+
+I can haz equations. Inline equations, such as the average is computed as $\frac{1}{n} \sum_{i=1}^{n} x_{i}$. Or display equations like this:
+
+$$
+\begin{equation*}
+|x|= 
+\begin{cases} x & \text{if $x\ge 0$,} \\
+-x &\text{if $x\lt 0$.}
+\end{cases}
+\end{equation*}
+$$
+</pre>
+
+<div class="right-column">
+This is a Markdown document.
+
+<h2>Medium header</h2>
+
+It's easy to do *italics* or __make things bold__.
+
+> All models are wrong, but some are useful. An approximate answer to the right problem is worth a good deal more than an exact answer to an approximate problem. 
+
+Code block below. Just affects formatting here.
+
+```
+x <- 3 * 4
+```
+
+I can haz equations. Inline equations, such as the average is computed as $\frac{1}{n} \sum_{i=1}^{n} x_{i}$. Or display equations like this:
+
+$$
+\begin{equation*}
+|x|= 
+\begin{cases} x & \text{if $x\ge 0$,} \\\\
+-x &\text{if $x\lt 0$.}
+\end{cases}
+\end{equation*}
+$$
+</div>
+<img style="max-width: 80px; position: absolute; left: 50%; top: 4.1em; margin-left: -85px;" src="media/smiley-face-clipart.png"/>
+<img style="max-width: 80px; position: absolute; left: 95%; top: 4.1em; margin-left: -80px;" src="media/smiley-face-clipart.png"/>
+
+## Markdown can be rendered to multiple formats
+
+* `pandoc` is a swiss-army knife tool for conversion
+
+<div style="margin-top: 1.5em; margin-left: -20%; text-align: center;">
+<img style="max-width: 120%;" src="media/pandoc-diagram.jpg"/>
+</div>
+
+# R Markdown
+
+## R Markdown is rendered to Markdown {.code-columns}
+
+<pre class="codesample" style="width: 40%; margin-right: 0;">
+This is an R Markdown document.
+
+```&#123;r&#125;
+x <- rnorm(1000)
+head(x)
+```
+
+`knitr` offers a lot of control over representing different types of output. We can also have inline R expressions computed on the fly. The mean $\bar{x} = \frac{1}{n} \sum_{i=1}^{n} x_{i}$ of the &#96;r length(x)&#96; random variates we generated is &#96;r round(mean(x), 3)&#96;. This figure is computed on-the-fly as well. No more copy-paste, including for figures:
+
+```&#123;r&#125;
+plot(density(x))
+```
+</pre>
+
+<pre class="codesample" style="width: 60%; margin-left: 0.3em;">
+This is an R Markdown document.
+
+```{r}
+x <- rnorm(1000)
+head(x)
+```
+
+`knitr` offers a lot of control over representing different types of output. We can also have inline R expressions computed on the fly. The mean $\bar{x} = \frac{1}{n} \sum_{i=1}^{n} x_{i}$ of the `r length(x)` random variates we generated is `r round(mean(x), 3)`. This figure is computed on-the-fly as well. No more copy-paste, including for figures:
+
+```r
+plot(density(x))
+```
+![plot of chunk unnamed-chunk-2](figure/unnamed-chunk-2.png)
+</pre>
+
+## Ideas, code, and generated results tied together {.code-columns}
+
+<pre class="codesample" style="width: 40%; margin-right: 0;">
+This is an R Markdown document.
+
+```&#123;r&#125;
+x <- rnorm(1000)
+head(x)
+```
+
+`knitr` offers a lot of control over representing different types of output. We can also have inline R expressions computed on the fly. The mean $\bar{x} = \frac{1}{n} \sum_{i=1}^{n} x_{i}$ of the &#96;r length(x)&#96; random variates we generated is &#96;r round(mean(x), 3)&#96;. This figure is computed on-the-fly as well. No more copy-paste, including for figures:
+
+```&#123;r&#125;
+plot(density(x))
+```
+</pre>
+
+<div class="right-column" style="width: 60%">
+This is an R Markdown document.
+
+```{r}
+x <- rnorm(1000)
+head(x)
+```
+
+`knitr` offers a lot of control over representing different types of output. We can also have inline R expressions computed on the fly. The mean $\bar{x} = \frac{1}{n} \sum_{i=1}^{n} x_{i}$ of the `r length(x)` random variates we generated is `r round(mean(x), 3)`. No more copy-paste, including for figures:
+
+```{r}
+plot(density(x))
+```
+</div>
+
+## Can be rendered interactively in RStudio
+
+<div style="margin-top: 1em; text-align: center;">
+<img style="max-width: 96%;" src="media/knitrButton-screenshot.png"/>
+</div>
+
+## Rendering can be automated is thus repeatable
+
+<div style="margin-top: 4em;"/>
+
+From within R:
+```r
+rmarkdown::render("filename.Rmd")
+```
+
+From the command line:
+```bash
+$ Rscript -e "rmarkdown::render('filename.Rmd')"
+```
+
+## Summary
+
+* R Markdown enables ideas and questions, the code that implements them, and the results generated by the implementation, to all stay together.
+
+* R Markdown toolchain allows automated, repeatable rendering
+    * for publishing to the web and viewing through a browser,
+    * and (through LaTeX) to obtain a submittable manuscript (in PDF or Word).
+
+* `knitr` is not limited to executing R code. See the book _Dynamic documents with R and knitr_ by Yihui Xie, part of the CRC Press / Chapman & Hall R Series (2013). ISBN: [9781482203530](http://www.isbnsearch.org/isbn/9781482203530).

slides.css

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+
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+}
+
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+}
+
+.right-column img {
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+
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+
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+
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+