diff --git a/02_RProgramming/DataTypes/Introduction to the R Language.pdf b/02_RProgramming/DataTypes/Introduction to the R Language.pdf
index cec046b60..b8f1bc492 100644
Binary files a/02_RProgramming/DataTypes/Introduction to the R Language.pdf and b/02_RProgramming/DataTypes/Introduction to the R Language.pdf differ
diff --git a/02_RProgramming/DataTypes/index.Rmd b/02_RProgramming/DataTypes/index.Rmd
index 65eb1ce54..19f8f1af4 100644
--- a/02_RProgramming/DataTypes/index.Rmd
+++ b/02_RProgramming/DataTypes/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}
@@ -200,7 +200,9 @@ NAs introduced by coercion
> as.logical(x)
[1] NA NA NA
> as.complex(x)
-[1] 0+0i 1+0i 2+0i 3+0i 4+0i 5+0i 6+0i
+[1] NA NA NA
+Warning message:
+NAs introduced by coercion
```
---
@@ -472,4 +474,4 @@ Data Types
- data frames
-- names
\ No newline at end of file
+- names
diff --git a/02_RProgramming/DataTypes/index.html b/02_RProgramming/DataTypes/index.html
index 9b50617cb..00c65c081 100644
--- a/02_RProgramming/DataTypes/index.html
+++ b/02_RProgramming/DataTypes/index.html
@@ -8,46 +8,46 @@
<meta name="generator" content="slidify" />
<meta name="apple-mobile-web-app-capable" content="yes">
<meta http-equiv="X-UA-Compatible" content="chrome=1">
- <link rel="stylesheet" href="../../libraries/frameworks/io2012/css/default.css" media="all" >
- <link rel="stylesheet" href="../../libraries/frameworks/io2012/phone.css"
+ <link rel="stylesheet" href="../../librariesNew/frameworks/io2012/css/default.css" media="all" >
+ <link rel="stylesheet" href="../../librariesNew/frameworks/io2012/css/phone.css"
media="only screen and (max-device-width: 480px)" >
- <link rel="stylesheet" href="../../libraries/frameworks/io2012/css/slidify.css" >
- <link rel="stylesheet" href="../../libraries/highlighters/highlight.js/css/tomorrow.css" />
- <base target="_blank"> <!-- This amazingness opens all links in a new tab. -->
- <script data-main="../../libraries/frameworks/io2012/js/slides"
- src="../../libraries/frameworks/io2012/js/require-1.0.8.min.js">
+ <link rel="stylesheet" href="../../librariesNew/frameworks/io2012/css/slidify.css" >
+ <link rel="stylesheet" href="../../librariesNew/highlighters/highlight.js/css/tomorrow.css" />
+ <base target="_blank"> <!-- This amazingness opens all links in a new tab. -->
+
+ <!-- Grab CDN jQuery, fall back to local if offline -->
+ <script src="http://ajax.aspnetcdn.com/ajax/jQuery/jquery-1.7.min.js"></script>
+ <script>window.jQuery || document.write('<script src="../../librariesNew/widgets/quiz/js/jquery.js"><\/script>')</script>
+ <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>Data Types and Basic Operations</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>Data Types and Basic Operations</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>Objects</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>R has five basic or “atomic” classes of objects:</p>
<ul>
@@ -73,11 +73,11 @@ <h2>Objects</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-2" style="background:;">
+<slide class="" id="slide-2" style="background:;">
<hgroup>
<h2>Numbers</h2>
</hgroup>
- <article>
+ <article data-timings="">
<ul>
<li><p>Numbers in R a generally treated as numeric objects (i.e. double
precision real numbers)</p></li>
@@ -97,11 +97,11 @@ <h2>Numbers</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-3" style="background:;">
+<slide class="" id="slide-3" style="background:;">
<hgroup>
<h2>Attributes</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>R objects can have attributes</p>
<ul>
@@ -119,11 +119,11 @@ <h2>Attributes</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-4" style="background:;">
+<slide class="" id="slide-4" style="background:;">
<hgroup>
<h2>Entering Input</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>At the R prompt we type expressions. The <code><-</code> symbol is the assignment operator.</p>
<pre><code class="r">> x <- 1
@@ -145,11 +145,11 @@ <h2>Entering Input</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-5" style="background:;">
+<slide class="" id="slide-5" style="background:;">
<hgroup>
<h2>Evaluation</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>When a complete expression is entered at the prompt, it is evaluated and the result of the evaluated expression is returned. The result may be auto-printed.</p>
<pre><code class="r">> x <- 5 ## nothing printed
@@ -165,11 +165,11 @@ <h2>Evaluation</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-6" style="background:;">
+<slide class="" id="slide-6" style="background:;">
<hgroup>
<h2>Printing</h2>
</hgroup>
- <article>
+ <article data-timings="">
<pre><code class="r">> x <- 1:20
> x
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
@@ -182,11 +182,11 @@ <h2>Printing</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-7" style="background:;">
+<slide class="" id="slide-7" style="background:;">
<hgroup>
<h2>Creating Vectors</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>The <code>c()</code> function can be used to create vectors of objects.</p>
<pre><code class="r">> x <- c(0.5, 0.6) ## numeric
@@ -208,11 +208,11 @@ <h2>Creating Vectors</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-8" style="background:;">
+<slide class="" id="slide-8" style="background:;">
<hgroup>
<h2>Mixing Objects</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>What about the following?</p>
<pre><code class="r">> y <- c(1.7, "a") ## character
@@ -226,11 +226,11 @@ <h2>Mixing Objects</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-9" style="background:;">
+<slide class="" id="slide-9" style="background:;">
<hgroup>
<h2>Explicit Coercion</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Objects can be explicitly coerced from one class to another using the <code>as.*</code> functions, if available.</p>
<pre><code class="r">> x <- 0:6
@@ -248,11 +248,11 @@ <h2>Explicit Coercion</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-10" style="background:;">
+<slide class="" id="slide-10" style="background:;">
<hgroup>
<h2>Explicit Coercion</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Nonsensical coercion results in <code>NA</code>s.</p>
<pre><code class="r">> x <- c("a", "b", "c")
@@ -263,18 +263,20 @@ <h2>Explicit Coercion</h2>
> as.logical(x)
[1] NA NA NA
> as.complex(x)
-[1] 0+0i 1+0i 2+0i 3+0i 4+0i 5+0i 6+0i
+[1] NA NA NA
+Warning message:
+NAs introduced by coercion
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-11" style="background:;">
+<slide class="" id="slide-11" style="background:;">
<hgroup>
<h2>Matrices</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Matrices are vectors with a <em>dimension</em> attribute. The dimension attribute is itself an integer vector of length 2 (nrow, ncol)</p>
<pre><code class="r">> m <- matrix(nrow = 2, ncol = 3)
@@ -293,11 +295,11 @@ <h2>Matrices</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-12" style="background:;">
+<slide class="" id="slide-12" style="background:;">
<hgroup>
<h2>Matrices (cont’d)</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Matrices are constructed <em>column-wise</em>, so entries can be thought of starting in the “upper left” corner and running down the columns.</p>
<pre><code class="r">> m <- matrix(1:6, nrow = 2, ncol = 3)
@@ -311,11 +313,11 @@ <h2>Matrices (cont’d)</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-13" style="background:;">
+<slide class="" id="slide-13" style="background:;">
<hgroup>
<h2>Matrices (cont’d)</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Matrices can also be created directly from vectors by adding a dimension attribute.</p>
<pre><code class="r">> m <- 1:10
@@ -332,11 +334,11 @@ <h2>Matrices (cont’d)</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-14" style="background:;">
+<slide class="" id="slide-14" style="background:;">
<hgroup>
<h2>cbind-ing and rbind-ing</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Matrices can be created by <em>column-binding</em> or <em>row-binding</em> with <code>cbind()</code> and <code>rbind()</code>.</p>
<pre><code class="r">> x <- 1:3
@@ -356,11 +358,11 @@ <h2>cbind-ing and rbind-ing</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-15" style="background:;">
+<slide class="" id="slide-15" style="background:;">
<hgroup>
<h2>Lists</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Lists are a special type of vector that can contain elements of different classes. Lists are a very important data type in R and you should get to know them well.</p>
<pre><code class="r">> x <- list(1, "a", TRUE, 1 + 4i)
@@ -382,11 +384,11 @@ <h2>Lists</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-16" style="background:;">
+<slide class="" id="slide-16" style="background:;">
<hgroup>
<h2>Factors</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Factors are used to represent categorical data. Factors can be unordered or ordered. One can think of a factor as an integer vector where each integer has a <em>label</em>.</p>
<ul>
@@ -398,11 +400,11 @@ <h2>Factors</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-17" style="background:;">
+<slide class="" id="slide-17" style="background:;">
<hgroup>
<h2>Factors</h2>
</hgroup>
- <article>
+ <article data-timings="">
<pre><code class="r">> x <- factor(c("yes", "yes", "no", "yes", "no"))
> x
[1] yes yes no yes no
@@ -421,11 +423,11 @@ <h2>Factors</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-18" style="background:;">
+<slide class="" id="slide-18" style="background:;">
<hgroup>
<h2>Factors</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>The order of the levels can be set using the <code>levels</code> argument to <code>factor()</code>. This can be important in linear modelling because the first level is used as the baseline level.</p>
<pre><code class="r">> x <- factor(c("yes", "yes", "no", "yes", "no"),
@@ -439,11 +441,11 @@ <h2>Factors</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-19" style="background:;">
+<slide class="" id="slide-19" style="background:;">
<hgroup>
<h2>Missing Values</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Missing values are denoted by <code>NA</code> or <code>NaN</code> for undefined mathematical operations. </p>
<ul>
@@ -457,11 +459,11 @@ <h2>Missing Values</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-20" style="background:;">
+<slide class="" id="slide-20" style="background:;">
<hgroup>
<h2>Missing Values</h2>
</hgroup>
- <article>
+ <article data-timings="">
<pre><code class="r">> x <- c(1, 2, NA, 10, 3)
> is.na(x)
[1] FALSE FALSE TRUE FALSE FALSE
@@ -478,11 +480,11 @@ <h2>Missing Values</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-21" style="background:;">
+<slide class="" id="slide-21" style="background:;">
<hgroup>
<h2>Data Frames</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Data frames are used to store tabular data</p>
<ul>
@@ -498,11 +500,11 @@ <h2>Data Frames</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-22" style="background:;">
+<slide class="" id="slide-22" style="background:;">
<hgroup>
<h2>Data Frames</h2>
</hgroup>
- <article>
+ <article data-timings="">
<pre><code class="r">> x <- data.frame(foo = 1:4, bar = c(T, T, F, F))
> x
foo bar
@@ -520,11 +522,11 @@ <h2>Data Frames</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-23" style="background:;">
+<slide class="" id="slide-23" style="background:;">
<hgroup>
<h2>Names</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>R objects can also have names, which is very useful for writing readable code and self-describing objects.</p>
<pre><code class="r">> x <- 1:3
@@ -542,11 +544,11 @@ <h2>Names</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-24" style="background:;">
+<slide class="" id="slide-24" style="background:;">
<hgroup>
<h2>Names</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Lists can also have names.</p>
<pre><code class="r">> x <- list(a = 1, b = 2, c = 3)
@@ -565,11 +567,11 @@ <h2>Names</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-25" style="background:;">
+<slide class="" id="slide-25" style="background:;">
<hgroup>
<h2>Names</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>And matrices.</p>
<pre><code class="r">> m <- matrix(1:4, nrow = 2, ncol = 2)
@@ -584,11 +586,11 @@ <h2>Names</h2>
<!-- Presenter Notes -->
</slide>
- <slide class="" id="slide-26" style="background:;">
+<slide class="" id="slide-26" style="background:;">
<hgroup>
<h2>Summary</h2>
</hgroup>
- <article>
+ <article data-timings="">
<p>Data Types</p>
<ul>
@@ -606,34 +608,191 @@ <h2>Summary</h2>
<slide class="backdrop"></slide>
</slides>
-
- <!--[if IE]>
+ <div class="pagination pagination-small" id='io2012-ptoc' style="display:none;">
+ <ul>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=1 title='Objects'>
+ 1
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=2 title='Numbers'>
+ 2
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=3 title='Attributes'>
+ 3
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=4 title='Entering Input'>
+ 4
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=5 title='Evaluation'>
+ 5
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=6 title='Printing'>
+ 6
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=7 title='Creating Vectors'>
+ 7
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=8 title='Mixing Objects'>
+ 8
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=9 title='Explicit Coercion'>
+ 9
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=10 title='Explicit Coercion'>
+ 10
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=11 title='Matrices'>
+ 11
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=12 title='Matrices (cont’d)'>
+ 12
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=13 title='Matrices (cont’d)'>
+ 13
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=14 title='cbind-ing and rbind-ing'>
+ 14
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=15 title='Lists'>
+ 15
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=16 title='Factors'>
+ 16
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=17 title='Factors'>
+ 17
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=18 title='Factors'>
+ 18
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=19 title='Missing Values'>
+ 19
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=20 title='Missing Values'>
+ 20
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=21 title='Data Frames'>
+ 21
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=22 title='Data Frames'>
+ 22
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=23 title='Names'>
+ 23
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=24 title='Names'>
+ 24
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=25 title='Names'>
+ 25
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=26 title='Summary'>
+ 26
+ </a>
+ </li>
+ </ul>
+ </div> <!--[if IE]>
<script
src="http://ajax.googleapis.com/ajax/libs/chrome-frame/1/CFInstall.min.js">
</script>
<script>CFInstall.check({mode: 'overlay'});</script>
<![endif]-->
</body>
-<!-- Grab CDN jQuery, fall back to local if offline -->
-<script src="http://ajax.aspnetcdn.com/ajax/jQuery/jquery-1.7.min.js"></script>
-<script>window.jQuery || document.write('<script src="../../libraries/widgets/quiz/js/jquery-1.7.min.js"><\/script>')</script>
-<!-- Load Javascripts for Widgets -->
-<!-- MathJax: Fall back to local if CDN offline but local image fonts are not supported (saves >100MB) -->
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [['$','$'], ['\\(','\\)']],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-<!-- <script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
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+ <!-- Load Javascripts for Widgets -->
+
+ <!-- MathJax: Fall back to local if CDN offline but local image fonts are not supported (saves >100MB) -->
+ <script type="text/x-mathjax-config">
+ MathJax.Hub.Config({
+ tex2jax: {
+ inlineMath: [['$','$'], ['\\(','\\)']],
+ processEscapes: true
+ }
+ });
+ </script>
+ <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+ <!-- <script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+ </script> -->
+ <script>window.MathJax || document.write('<script type="text/x-mathjax-config">MathJax.Hub.Config({"HTML-CSS":{imageFont:null}});<\/script><script src="../../librariesNew/widgets/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"><\/script>')
</script>
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-<script src="../../libraries/highlighters/highlight.js/highlight.pack.js"></script>
-<script>hljs.initHighlightingOnLoad();</script>
-<!-- DONE LOADING HIGHLIGHTER JS FILES -->
-</html>
\ No newline at end of file
+ <script src="../../librariesNew/highlighters/highlight.js/highlight.pack.js"></script>
+ <script>hljs.initHighlightingOnLoad();</script>
+ <!-- DONE LOADING HIGHLIGHTER JS FILES -->
+
+ </html>
\ No newline at end of file
diff --git a/02_RProgramming/DataTypes/index.md b/02_RProgramming/DataTypes/index.md
index ccd9ff364..19f8f1af4 100644
--- a/02_RProgramming/DataTypes/index.md
+++ b/02_RProgramming/DataTypes/index.md
@@ -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}
@@ -200,7 +200,9 @@ NAs introduced by coercion
> as.logical(x)
[1] NA NA NA
> as.complex(x)
-[1] 0+0i 1+0i 2+0i 3+0i 4+0i 5+0i 6+0i
+[1] NA NA NA
+Warning message:
+NAs introduced by coercion
```
---
diff --git a/03_GettingData/dplyr/chicago.zip b/03_GettingData/dplyr/chicago.zip
new file mode 100644
index 000000000..d0eb3a7fd
Binary files /dev/null and b/03_GettingData/dplyr/chicago.zip differ
diff --git a/04_ExploratoryAnalysis/ggplot2/ppt/ggplot2.pdf b/04_ExploratoryAnalysis/ggplot2/ppt/ggplot2.pdf
index 092a7e4c4..a04ed124a 100644
Binary files a/04_ExploratoryAnalysis/ggplot2/ppt/ggplot2.pdf and b/04_ExploratoryAnalysis/ggplot2/ppt/ggplot2.pdf differ
diff --git a/04_ExploratoryAnalysis/ggplot2/ppt/ggplot2.pptx b/04_ExploratoryAnalysis/ggplot2/ppt/ggplot2.pptx
index 44e98c5d4..7c3ec5979 100644
Binary files a/04_ExploratoryAnalysis/ggplot2/ppt/ggplot2.pptx and b/04_ExploratoryAnalysis/ggplot2/ppt/ggplot2.pptx differ
diff --git a/05_ReproducibleResearch/organizingADataAnalysis/index.Rmd b/05_ReproducibleResearch/organizingADataAnalysis/index.Rmd
index eae99fc98..e2db82a63 100644
--- a/05_ReproducibleResearch/organizingADataAnalysis/index.Rmd
+++ b/05_ReproducibleResearch/organizingADataAnalysis/index.Rmd
@@ -110,7 +110,7 @@ mode : selfcontained # {standalone, draft}
* Not necessary if you use R markdown
* Should contain step-by-step instructions for analysis
-* Here is an example [https://github.com/jtleek/swfdr/blob/master/README](https://github.com/jtleek/swfdr/blob/master/README)
+* Here is an example [https://github.com/jtleek/swfdr/blob/master/README.md](https://github.com/jtleek/swfdr/blob/master/README.md)
---
diff --git a/05_ReproducibleResearch/organizingADataAnalysis/index.html b/05_ReproducibleResearch/organizingADataAnalysis/index.html
index 027e1d484..ab751d4e7 100644
--- a/05_ReproducibleResearch/organizingADataAnalysis/index.html
+++ b/05_ReproducibleResearch/organizingADataAnalysis/index.html
@@ -1,59 +1,171 @@
<!DOCTYPE html>
<html>
<head>
- <title>Organizing a Data Analysis</title>
- <meta charset="utf-8">
- <meta name="description" content="Organizing a Data Analysis">
- <meta name="author" content="Roger D. Peng, Associate Professor of Biostatistics">
- <meta name="generator" content="slidify" />
- <meta name="apple-mobile-web-app-capable" content="yes">
- <meta http-equiv="X-UA-Compatible" content="chrome=1">
- <link rel="stylesheet" href="../../libraries/frameworks/io2012/css/default.css" media="all" >
- <link rel="stylesheet" href="../../libraries/frameworks/io2012/phone.css"
- media="only screen and (max-device-width: 480px)" >
- <link rel="stylesheet" href="../../libraries/frameworks/io2012/css/slidify.css" >
- <link rel="stylesheet" href="../../libraries/highlighters/highlight.js/css/zenburn.css" />
- <base target="_blank"> <!-- This amazingness opens all links in a new tab. -->
- <script data-main="../../libraries/frameworks/io2012/js/slides"
- src="../../libraries/frameworks/io2012/js/require-1.0.8.min.js">
- </script>
-
- <link rel="stylesheet" href = "../../assets/css/custom.css">
-<link rel="stylesheet" href = "../../assets/css/custom.css.BACKUP.546.css">
-<link rel="stylesheet" href = "../../assets/css/custom.css.BASE.546.css">
-<link rel="stylesheet" href = "../../assets/css/custom.css.LOCAL.546.css">
-<link rel="stylesheet" href = "../../assets/css/custom.css.orig">
-<link rel="stylesheet" href = "../../assets/css/custom.css.REMOTE.546.css">
-<link rel="stylesheet" href = "../../assets/css/ribbons.css">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+
+<title>Data analysis files</title>
+
+<script type="text/javascript">
+window.onload = function() {
+ var imgs = document.getElementsByTagName('img'), i, img;
+ for (i = 0; i < imgs.length; i++) {
+ img = imgs[i];
+ // center an image if it is the only element of its parent
+ if (img.parentElement.childElementCount === 1)
+ img.parentElement.style.textAlign = 'center';
+ }
+};
+</script>
+
+
+
+
+
+<style type="text/css">
+body, td {
+ font-family: sans-serif;
+ background-color: white;
+ font-size: 13px;
+}
+
+body {
+ max-width: 800px;
+ margin: auto;
+ padding: 1em;
+ line-height: 20px;
+}
+
+tt, code, pre {
+ font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace;
+}
+
+h1 {
+ font-size:2.2em;
+}
+
+h2 {
+ font-size:1.8em;
+}
+
+h3 {
+ font-size:1.4em;
+}
+
+h4 {
+ font-size:1.0em;
+}
+
+h5 {
+ font-size:0.9em;
+}
+
+h6 {
+ font-size:0.8em;
+}
+
+a:visited {
+ color: rgb(50%, 0%, 50%);
+}
+
+pre, img {
+ max-width: 100%;
+}
+pre {
+ overflow-x: auto;
+}
+pre code {
+ display: block; padding: 0.5em;
+}
+
+code {
+ font-size: 92%;
+ border: 1px solid #ccc;
+}
+
+code[class] {
+ background-color: #F8F8F8;
+}
+
+table, td, th {
+ border: none;
+}
+
+blockquote {
+ color:#666666;
+ margin:0;
+ padding-left: 1em;
+ border-left: 0.5em #EEE solid;
+}
+
+hr {
+ height: 0px;
+ border-bottom: none;
+ border-top-width: thin;
+ border-top-style: dotted;
+ border-top-color: #999999;
+}
+
+@media print {
+ * {
+ background: transparent !important;
+ color: black !important;
+ filter:none !important;
+ -ms-filter: none !important;
+ }
+
+ body {
+ font-size:12pt;
+ max-width:100%;
+ }
+
+ a, a:visited {
+ text-decoration: underline;
+ }
+
+ hr {
+ visibility: hidden;
+ page-break-before: always;
+ }
+
+ pre, blockquote {
+ padding-right: 1em;
+ page-break-inside: avoid;
+ }
+
+ tr, img {
+ page-break-inside: avoid;
+ }
+
+ img {
+ max-width: 100% !important;
+ }
+
+ @page :left {
+ margin: 15mm 20mm 15mm 10mm;
+ }
+
+ @page :right {
+ margin: 15mm 10mm 15mm 20mm;
+ }
+
+ p, h2, h3 {
+ orphans: 3; widows: 3;
+ }
+
+ h2, h3 {
+ page-break-after: avoid;
+ }
+}
+</style>
+
+
</head>
-<body style="opacity: 0">
- <slides class="layout-widescreen">
-
- <!-- LOGO SLIDE -->
- <!-- END LOGO 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>Organizing a Data Analysis</h1>
- <h2></h2>
- <p>Roger D. Peng, Associate Professor of Biostatistics<br/>Johns Hopkins Bloomberg School of Public Health</p>
- </hgroup>
- </slide>
-
- <!-- SLIDES -->
- <slide class="" id="slide-1" style="background:;">
- <hgroup>
- <h2>Data analysis files</h2>
- </hgroup>
- <article>
- <ul>
+
+<body>
+<h2>Data analysis files</h2>
+
+<ul>
<li>Data
<ul>
@@ -81,32 +193,22 @@ <h2>Data analysis files</h2>
</ul></li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
+<hr/>
- <slide class="" id="slide-2" style="background:;">
- <hgroup>
- <h2>Raw Data</h2>
- </hgroup>
- <article>
- <p><img class=center src=../../assets/img/medicalrecord.png height='400'/></p>
+<h2>Raw Data</h2>
+
+<p><img class=center src=../../assets/img/medicalrecord.png height='400'/></p>
<ul>
<li>Should be stored in your analysis folder</li>
<li>If accessed from the web, include url, description, and date accessed in README</li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
+<hr/>
+
+<h2>Processed data</h2>
- <slide class="" id="slide-3" style="background:;">
- <hgroup>
- <h2>Processed data</h2>
- </hgroup>
- <article>
- <p><img class=center src=../../assets/img/excel.png height='400'/></p>
+<p><img class=center src=../../assets/img/excel.png height='400'/></p>
<ul>
<li>Processed data should be named so it is easy to see which script generated the data. </li>
@@ -114,32 +216,22 @@ <h2>Processed data</h2>
<li>Processed data should be <a href="http://vita.had.co.nz/papers/tidy-data.pdf">tidy</a></li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
+<hr/>
+
+<h2>Exploratory figures</h2>
- <slide class="" id="slide-4" style="background:;">
- <hgroup>
- <h2>Exploratory figures</h2>
- </hgroup>
- <article>
- <p><img class=center src=../../assets/img/example10.png height='400'/></p>
+<p><img class=center src=../../assets/img/example10.png height='400'/></p>
<ul>
<li>Figures made during the course of your analysis, not necessarily part of your final report.</li>
-<li>They do not need to be "pretty"</li>
+<li>They do not need to be “pretty”</li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
+<hr/>
- <slide class="" id="slide-5" style="background:;">
- <hgroup>
- <h2>Final Figures</h2>
- </hgroup>
- <article>
- <p><img class=center src=../../assets/img/figure1final.png height='400'/></p>
+<h2>Final Figures</h2>
+
+<p><img class=center src=../../assets/img/figure1final.png height='400'/></p>
<ul>
<li>Usually a small subset of the original figures</li>
@@ -147,16 +239,11 @@ <h2>Final Figures</h2>
<li>Possibly multiple panels</li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
+<hr/>
+
+<h2>Raw scripts</h2>
- <slide class="" id="slide-6" style="background:;">
- <hgroup>
- <h2>Raw scripts</h2>
- </hgroup>
- <article>
- <p><img class=center src=../../assets/img/rawcode.png height='350'/></p>
+<p><img class=center src=../../assets/img/rawcode.png height='350'/></p>
<ul>
<li>May be less commented (but comments help you!)</li>
@@ -164,16 +251,11 @@ <h2>Raw scripts</h2>
<li>May include analyses that are later discarded</li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
+<hr/>
- <slide class="" id="slide-7" style="background:;">
- <hgroup>
- <h2>Final scripts</h2>
- </hgroup>
- <article>
- <p><img class=center src=../../assets/img/finalscript2.png height='300'/></p>
+<h2>Final scripts</h2>
+
+<p><img class=center src=../../assets/img/finalscript2.png height='300'/></p>
<ul>
<li>Clearly commented
@@ -186,16 +268,11 @@ <h2>Final scripts</h2>
<li>Only analyses that appear in the final write-up</li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
+<hr/>
+
+<h2>R markdown files</h2>
- <slide class="" id="slide-8" style="background:;">
- <hgroup>
- <h2>R markdown files</h2>
- </hgroup>
- <article>
- <p><img class=center src=../../assets/img/rmd.png height='400'/></p>
+<p><img class=center src=../../assets/img/rmd.png height='400'/></p>
<ul>
<li><a href="http://www.rstudio.com/ide/docs/authoring/using_markdown">R markdown</a> files can be used to generate reproducible reports</li>
@@ -203,33 +280,23 @@ <h2>R markdown files</h2>
<li>Very easy to create in <a href="http://www.rstudio.com/">Rstudio</a></li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
+<hr/>
- <slide class="" id="slide-9" style="background:;">
- <hgroup>
- <h2>Readme files</h2>
- </hgroup>
- <article>
- <p><img class=center src=../../assets/img/readme.png height='400'/></p>
+<h2>Readme files</h2>
+
+<p><img class=center src=../../assets/img/readme.png height='400'/></p>
<ul>
<li>Not necessary if you use R markdown</li>
<li>Should contain step-by-step instructions for analysis</li>
-<li>Here is an example <a href="https://github.com/jtleek/swfdr/blob/master/README">https://github.com/jtleek/swfdr/blob/master/README</a></li>
+<li>Here is an example <a href="https://github.com/jtleek/swfdr/blob/master/README.md">https://github.com/jtleek/swfdr/blob/master/README.md</a></li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
+<hr/>
+
+<h2>Text of the document</h2>
- <slide class="" id="slide-10" style="background:;">
- <hgroup>
- <h2>Text of the document</h2>
- </hgroup>
- <article>
- <p><img class=center src=../../assets/img/swfdr.png height='350'/></p>
+<p><img class=center src=../../assets/img/swfdr.png height='350'/></p>
<ul>
<li>It should include a title, introduction (motivation), methods (statistics you used), results (including measures of uncertainty), and conclusions (including potential problems)</li>
@@ -238,56 +305,17 @@ <h2>Text of the document</h2>
<li>References should be included for statistical methods</li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
+<hr/>
+
+<h2>Further resources</h2>
- <slide class="" id="slide-11" style="background:;">
- <hgroup>
- <h2>Further resources</h2>
- </hgroup>
- <article>
- <ul>
+<ul>
<li>Information about a non-reproducible study that led to cancer patients being mistreated: <a href="http://simplystatistics.org/2012/02/27/the-duke-saga-starter-set/">The Duke Saga Starter Set</a></li>
<li><a href="http://biostatistics.oxfordjournals.org/content/10/3/405.full">Reproducible research and Biostatistics</a></li>
<li><a href="http://www.r-statistics.com/2010/09/managing-a-statistical-analysis-project-guidelines-and-best-practices/">Managing a statistical analysis project guidelines and best practices</a></li>
<li><a href="http://projecttemplate.net/">Project template</a> - a pre-organized set of files for data analysis</li>
</ul>
- </article>
- <!-- Presenter Notes -->
-</slide>
-
- <slide class="backdrop"></slide>
- </slides>
-
- <!--[if IE]>
- <script
- src="http://ajax.googleapis.com/ajax/libs/chrome-frame/1/CFInstall.min.js">
- </script>
- <script>CFInstall.check({mode: 'overlay'});</script>
- <![endif]-->
</body>
-<!-- Grab CDN jQuery, fall back to local if offline -->
-<script src="http://ajax.aspnetcdn.com/ajax/jQuery/jquery-1.7.min.js"></script>
-<script>window.jQuery || document.write('<script src="../../libraries/widgets/quiz/js/jquery-1.7.min.js"><\/script>')</script>
-<!-- Load Javascripts for Widgets -->
-<!-- MathJax: Fall back to local if CDN offline but local image fonts are not supported (saves >100MB) -->
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [['$','$'], ['\\(','\\)']],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-<!-- <script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script> -->
-<script>window.MathJax || document.write('<script type="text/x-mathjax-config">MathJax.Hub.Config({"HTML-CSS":{imageFont:null}});<\/script><script src="../../libraries/widgets/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"><\/script>')
-</script>
-<!-- LOAD HIGHLIGHTER JS FILES -->
-<script src="../../libraries/highlighters/highlight.js/highlight.pack.js"></script>
-<script>hljs.initHighlightingOnLoad();</script>
-<!-- DONE LOADING HIGHLIGHTER JS FILES -->
-</html>
\ No newline at end of file
+
+</html>
diff --git a/05_ReproducibleResearch/organizingADataAnalysis/index.md b/05_ReproducibleResearch/organizingADataAnalysis/index.md
index eae99fc98..e2db82a63 100644
--- a/05_ReproducibleResearch/organizingADataAnalysis/index.md
+++ b/05_ReproducibleResearch/organizingADataAnalysis/index.md
@@ -110,7 +110,7 @@ mode : selfcontained # {standalone, draft}
* Not necessary if you use R markdown
* Should contain step-by-step instructions for analysis
-* Here is an example [https://github.com/jtleek/swfdr/blob/master/README](https://github.com/jtleek/swfdr/blob/master/README)
+* Here is an example [https://github.com/jtleek/swfdr/blob/master/README.md](https://github.com/jtleek/swfdr/blob/master/README.md)
---
diff --git a/06_StatisticalInference/homework/hw1.Rmd b/06_StatisticalInference/homework/hw1.Rmd
index 7f31c63a0..f5476f5c7 100644
--- a/06_StatisticalInference/homework/hw1.Rmd
+++ b/06_StatisticalInference/homework/hw1.Rmd
@@ -40,22 +40,22 @@ Creating Data Products
--- &radio
-Consider influenza epidemics for two parent heterosexual families. Suppose that the probability is 15% that at least one of the parents has contracted the disease. The probability that the father has contracted influenza is 6% while that the mother contracted the disease is 5%. What is the probability that both contracted influenza expressed as a whole number percentage?
+Consider influenza epidemics for two parent heterosexual families. Suppose that the probability is 15% that at least one of the parents has contracted the disease. The probability that the father has contracted influenza is 10% while that the mother contracted the disease is 9%. What is the probability that both contracted influenza expressed as a whole number percentage?
1. 15%
-2. 6%
-3. 5%
-4. _2%_
+2. 10%
+3. 9%
+4. _4%_
*** .hint
-$A = Father$, $P(A) = .06$, $B = Mother$, $P(B) = .05$
+$A = Father$, $P(A) = .10$, $B = Mother$, $P(B) = .09$
$P(A\cup B) = .15$,
*** .explanation
-$P(A\cup B) = P(A) + P(B) - 2 P(AB)$ thus
-$$.15 = .06 + .05 - 2 P(AB)$$
+$P(A\cup B) = P(A) + P(B) - P(AB)$ thus
+$$.15 = .10 + .09 - P(AB)$$
```{r}
-(0.15 - .06 - .05) / 2
+.10 + .09 - .15
```
--- &radio
diff --git a/06_StatisticalInference/homework/hw1.html b/06_StatisticalInference/homework/hw1.html
index e2e14b4a6..3db02f1ae 100644
--- a/06_StatisticalInference/homework/hw1.html
+++ b/06_StatisticalInference/homework/hw1.html
@@ -63,13 +63,13 @@ <h2>About these slides</h2>
<article data-timings="">
<div class="quiz quiz-single well ">
- <p>Consider influenza epidemics for two parent heterosexual families. Suppose that the probability is 15% that at least one of the parents has contracted the disease. The probability that the father has contracted influenza is 6% while that the mother contracted the disease is 5%. What is the probability that both contracted influenza expressed as a whole number percentage?</p>
+ <p>Consider influenza epidemics for two parent heterosexual families. Suppose that the probability is 15% that at least one of the parents has contracted the disease. The probability that the father has contracted influenza is 10% while that the mother contracted the disease is 9%. What is the probability that both contracted influenza expressed as a whole number percentage?</p>
<ol>
<li>15%</li>
-<li>6%</li>
-<li>5%</li>
-<li><em>2%</em></li>
+<li>10%</li>
+<li>9%</li>
+<li><em>4%</em></li>
</ol>
<button class="quiz-submit btn btn-primary">Submit</button>
@@ -78,18 +78,18 @@ <h2>About these slides</h2>
<button class="quiz-clear btn btn-danger">Clear</button>
<div class="quiz-hint">
- <p>\(A = Father\), \(P(A) = .06\), \(B = Mother\), \(P(B) = .05\)
+ <p>\(A = Father\), \(P(A) = .10\), \(B = Mother\), \(P(B) = .09\)
\(P(A\cup B) = .15\), </p>
</div>
<div class="quiz-explanation">
- <p>\(P(A\cup B) = P(A) + P(B) - 2 P(AB)\) thus
-\[.15 = .06 + .05 - 2 P(AB)\]</p>
+ <p>\(P(A\cup B) = P(A) + P(B) - P(AB)\) thus
+\[.15 = .10 + .09 - P(AB)\]</p>
-<pre><code class="r">(0.15 - .06 - .05) / 2
+<pre><code class="r">.10 + .09 - .15
</code></pre>
-<pre><code>[1] 0.02
+<pre><code>[1] 0.04
</code></pre>
</div>
@@ -107,7 +107,7 @@ <h2>About these slides</h2>
<ol>
<li>1.00</li>
<li>0.75</li>
-<li>0.50</li>
+<li><em>0.50</em></li>
<li>0.25</li>
</ol>
diff --git a/06_StatisticalInference/homework/hw1.md b/06_StatisticalInference/homework/hw1.md
index 4a7add5f0..0025d9fc3 100644
--- a/06_StatisticalInference/homework/hw1.md
+++ b/06_StatisticalInference/homework/hw1.md
@@ -25,27 +25,27 @@ Creating Data Products
--- &radio
-Consider influenza epidemics for two parent heterosexual families. Suppose that the probability is 15% that at least one of the parents has contracted the disease. The probability that the father has contracted influenza is 6% while that the mother contracted the disease is 5%. What is the probability that both contracted influenza expressed as a whole number percentage?
+Consider influenza epidemics for two parent heterosexual families. Suppose that the probability is 15% that at least one of the parents has contracted the disease. The probability that the father has contracted influenza is 10% while that the mother contracted the disease is 9%. What is the probability that both contracted influenza expressed as a whole number percentage?
1. 15%
-2. 6%
-3. 5%
-4. _2%_
+2. 10%
+3. 9%
+4. _4%_
*** .hint
-$A = Father$, $P(A) = .06$, $B = Mother$, $P(B) = .05$
+$A = Father$, $P(A) = .10$, $B = Mother$, $P(B) = .09$
$P(A\cup B) = .15$,
*** .explanation
-$P(A\cup B) = P(A) + P(B) - 2 P(AB)$ thus
-$$.15 = .06 + .05 - 2 P(AB)$$
+$P(A\cup B) = P(A) + P(B) - P(AB)$ thus
+$$.15 = .10 + .09 - P(AB)$$
```r
-(0.15 - .06 - .05) / 2
+.10 + .09 - .15
```
```
-[1] 0.02
+[1] 0.04
```
@@ -55,7 +55,7 @@ A random variable, $X$, is uniform, a box from $0$ to $1$ of height $1$. (So tha
1. 1.00
2. 0.75
-3. 0.50
+3. _0.50_
4. 0.25
*** .hint
diff --git a/06_StatisticalInference/homework/hw2.Rmd b/06_StatisticalInference/homework/hw2.Rmd
index 3a568425c..b38eab299 100644
--- a/06_StatisticalInference/homework/hw2.Rmd
+++ b/06_StatisticalInference/homework/hw2.Rmd
@@ -157,10 +157,10 @@ Let $p=.5$ and $X$ be binomial
*** .explanation
-<span class="answer">`r round(pbinom(4, prob = .5, size = 6, lower.tail = TRUE) * 100, 1)`</span>
+<span class="answer">`r round(pbinom(4, prob = .5, size = 6, lower.tail = FALSE) * 100, 1)`</span>
```{r}
-round(pbinom(4, prob = .5, size = 6, lower.tail = TRUE) * 100, 1)
+round(pbinom(4, prob = .5, size = 6, lower.tail = FALSE) * 100, 1)
```
--- &multitext
@@ -210,9 +210,9 @@ If you roll ten standard dice, take their average, then repeat this process over
$$Var(\bar X) = \sigma^2 /n$$
*** .explanation
-The answer will be <span class="answer">`r round( mean(1 : 6 - 3.5) ^2 / 100, 3)`</span>
-since the variance of the sampling distribution of the mean is $\sigma^2/12$
-and the variance of a die roll is
+The answer will be <span class="answer">`r round( mean( (1 : 6 - 3.5) ^2) / 10, 3)`</span>
+since the variance of the sampling distribution of the mean is $\sigma^2/10$
+where $\sigma^2$ is the variance of a single die roll, which is
```{r}
mean((1 : 6 - 3.5)^2)
diff --git a/06_StatisticalInference/homework/hw2.html b/06_StatisticalInference/homework/hw2.html
index 5bab28043..e7a3d6a50 100644
--- a/06_StatisticalInference/homework/hw2.html
+++ b/06_StatisticalInference/homework/hw2.html
@@ -48,12 +48,11 @@ <h2>About these slides</h2>
</hgroup>
<article data-timings="">
<ul>
-<li>These are some practice problems for Statistical Inference Quiz 1</li>
+<li>These are some practice problems for Statistical Inference Quiz 2</li>
<li>They were created using slidify interactive which you will learn in
Creating Data Products</li>
<li>Please help improve this with pull requests here
-(<a href="https://github.com/bcaffo/courses">https://github.com/bcaffo/courses</a>)
-runif(1)</li>
+(<a href="https://github.com/bcaffo/courses">https://github.com/bcaffo/courses</a>)</li>
</ul>
</article>
@@ -288,12 +287,12 @@ <h2>About these slides</h2>
</div>
<div class="quiz-explanation">
- <p><span class="answer">89.1</span></p>
+ <p><span class="answer">10.9</span></p>
-<pre><code class="r">round(pbinom(4, prob = .5, size = 6, lower.tail = TRUE) * 100, 1)
+<pre><code class="r">round(pbinom(4, prob = .5, size = 6, lower.tail = FALSE) * 100, 1)
</code></pre>
-<pre><code>[1] 89.1
+<pre><code>[1] 10.9
</code></pre>
</div>
@@ -388,9 +387,9 @@ <h2>About these slides</h2>
</div>
<div class="quiz-explanation">
- <p>The answer will be <span class="answer">0</span>
-since the variance of the sampling distribution of the mean is \(\sigma^2/12\)
-and the variance of a die roll is </p>
+ <p>The answer will be <span class="answer">0.292</span>
+since the variance of the sampling distribution of the mean is \(\sigma^2/10\)
+where \(\sigma^2\) is the variance of a single die roll, which is </p>
<pre><code class="r">mean((1 : 6 - 3.5)^2)
</code></pre>
diff --git a/06_StatisticalInference/homework/hw2.md b/06_StatisticalInference/homework/hw2.md
index 32ef6b25f..44ecbe56b 100644
--- a/06_StatisticalInference/homework/hw2.md
+++ b/06_StatisticalInference/homework/hw2.md
@@ -16,12 +16,11 @@ mode : selfcontained # {standalone, draft}
## About these slides
-- These are some practice problems for Statistical Inference Quiz 1
+- These are some practice problems for Statistical Inference Quiz 2
- They were created using slidify interactive which you will learn in
Creating Data Products
- Please help improve this with pull requests here
(https://github.com/bcaffo/courses)
-runif(1)
--- &radio
The probability that a manuscript gets accepted to a journal is 12% (say). However,
@@ -182,15 +181,15 @@ Let $p=.5$ and $X$ be binomial
*** .explanation
-<span class="answer">89.1</span>
+<span class="answer">10.9</span>
```r
-round(pbinom(4, prob = .5, size = 6, lower.tail = TRUE) * 100, 1)
+round(pbinom(4, prob = .5, size = 6, lower.tail = FALSE) * 100, 1)
```
```
-[1] 89.1
+[1] 10.9
```
@@ -247,9 +246,9 @@ If you roll ten standard dice, take their average, then repeat this process over
$$Var(\bar X) = \sigma^2 /n$$
*** .explanation
-The answer will be <span class="answer">0</span>
-since the variance of the sampling distribution of the mean is $\sigma^2/12$
-and the variance of a die roll is
+The answer will be <span class="answer">0.292</span>
+since the variance of the sampling distribution of the mean is $\sigma^2/10$
+where $\sigma^2$ is the variance of a single die roll, which is
```r
diff --git a/06_StatisticalInference/homework/hw3.Rmd b/06_StatisticalInference/homework/hw3.Rmd
new file mode 100644
index 000000000..df1866fc0
--- /dev/null
+++ b/06_StatisticalInference/homework/hw3.Rmd
@@ -0,0 +1,206 @@
+---
+title : Homework 3 for Stat Inference
+subtitle : Extra problems for Stat Inference
+author : Brian Caffo
+job : Johns Hopkins Bloomberg School of Public Health
+framework : io2012
+highlighter : highlight.js
+hitheme : tomorrow
+#url:
+# lib: ../../librariesNew #Remove new if using old slidify
+# assets: ../../assets
+widgets : [mathjax, quiz, bootstrap]
+mode : selfcontained # {standalone, draft}
+---
+```{r setup, cache = F, echo = F, message = F, warning = F, tidy = F, results='hide'}
+# make this an external chunk that can be included in any file
+library(knitr)
+options(width = 100)
+opts_chunk$set(message = F, error = F, warning = F, comment = NA, fig.align = 'center', dpi = 100, tidy = F, cache.path = '.cache/', fig.path = 'fig/')
+
+options(xtable.type = 'html')
+knit_hooks$set(inline = function(x) {
+ if(is.numeric(x)) {
+ round(x, getOption('digits'))
+ } else {
+ paste(as.character(x), collapse = ', ')
+ }
+})
+knit_hooks$set(plot = knitr:::hook_plot_html)
+```
+
+## About these slides
+- These are some practice problems for Statistical Inference Quiz 3
+- They were created using slidify interactive which you will learn in
+Creating Data Products
+- Please help improve this with pull requests here
+(https://github.com/bcaffo/courses)
+
+
+
+--- &multitext
+Load the data set `mtcars` in the `datasets` R package. Calculate a
+95% confidence interval to the nearest MPG.
+
+1. What is the lower endpoint of the interval?
+2. What is the upper endpoint of the interval?
+
+*** .hint
+Do `library(datasets)` and then `data(mtcars)` to get the data.
+Consider `t.test` for calculations. You may have to install
+the datasets package.
+
+
+*** .explanation
+```{r}
+library(datasets); data(mtcars)
+round(t.test(mtcars$mpg)$conf.int)
+```
+
+<span class="answer">`r round(min(t.test(mtcars$mpg)$conf.int))`</span>
+<span class="answer">`r round(max(t.test(mtcars$mpg)$conf.int))`</span>
+
+--- &multitext
+Suppose that data of 9 paired differences has a standard error of $1$, what value would the average difference have to be to have the lower endpoint of a 95%
+students t confidence interval touch zero?
+
+1. Give the number here to two decimal places
+
+*** .hint
+The t interval is $\bar x t_{.95, 8}\pm s /sqrt{n}$
+
+*** .explanation
+<span class="answer">`r round(qt(.95, df = 8) * 1 / 3, 2)`</span>
+
+We want $\bar x = t_{.95} s / sqrt{n}$
+```{r}
+round(qt(.95, df = 8) * 1 / 3, 2)
+```
+
+
+--- &radio
+An independent group Student's T interval is used over
+a paired T interval when:
+
+1. The observations are paired between the groups.
+2. _The observations between the groups are natually assumed to be statistically independent_
+3. As long as you do it correctly, either is fine.
+4. More details are needed to answer this question
+
+*** .hint
+A paired interval is for paired observations.
+
+*** .explanation
+We can't pair them if the groups are independent of each other as well as independent within themselves.
+
+
+--- &multitext
+Consider the `mtcars` dataset. Construct a 95% T interval for MPG comparing
+4 to 6 cylinder cars (subtracting in the order of 4 - 6)
+assume a constant variance.
+
+1. What is the lower endpoint of the interval to 1 decimal place?
+2. What is the upper endpoint of the interval to 1 decimal place?
+
+*** .hint
+Use `t.test` with `var.equal=TRUE`
+
+*** .explanation
+
+```{r}
+m4 <- mtcars$mpg[mtcars$cyl == 4]
+m6 <- mtcars$mpg[mtcars$cyl == 6]
+#this does 4 - 6
+confint <- as.vector(t.test(m4, m6, var.equal = TRUE)$conf.int)
+```
+
+<span class="answer">`r round(min(confint), 1)`</span>
+<span class="answer">`r round(max(confint), 1)`</span>
+
+
+--- &radio
+If someone put a gun to your head and said "Your confidence interval
+must contain what it's estimating or I'll pull the trigger", what would
+be the smart thing to do?
+
+1. _Make your interval as wide as possible_
+2. Make your interval as small as possible
+3. Call the authorities
+
+*** .hint
+C'mon. You don't need a hint
+
+*** .explanation
+This is just an example of what happens to confidence intervals as you
+increase the confidence level. You want to be quite sure in your interval (i.e.
+have a large confidence level) and so you would increase the interval's width
+
+--- &radio
+
+Refer back to comparing MPG for 4 versus 6 cylinders. What do you conclude?
+
+1. The interval is above zero, suggesting 6 is better than 4 in the terms of MPG
+2. _The interval is above zero, suggesting 4 is better than 6 in the terms of MPG_
+3. The interval does not tell you anything about the hypothesis test; you have to do the test.
+4. The interval contains 0 suggesting no difference.
+
+*** .hint
+Refer back to the problem, consider the implications of the interval being
+larger than 0, double check the order in which things were subtracted and
+make sure the results make sense in the context of the problem.
+
+*** .explanation
+The interval was conducted subtracting 4 - 6 and was entirely above zero.
+
+--- &multitext
+Suppose that 18 obese subjects were randomized, 9 each, to a new diet pill and a placebo. Subjects' body mass indices (BMIs) were measured at a baseline and again after having received the treatment or placebo for four weeks. The average difference from follow-up to the baseline (followup - baseline) was 3 kg/m2 for the treated group and 1 kg/m2 for the placebo group. The corresponding standard deviations of the differences was 1.5 kg/m2 for the treatment group and 1.8 kg/m2 for the placebo group. The study aims to answer whether the change in BMI over the four week period appear to differ between the treated and placebo groups.
+
+What is the pooled variance estimate? (to 2 decimal places)
+
+
+*** .hint
+The sample sizes are equal, so the pooled variance is the average of the
+individual variances
+
+
+*** .explanation
+```{r}
+n1 <- n2 <- 9
+x1 <- -3 ##treated
+x2 <- 1 ##placebo
+s1 <- 1.5 ##treated
+s2 <- 1.8 ##placebo
+spsq <- ( (n1 - 1) * s1^2 + (n2 - 1) * s2^2) / (n1 + n2 - 2)
+```
+<span class="answer">`r round(spsq, 2)`</span>
+
+
+--- &radio
+
+For Binomial data the maximum likelihood estimate for the probability of
+a success is
+
+1. _The proportion of successes_
+2. The proportion of failures
+3. A shrunken version of the proportion of successes
+4. A shrunken version of the proportion of failures
+
+*** .hint
+Look back at the notes about likelihood.
+
+*** .explanation
+The MLE for binomial data is always the proportion of successes.
+
+--- &radio
+
+Bayesian inference requires
+
+1. A type I error rate
+2. Setting your confidence level
+3. _Assigning a prior probability distribution_
+4. Evaluating frequency error rates
+
+*** .explanation
+All of the other answers discuss frequentist concepts. All Bayesian analyses requiring setting a prior.
+
+
diff --git a/06_StatisticalInference/homework/hw3.html b/06_StatisticalInference/homework/hw3.html
new file mode 100644
index 000000000..6e54ea85e
--- /dev/null
+++ b/06_StatisticalInference/homework/hw3.html
@@ -0,0 +1,476 @@
+<!DOCTYPE html>
+<html>
+<head>
+ <title>Homework 3 for Stat Inference</title>
+ <meta charset="utf-8">
+ <meta name="description" content="Homework 3 for Stat Inference">
+ <meta name="author" content="Brian Caffo">
+ <meta name="generator" content="slidify" />
+ <meta name="apple-mobile-web-app-capable" content="yes">
+ <meta http-equiv="X-UA-Compatible" content="chrome=1">
+ <link rel="stylesheet" href="libraries/frameworks/io2012/css/default.css" media="all" >
+ <link rel="stylesheet" href="libraries/frameworks/io2012/css/phone.css"
+ media="only screen and (max-device-width: 480px)" >
+ <link rel="stylesheet" href="libraries/frameworks/io2012/css/slidify.css" >
+ <link rel="stylesheet" href="libraries/highlighters/highlight.js/css/tomorrow.css" />
+ <base target="_blank"> <!-- This amazingness opens all links in a new tab. --> <link rel=stylesheet href="libraries/widgets/quiz/css/demo.css"></link>
+<link rel=stylesheet href="libraries/widgets/bootstrap/css/bootstrap.css"></link>
+
+
+ <!-- Grab CDN jQuery, fall back to local if offline -->
+ <script src="http://ajax.aspnetcdn.com/ajax/jQuery/jquery-1.7.min.js"></script>
+ <script>window.jQuery || document.write('<script src="libraries/widgets/quiz/js/jquery.js"><\/script>')</script>
+ <script data-main="libraries/frameworks/io2012/js/slides"
+ src="libraries/frameworks/io2012/js/require-1.0.8.min.js">
+ </script>
+
+
+
+</head>
+<body style="opacity: 0">
+ <slides class="layout-widescreen">
+
+ <!-- LOGO SLIDE -->
+ <slide class="title-slide segue nobackground">
+ <hgroup class="auto-fadein">
+ <h1>Homework 3 for Stat Inference</h1>
+ <h2>Extra problems for Stat Inference</h2>
+ <p>Brian Caffo<br/>Johns Hopkins Bloomberg School of Public Health</p>
+ </hgroup>
+ <article></article>
+</slide>
+
+
+ <!-- SLIDES -->
+ <slide class="" id="slide-1" style="background:;">
+ <hgroup>
+ <h2>About these slides</h2>
+ </hgroup>
+ <article data-timings="">
+ <ul>
+<li>These are some practice problems for Statistical Inference Quiz 3</li>
+<li>They were created using slidify interactive which you will learn in
+Creating Data Products</li>
+<li>Please help improve this with pull requests here
+(<a href="https://github.com/bcaffo/courses">https://github.com/bcaffo/courses</a>)</li>
+</ul>
+
+ </article>
+ <!-- Presenter Notes -->
+</slide>
+
+<slide class="" id="slide-2" style="background:;">
+ <article data-timings="">
+
+<div class="quiz-text quiz-multitext well">
+ <p>Load the data set <code>mtcars</code> in the <code>datasets</code> R package. Calculate a
+95% confidence interval to the nearest MPG.</p>
+
+<ol>
+<li>What is the lower endpoint of the interval?</li>
+<li>What is the upper endpoint of the interval?</li>
+</ol>
+
+ <button class="quiz-submit btn btn-primary">Submit</button>
+ <button class="quiz-toggle-hint btn btn-info">Show Hint</button>
+ <button class="quiz-show-answer btn btn-success">Show Answer</button>
+ <button class="quiz-clear btn btn-danger">Clear</button>
+
+ <div class="quiz-hint">
+ <p>Do <code>library(datasets)</code> and then <code>data(mtcars)</code> to get the data.
+Consider <code>t.test</code> for calculations. You may have to install
+the datasets package.</p>
+
+</div>
+<div class="quiz-explanation">
+ <pre><code class="r">library(datasets); data(mtcars)
+round(t.test(mtcars$mpg)$conf.int)
+</code></pre>
+
+<pre><code>[1] 18 22
+attr(,"conf.level")
+[1] 0.95
+</code></pre>
+
+<p><span class="answer">18</span>
+<span class="answer">22</span></p>
+
+</div>
+</div>
+ </article>
+ <!-- Presenter Notes -->
+</slide>
+
+<slide class="" id="slide-3" style="background:;">
+ <article data-timings="">
+
+<div class="quiz-text quiz-multitext well">
+ <p>Suppose that data of 9 paired differences has a standard error of \(1\), what value would the average difference have to be to have the lower endpoint of a 95%
+students t confidence interval touch zero?</p>
+
+<ol>
+<li>Give the number here to two decimal places</li>
+</ol>
+
+ <button class="quiz-submit btn btn-primary">Submit</button>
+ <button class="quiz-toggle-hint btn btn-info">Show Hint</button>
+ <button class="quiz-show-answer btn btn-success">Show Answer</button>
+ <button class="quiz-clear btn btn-danger">Clear</button>
+
+ <div class="quiz-hint">
+ <p>The t interval is \(\bar x t_{.95, 8}\pm s /sqrt{n}\)</p>
+
+</div>
+<div class="quiz-explanation">
+ <p><span class="answer">0.62</span></p>
+
+<p>We want \(\bar x = t_{.95} s / sqrt{n}\)</p>
+
+<pre><code class="r">round(qt(.95, df = 8) * 1 / 3, 2)
+</code></pre>
+
+<pre><code>[1] 0.62
+</code></pre>
+
+</div>
+</div>
+ </article>
+ <!-- Presenter Notes -->
+</slide>
+
+<slide class="" id="slide-4" style="background:;">
+ <article data-timings="">
+
+<div class="quiz quiz-single well ">
+ <p>An independent group Student's T interval is used over
+a paired T interval when:</p>
+
+<ol>
+<li>The observations are paired between the groups.</li>
+<li><em>The observations between the groups are natually assumed to be statistically independent</em></li>
+<li>As long as you do it correctly, either is fine.</li>
+<li>More details are needed to answer this question</li>
+</ol>
+
+ <button class="quiz-submit btn btn-primary">Submit</button>
+ <button class="quiz-toggle-hint btn btn-info">Show Hint</button>
+ <button class="quiz-show-answer btn btn-success">Show Answer</button>
+ <button class="quiz-clear btn btn-danger">Clear</button>
+
+ <div class="quiz-hint">
+ <p>A paired interval is for paired observations.</p>
+
+</div>
+<div class="quiz-explanation">
+ <p>We can't pair them if the groups are independent of each other as well as independent within themselves.</p>
+
+</div>
+</div>
+ </article>
+ <!-- Presenter Notes -->
+</slide>
+
+<slide class="" id="slide-5" style="background:;">
+ <article data-timings="">
+
+<div class="quiz-text quiz-multitext well">
+ <p>Consider the <code>mtcars</code> dataset. Construct a 95% T interval for MPG comparing
+4 to 6 cylinder cars (subtracting in the order of 4 - 6)
+assume a constant variance.</p>
+
+<ol>
+<li>What is the lower endpoint of the interval to 1 decimal place?</li>
+<li>What is the upper endpoint of the interval to 1 decimal place?</li>
+</ol>
+
+ <button class="quiz-submit btn btn-primary">Submit</button>
+ <button class="quiz-toggle-hint btn btn-info">Show Hint</button>
+ <button class="quiz-show-answer btn btn-success">Show Answer</button>
+ <button class="quiz-clear btn btn-danger">Clear</button>
+
+ <div class="quiz-hint">
+ <p>Use <code>t.test</code> with <code>var.equal=TRUE</code></p>
+
+</div>
+<div class="quiz-explanation">
+ <pre><code class="r">m4 <- mtcars$mpg[mtcars$cyl == 4]
+m6 <- mtcars$mpg[mtcars$cyl == 6]
+#this does 4 - 6
+confint <- as.vector(t.test(m4, m6, var.equal = TRUE)$conf.int)
+</code></pre>
+
+<p><span class="answer">3.2</span>
+<span class="answer">10.7</span></p>
+
+</div>
+</div>
+ </article>
+ <!-- Presenter Notes -->
+</slide>
+
+<slide class="" id="slide-6" style="background:;">
+ <article data-timings="">
+
+<div class="quiz quiz-single well ">
+ <p>If someone put a gun to your head and said "Your confidence interval
+must contain what it's estimating or I'll pull the trigger", what would
+be the smart thing to do?</p>
+
+<ol>
+<li><em>Make your interval as wide as possible</em></li>
+<li>Make your interval as small as possible</li>
+<li>Call the authorities</li>
+</ol>
+
+ <button class="quiz-submit btn btn-primary">Submit</button>
+ <button class="quiz-toggle-hint btn btn-info">Show Hint</button>
+ <button class="quiz-show-answer btn btn-success">Show Answer</button>
+ <button class="quiz-clear btn btn-danger">Clear</button>
+
+ <div class="quiz-hint">
+ <p>C'mon. You don't need a hint</p>
+
+</div>
+<div class="quiz-explanation">
+ <p>This is just an example of what happens to confidence intervals as you
+increase the confidence level. You want to be quite sure in your interval (i.e.
+have a large confidence level) and so you would increase the interval's width</p>
+
+</div>
+</div>
+ </article>
+ <!-- Presenter Notes -->
+</slide>
+
+<slide class="" id="slide-7" style="background:;">
+ <article data-timings="">
+
+<div class="quiz quiz-single well ">
+ <p>Refer back to comparing MPG for 4 versus 6 cylinders. What do you conclude?</p>
+
+<ol>
+<li>The interval is above zero, suggesting 6 is better than 4 in the terms of MPG</li>
+<li><em>The interval is above zero, suggesting 4 is better than 6 in the terms of MPG</em></li>
+<li>The interval does not tell you anything about the hypothesis test; you have to do the test.</li>
+<li>The interval contains 0 suggesting no difference.</li>
+</ol>
+
+ <button class="quiz-submit btn btn-primary">Submit</button>
+ <button class="quiz-toggle-hint btn btn-info">Show Hint</button>
+ <button class="quiz-show-answer btn btn-success">Show Answer</button>
+ <button class="quiz-clear btn btn-danger">Clear</button>
+
+ <div class="quiz-hint">
+ <p>Refer back to the problem, consider the implications of the interval being
+larger than 0, double check the order in which things were subtracted and
+make sure the results make sense in the context of the problem.</p>
+
+</div>
+<div class="quiz-explanation">
+ <p>The interval was conducted subtracting 4 - 6 and was entirely above zero.</p>
+
+</div>
+</div>
+ </article>
+ <!-- Presenter Notes -->
+</slide>
+
+<slide class="" id="slide-8" style="background:;">
+ <article data-timings="">
+
+<div class="quiz-text quiz-multitext well">
+ <p>Suppose that 18 obese subjects were randomized, 9 each, to a new diet pill and a placebo. Subjects' body mass indices (BMIs) were measured at a baseline and again after having received the treatment or placebo for four weeks. The average difference from follow-up to the baseline (followup - baseline) was 3 kg/m2 for the treated group and 1 kg/m2 for the placebo group. The corresponding standard deviations of the differences was 1.5 kg/m2 for the treatment group and 1.8 kg/m2 for the placebo group. The study aims to answer whether the change in BMI over the four week period appear to differ between the treated and placebo groups. </p>
+
+<p>What is the pooled variance estimate? (to 2 decimal places)</p>
+
+ <button class="quiz-submit btn btn-primary">Submit</button>
+ <button class="quiz-toggle-hint btn btn-info">Show Hint</button>
+ <button class="quiz-show-answer btn btn-success">Show Answer</button>
+ <button class="quiz-clear btn btn-danger">Clear</button>
+
+ <div class="quiz-hint">
+ <p>The sample sizes are equal, so the pooled variance is the average of the
+individual variances</p>
+
+</div>
+<div class="quiz-explanation">
+ <pre><code class="r">n1 <- n2 <- 9
+x1 <- -3 ##treated
+x2 <- 1 ##placebo
+s1 <- 1.5 ##treated
+s2 <- 1.8 ##placebo
+spsq <- ( (n1 - 1) * s1^2 + (n2 - 1) * s2^2) / (n1 + n2 - 2)
+</code></pre>
+
+<p><span class="answer">2.75</span></p>
+
+</div>
+</div>
+ </article>
+ <!-- Presenter Notes -->
+</slide>
+
+<slide class="" id="slide-9" style="background:;">
+ <article data-timings="">
+
+<div class="quiz quiz-single well ">
+ <p>For Binomial data the maximum likelihood estimate for the probability of
+a success is</p>
+
+<ol>
+<li><em>The proportion of successes</em></li>
+<li>The proportion of failures</li>
+<li>A shrunken version of the proportion of successes</li>
+<li>A shrunken version of the proportion of failures</li>
+</ol>
+
+ <button class="quiz-submit btn btn-primary">Submit</button>
+ <button class="quiz-toggle-hint btn btn-info">Show Hint</button>
+ <button class="quiz-show-answer btn btn-success">Show Answer</button>
+ <button class="quiz-clear btn btn-danger">Clear</button>
+
+ <div class="quiz-hint">
+ <p>Look back at the notes about likelihood.</p>
+
+</div>
+<div class="quiz-explanation">
+ <p>The MLE for binomial data is always the proportion of successes.</p>
+
+</div>
+</div>
+ </article>
+ <!-- Presenter Notes -->
+</slide>
+
+<slide class="" id="slide-10" style="background:;">
+ <article data-timings="">
+
+<div class="quiz quiz-single well ">
+ <p>Bayesian inference requires</p>
+
+<ol>
+<li>A type I error rate</li>
+<li>Setting your confidence level</li>
+<li><em>Assigning a prior probability distribution</em></li>
+<li>Evaluating frequency error rates</li>
+</ol>
+
+ <button class="quiz-submit btn btn-primary">Submit</button>
+ <button class="quiz-toggle-hint btn btn-info">Show Hint</button>
+ <button class="quiz-show-answer btn btn-success">Show Answer</button>
+ <button class="quiz-clear btn btn-danger">Clear</button>
+
+ <div class="quiz-explanation">
+ <p>All of the other answers discuss frequentist concepts. All Bayesian analyses requiring setting a prior.</p>
+
+</div>
+</div>
+ </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='About these slides'>
+ 1
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=2 title=''>
+ 2
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=3 title=''>
+ 3
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=4 title=''>
+ 4
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=5 title=''>
+ 5
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=6 title=''>
+ 6
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=7 title=''>
+ 7
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=8 title=''>
+ 8
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=9 title=''>
+ 9
+ </a>
+ </li>
+ <li>
+ <a href="#" target="_self" rel='tooltip'
+ data-slide=10 title=''>
+ 10
+ </a>
+ </li>
+ </ul>
+ </div> <!--[if IE]>
+ <script
+ src="http://ajax.googleapis.com/ajax/libs/chrome-frame/1/CFInstall.min.js">
+ </script>
+ <script>CFInstall.check({mode: 'overlay'});</script>
+ <![endif]-->
+</body>
+ <!-- Load Javascripts for Widgets -->
+ <script src="libraries/widgets/quiz/js/jquery.quiz.js"></script>
+<script src="libraries/widgets/quiz/js/mustache.min.js"></script>
+<script src="libraries/widgets/quiz/js/quiz-app.js"></script>
+<script src="libraries/widgets/bootstrap/js/bootstrap.min.js"></script>
+<script src="libraries/widgets/bootstrap/js/bootbox.min.js"></script>
+
+ <!-- MathJax: Fall back to local if CDN offline but local image fonts are not supported (saves >100MB) -->
+ <script type="text/x-mathjax-config">
+ MathJax.Hub.Config({
+ tex2jax: {
+ inlineMath: [['$','$'], ['\\(','\\)']],
+ processEscapes: true
+ }
+ });
+ </script>
+ <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+ <!-- <script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+ </script> -->
+ <script>window.MathJax || document.write('<script type="text/x-mathjax-config">MathJax.Hub.Config({"HTML-CSS":{imageFont:null}});<\/script><script src="libraries/widgets/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"><\/script>')
+</script>
+<script>
+ $(function (){
+ $("#example").popover();
+ $("[rel='tooltip']").tooltip();
+ });
+ </script>
+ <!-- LOAD HIGHLIGHTER JS FILES -->
+ <script src="libraries/highlighters/highlight.js/highlight.pack.js"></script>
+ <script>hljs.initHighlightingOnLoad();</script>
+ <!-- DONE LOADING HIGHLIGHTER JS FILES -->
+
+ </html>
\ No newline at end of file
diff --git a/06_StatisticalInference/homework/hw3.md b/06_StatisticalInference/homework/hw3.md
new file mode 100644
index 000000000..93859ed5b
--- /dev/null
+++ b/06_StatisticalInference/homework/hw3.md
@@ -0,0 +1,210 @@
+---
+title : Homework 3 for Stat Inference
+subtitle : Extra problems for Stat Inference
+author : Brian Caffo
+job : Johns Hopkins Bloomberg School of Public Health
+framework : io2012
+highlighter : highlight.js
+hitheme : tomorrow
+#url:
+# lib: ../../librariesNew #Remove new if using old slidify
+# assets: ../../assets
+widgets : [mathjax, quiz, bootstrap]
+mode : selfcontained # {standalone, draft}
+---
+
+
+
+## About these slides
+- These are some practice problems for Statistical Inference Quiz 3
+- They were created using slidify interactive which you will learn in
+Creating Data Products
+- Please help improve this with pull requests here
+(https://github.com/bcaffo/courses)
+
+
+
+--- &multitext
+Load the data set `mtcars` in the `datasets` R package. Calculate a
+95% confidence interval to the nearest MPG.
+
+1. What is the lower endpoint of the interval?
+2. What is the upper endpoint of the interval?
+
+*** .hint
+Do `library(datasets)` and then `data(mtcars)` to get the data.
+Consider `t.test` for calculations. You may have to install
+the datasets package.
+
+
+*** .explanation
+
+```r
+library(datasets); data(mtcars)
+round(t.test(mtcars$mpg)$conf.int)
+```
+
+```
+[1] 18 22
+attr(,"conf.level")
+[1] 0.95
+```
+
+
+<span class="answer">18</span>
+<span class="answer">22</span>
+
+--- &multitext
+Suppose that data of 9 paired differences has a standard error of $1$, what value would the average difference have to be to have the lower endpoint of a 95%
+students t confidence interval touch zero?
+
+1. Give the number here to two decimal places
+
+*** .hint
+The t interval is $\bar x t_{.95, 8}\pm s /sqrt{n}$
+
+*** .explanation
+<span class="answer">0.62</span>
+
+We want $\bar x = t_{.95} s / sqrt{n}$
+
+```r
+round(qt(.95, df = 8) * 1 / 3, 2)
+```
+
+```
+[1] 0.62
+```
+
+
+
+--- &radio
+An independent group Student's T interval is used over
+a paired T interval when:
+
+1. The observations are paired between the groups.
+2. _The observations between the groups are natually assumed to be statistically independent_
+3. As long as you do it correctly, either is fine.
+4. More details are needed to answer this question
+
+*** .hint
+A paired interval is for paired observations.
+
+*** .explanation
+We can't pair them if the groups are independent of each other as well as independent within themselves.
+
+
+--- &multitext
+Consider the `mtcars` dataset. Construct a 95% T interval for MPG comparing
+4 to 6 cylinder cars (subtracting in the order of 4 - 6)
+assume a constant variance.
+
+1. What is the lower endpoint of the interval to 1 decimal place?
+2. What is the upper endpoint of the interval to 1 decimal place?
+
+*** .hint
+Use `t.test` with `var.equal=TRUE`
+
+*** .explanation
+
+
+```r
+m4 <- mtcars$mpg[mtcars$cyl == 4]
+m6 <- mtcars$mpg[mtcars$cyl == 6]
+#this does 4 - 6
+confint <- as.vector(t.test(m4, m6, var.equal = TRUE)$conf.int)
+```
+
+
+<span class="answer">3.2</span>
+<span class="answer">10.7</span>
+
+
+--- &radio
+If someone put a gun to your head and said "Your confidence interval
+must contain what it's estimating or I'll pull the trigger", what would
+be the smart thing to do?
+
+1. _Make your interval as wide as possible_
+2. Make your interval as small as possible
+3. Call the authorities
+
+*** .hint
+C'mon. You don't need a hint
+
+*** .explanation
+This is just an example of what happens to confidence intervals as you
+increase the confidence level. You want to be quite sure in your interval (i.e.
+have a large confidence level) and so you would increase the interval's width
+
+--- &radio
+
+Refer back to comparing MPG for 4 versus 6 cylinders. What do you conclude?
+
+1. The interval is above zero, suggesting 6 is better than 4 in the terms of MPG
+2. _The interval is above zero, suggesting 4 is better than 6 in the terms of MPG_
+3. The interval does not tell you anything about the hypothesis test; you have to do the test.
+4. The interval contains 0 suggesting no difference.
+
+*** .hint
+Refer back to the problem, consider the implications of the interval being
+larger than 0, double check the order in which things were subtracted and
+make sure the results make sense in the context of the problem.
+
+*** .explanation
+The interval was conducted subtracting 4 - 6 and was entirely above zero.
+
+--- &multitext
+Suppose that 18 obese subjects were randomized, 9 each, to a new diet pill and a placebo. Subjects' body mass indices (BMIs) were measured at a baseline and again after having received the treatment or placebo for four weeks. The average difference from follow-up to the baseline (followup - baseline) was 3 kg/m2 for the treated group and 1 kg/m2 for the placebo group. The corresponding standard deviations of the differences was 1.5 kg/m2 for the treatment group and 1.8 kg/m2 for the placebo group. The study aims to answer whether the change in BMI over the four week period appear to differ between the treated and placebo groups.
+
+What is the pooled variance estimate? (to 2 decimal places)
+
+
+*** .hint
+The sample sizes are equal, so the pooled variance is the average of the
+individual variances
+
+
+*** .explanation
+
+```r
+n1 <- n2 <- 9
+x1 <- -3 ##treated
+x2 <- 1 ##placebo
+s1 <- 1.5 ##treated
+s2 <- 1.8 ##placebo
+spsq <- ( (n1 - 1) * s1^2 + (n2 - 1) * s2^2) / (n1 + n2 - 2)
+```
+
+<span class="answer">2.75</span>
+
+
+--- &radio
+
+For Binomial data the maximum likelihood estimate for the probability of
+a success is
+
+1. _The proportion of successes_
+2. The proportion of failures
+3. A shrunken version of the proportion of successes
+4. A shrunken version of the proportion of failures
+
+*** .hint
+Look back at the notes about likelihood.
+
+*** .explanation
+The MLE for binomial data is always the proportion of successes.
+
+--- &radio
+
+Bayesian inference requires
+
+1. A type I error rate
+2. Setting your confidence level
+3. _Assigning a prior probability distribution_
+4. Evaluating frequency error rates
+
+*** .explanation
+All of the other answers discuss frequentist concepts. All Bayesian analyses requiring setting a prior.
+
+
diff --git a/06_StatisticalInference/homework/hw4.Rmd b/06_StatisticalInference/homework/hw4.Rmd
new file mode 100644
index 000000000..bf5a8da3b
--- /dev/null
+++ b/06_StatisticalInference/homework/hw4.Rmd
@@ -0,0 +1,37 @@
+---
+title : Homework 4 for Stat Inference
+subtitle : Extra problems for Stat Inference
+author : Brian Caffo
+job : Johns Hopkins Bloomberg School of Public Health
+framework : io2012
+highlighter : highlight.js
+hitheme : tomorrow
+#url:
+# lib: ../../librariesNew #Remove new if using old slidify
+# assets: ../../assets
+widgets : [mathjax, quiz, bootstrap]
+mode : selfcontained # {standalone, draft}
+---
+```{r setup, cache = F, echo = F, message = F, warning = F, tidy = F, results='hide'}
+# make this an external chunk that can be included in any file
+library(knitr)
+options(width = 100)
+opts_chunk$set(message = F, error = F, warning = F, comment = NA, fig.align = 'center', dpi = 100, tidy = F, cache.path = '.cache/', fig.path = 'fig/')
+
+options(xtable.type = 'html')
+knit_hooks$set(inline = function(x) {
+ if(is.numeric(x)) {
+ round(x, getOption('digits'))
+ } else {
+ paste(as.character(x), collapse = ', ')
+ }
+})
+knit_hooks$set(plot = knitr:::hook_plot_html)
+```
+
+## About these slides
+- These are some practice problems for Statistical Inference Quiz 4
+- They were created using slidify interactive which you will learn in
+Creating Data Products
+- Please help improve this with pull requests here
+(https://github.com/bcaffo/courses)
diff --git a/06_StatisticalInference/homework/hw4.html b/06_StatisticalInference/homework/hw4.html
new file mode 100644
index 000000000..565621a6d
--- /dev/null
+++ b/06_StatisticalInference/homework/hw4.html
@@ -0,0 +1,112 @@
+<!DOCTYPE html>
+<html>
+<head>
+ <title>Homework 4 for Stat Inference</title>
+ <meta charset="utf-8">
+ <meta name="description" content="Homework 4 for Stat Inference">
+ <meta name="author" content="Brian Caffo">
+ <meta name="generator" content="slidify" />
+ <meta name="apple-mobile-web-app-capable" content="yes">
+ <meta http-equiv="X-UA-Compatible" content="chrome=1">
+ <link rel="stylesheet" href="libraries/frameworks/io2012/css/default.css" media="all" >
+ <link rel="stylesheet" href="libraries/frameworks/io2012/css/phone.css"
+ media="only screen and (max-device-width: 480px)" >
+ <link rel="stylesheet" href="libraries/frameworks/io2012/css/slidify.css" >
+ <link rel="stylesheet" href="libraries/highlighters/highlight.js/css/tomorrow.css" />
+ <base target="_blank"> <!-- This amazingness opens all links in a new tab. --> <link rel=stylesheet href="libraries/widgets/quiz/css/demo.css"></link>
+<link rel=stylesheet href="libraries/widgets/bootstrap/css/bootstrap.css"></link>
+
+
+ <!-- Grab CDN jQuery, fall back to local if offline -->
+ <script src="http://ajax.aspnetcdn.com/ajax/jQuery/jquery-1.7.min.js"></script>
+ <script>window.jQuery || document.write('<script src="libraries/widgets/quiz/js/jquery.js"><\/script>')</script>
+ <script data-main="libraries/frameworks/io2012/js/slides"
+ src="libraries/frameworks/io2012/js/require-1.0.8.min.js">
+ </script>
+
+
+
+</head>
+<body style="opacity: 0">
+ <slides class="layout-widescreen">
+
+ <!-- LOGO SLIDE -->
+ <slide class="title-slide segue nobackground">
+ <hgroup class="auto-fadein">
+ <h1>Homework 4 for Stat Inference</h1>
+ <h2>Extra problems for Stat Inference</h2>
+ <p>Brian Caffo<br/>Johns Hopkins Bloomberg School of Public Health</p>
+ </hgroup>
+ <article></article>
+</slide>
+
+
+ <!-- SLIDES -->
+ <slide class="" id="slide-1" style="background:;">
+ <hgroup>
+ <h2>About these slides</h2>
+ </hgroup>
+ <article data-timings="">
+ <ul>
+<li>These are some practice problems for Statistical Inference Quiz 4</li>
+<li>They were created using slidify interactive which you will learn in
+Creating Data Products</li>
+<li>Please help improve this with pull requests here
+(<a href="https://github.com/bcaffo/courses">https://github.com/bcaffo/courses</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='About these slides'>
+ 1
+ </a>
+ </li>
+ </ul>
+ </div> <!--[if IE]>
+ <script
+ src="http://ajax.googleapis.com/ajax/libs/chrome-frame/1/CFInstall.min.js">
+ </script>
+ <script>CFInstall.check({mode: 'overlay'});</script>
+ <![endif]-->
+</body>
+ <!-- Load Javascripts for Widgets -->
+ <script src="libraries/widgets/quiz/js/jquery.quiz.js"></script>
+<script src="libraries/widgets/quiz/js/mustache.min.js"></script>
+<script src="libraries/widgets/quiz/js/quiz-app.js"></script>
+<script src="libraries/widgets/bootstrap/js/bootstrap.min.js"></script>
+<script src="libraries/widgets/bootstrap/js/bootbox.min.js"></script>
+
+ <!-- MathJax: Fall back to local if CDN offline but local image fonts are not supported (saves >100MB) -->
+ <script type="text/x-mathjax-config">
+ MathJax.Hub.Config({
+ tex2jax: {
+ inlineMath: [['$','$'], ['\\(','\\)']],
+ processEscapes: true
+ }
+ });
+ </script>
+ <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+ <!-- <script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+ </script> -->
+ <script>window.MathJax || document.write('<script type="text/x-mathjax-config">MathJax.Hub.Config({"HTML-CSS":{imageFont:null}});<\/script><script src="libraries/widgets/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"><\/script>')
+</script>
+<script>
+ $(function (){
+ $("#example").popover();
+ $("[rel='tooltip']").tooltip();
+ });
+ </script>
+ <!-- LOAD HIGHLIGHTER JS FILES -->
+ <script src="libraries/highlighters/highlight.js/highlight.pack.js"></script>
+ <script>hljs.initHighlightingOnLoad();</script>
+ <!-- DONE LOADING HIGHLIGHTER JS FILES -->
+
+ </html>
\ No newline at end of file
diff --git a/06_StatisticalInference/homework/hw4.md b/06_StatisticalInference/homework/hw4.md
new file mode 100644
index 000000000..a22e64543
--- /dev/null
+++ b/06_StatisticalInference/homework/hw4.md
@@ -0,0 +1,23 @@
+---
+title : Homework 4 for Stat Inference
+subtitle : Extra problems for Stat Inference
+author : Brian Caffo
+job : Johns Hopkins Bloomberg School of Public Health
+framework : io2012
+highlighter : highlight.js
+hitheme : tomorrow
+#url:
+# lib: ../../librariesNew #Remove new if using old slidify
+# assets: ../../assets
+widgets : [mathjax, quiz, bootstrap]
+mode : selfcontained # {standalone, draft}
+---
+
+
+
+## About these slides
+- These are some practice problems for Statistical Inference Quiz 4
+- They were created using slidify interactive which you will learn in
+Creating Data Products
+- Please help improve this with pull requests here
+(https://github.com/bcaffo/courses)
diff --git a/08_PracticalMachineLearning/019predictingWithTrees/index.Rmd b/08_PracticalMachineLearning/019predictingWithTrees/index.Rmd
index a3cccb90f..1c4dc6e20 100644
--- a/08_PracticalMachineLearning/019predictingWithTrees/index.Rmd
+++ b/08_PracticalMachineLearning/019predictingWithTrees/index.Rmd
@@ -124,7 +124,7 @@ plot(x,y,xaxt="n",yaxt="n",cex=3,col=c(rep("blue",8),rep("red",8)),pch=19)
* __Misclassification:__ $8/16 = 0.5$
* __Gini:__ $1 - [(8/16)^2 + (8/16)^2] = 0.5$
-* __Information:__$-[1/16 \times log2(1/16) + 15/16 \times log2(15/16)] = 1$
+* __Information:__$-[8/16 \times log2(8/16) + 8/16 \times log2(8/16)] = 1$
diff --git a/08_PracticalMachineLearning/025combiningPredictors/index.Rmd b/08_PracticalMachineLearning/025combiningPredictors/index.Rmd
index 958b2c4d8..ca6ec2f93 100644
--- a/08_PracticalMachineLearning/025combiningPredictors/index.Rmd
+++ b/08_PracticalMachineLearning/025combiningPredictors/index.Rmd
@@ -67,7 +67,7 @@ BellKor = Combination of 107 predictors
Suppose we have 5 completely independent classifiers
If accuracy is 70% for each:
- * $10\times(0.7)^3(0.3)^2 + 5\times(0.7)^4(0.3)^2 + (0.7)^5$
+ * $10\times(0.7)^3(0.3)^2 + 5\times(0.7)^4(0.3)^1 + (0.7)^5$
* 83.7% majority vote accuracy
With 101 independent classifiers
diff --git a/09_DevelopingDataProducts/rStudioPresent/index.Rpres b/09_DevelopingDataProducts/rStudioPresent/index.Rpres
index a237721f7..00c9487c7 100644
--- a/09_DevelopingDataProducts/rStudioPresent/index.Rpres
+++ b/09_DevelopingDataProducts/rStudioPresent/index.Rpres
@@ -1,132 +1,132 @@
-RStudio Presenter
-===
-author: Brian Caffo, Jeff Leek Roger Peng
-date: `r format(Sys.Date(), format="%B %d %Y")`
-transition: rotate
-
-<small>
-Department of Biostatistics
-Bloomberg School of Public Health
-Johns Hopkins University
-Coursera Data Science Specialization
-</small>
-
-
-RStudio Presentation
-===
-- RStudio created a presentation authoring tool within their
-development environment.
-- If you are familiar with slidify, you will also be familiar with this tool
- - Code is authored in a generalized markdown format that allows for code chunks
- - The output is an html5 presentation
- - The file index for the presenter file is .Rpres, which gets converted to an .md file and then to an html file if desired
- - There's a preview tool in RStudio and GUIs for publishing to Rpubs or viewing/creating an html file
-
-Authoring content
-===
-- This is a fairly complete guide
- - http://www.rstudio.com/ide/docs/presentations/overview
-- Quick start is
- - `file` then `New File` then `R Presentation`
- - (`alt-f` then `f` then `p` if you want key strokes)
- - Use basically the same R markdown format for authoring as slidify/knitr
- - Single quotes for inline code
- - Tripple qutoes for block code
- - Same options for code evaluation, caching, hiding etcetera
-
-Compiling and tools
-===
-- R Studio auto formats and runs the code when you save the document
-- Mathjax JS library is loaded by default so that `$x^2$` yields $x^2$
-- Slide navigation button on the preview; clicking on the notepad icon takes you to that slide in the deck
-- Clicking on `more` yields options for
- - Clearning the knitr cache
- - Viewing in a browser (creates a temporay html file in `AppData/local/temp` for me)
- - Create a html file to save where you want)
-- A refresh button
-- A zoom button that brings up a full window
-
-Visuals
-===
-transition: linear
-
-- R Studio has made it easy to get some cool html5 effects, like cube transitions
-with simple options in YAML-like code after the first slide such as
-`transition: rotate`
-- You can specify it in a slide-by-slide basis
-
-Here's the option "linear"
-===
-transition: linear
-
-- Just put `transition: linear` right after the slide creation (three equal signs or more in a row)
-- Tansition options
- - http://www.rstudio.com/ide/docs/presentations/slide_transitions_and_navigation
-
-Hierarchical organization
-===
-type: section
-- If you want a hierarchical organization structure, just add a `type: typename` option after the slide
-- This changes the default appearance
- - http://www.rstudio.com/ide/docs/presentations/slide_transitions_and_navigation
-- This is of type `section`
-
-Here's a subsection
-===
-type: subsection
-
-Two columns
-===
-- Do whatever for column one
-- Then put `***` on a line by itself with blank lines before and after
-
-***
-
-- Then do whatever for column two
-
-
-Changing the slide font
-==========================================================
-font-import: http://fonts.googleapis.com/css?family=Risque
-font-family: 'Risque'
-
-- Add a `font-family: fontname` option after the slide
- - http://www.rstudio.com/ide/docs/presentations/customizing_fonts_and_appearance
-- Specified in the same way as css font families
- - http://www.w3schools.com/cssref/css_websafe_fonts.asp
-- Use `font-import: url` to import fonts
-- Important caveats
- - Fonts must be present on the system that you're presenting on, or it will go to a fallback font
- - You have to be connected to the internet to use an imported font (so don't rely on this for offline presentations)
-- This is the `Risque`
- - http://fonts.googleapis.com/css?family=Risque
-
-Really changing things
-===
-- If you know html5 and CSS well, then you can basically change whatever you want
-- A css file with the same names as your presentation will be autoimported
-- You can use `css: file.css` to import a css file
-- You have to create named classes and then use `class: classname` to get slide-specific style control from your css
- - (Or you can apply then within a `<span>`)
-- Ultimately, you have an html file, that you can edit as you wish
- - This should be viewed as a last resort, as the whole point is to have reproducible presentations, but may be the easiest way to get the exact style control you want for a final product
-
-Slidify versus R Studio Presenter
-===
-**Slidify**
-- Flexible control from the R MD file
-- Under rapid ongoing development
-- Large user base
-- Lots and lots of styles and options
-- Steeper learning curve
-- More command-line oriented
-
-***
-**R Studio Presenter**
-- Embedded in R Studio
-- More GUI oriented
-- Very easy to get started
-- Smaller set of easy styles and options
-- Default styles look very nice
-- Ultimately as flexible as slidify with a little CSS and HTML knowledge
-
+RStudio Presenter
+===
+author: Brian Caffo, Jeff Leek Roger Peng
+date: `r format(Sys.Date(), format="%B %d %Y")`
+transition: rotate
+
+<small>
+Department of Biostatistics
+Bloomberg School of Public Health
+Johns Hopkins University
+Coursera Data Science Specialization
+</small>
+
+
+RStudio Presentation
+===
+- RStudio created a presentation authoring tool within their
+development environment.
+- If you are familiar with slidify, you will also be familiar with this tool
+ - Code is authored in a generalized markdown format that allows for code chunks
+ - The output is an html5 presentation
+ - The file index for the presenter file is .Rpres, which gets converted to an .md file and then to an html file if desired
+ - There's a preview tool in RStudio and GUIs for publishing to Rpubs or viewing/creating an html file
+
+Authoring content
+===
+- This is a fairly complete guide
+ - http://www.rstudio.com/ide/docs/presentations/overview
+- Quick start is
+ - `file` then `New File` then `R Presentation`
+ - (`alt-f` then `f` then `p` if you want key strokes)
+ - Use basically the same R markdown format for authoring as slidify/knitr
+ - Single quotes for inline code
+ - Tripple qutoes for block code
+ - Same options for code evaluation, caching, hiding etcetera
+
+Compiling and tools
+===
+- R Studio auto formats and runs the code when you save the document
+- Mathjax JS library is loaded by default so that `$x^2$` yields $x^2$
+- Slide navigation button on the preview; clicking on the notepad icon takes you to that slide in the deck
+- Clicking on `more` yields options for
+ - Clearning the knitr cache
+ - Viewing in a browser (creates a temporay html file in `AppData/local/temp` for me)
+ - Create a html file to save where you want)
+- A refresh button
+- A zoom button that brings up a full window
+
+Visuals
+===
+transition: linear
+
+- R Studio has made it easy to get some cool html5 effects, like cube transitions
+with simple options in YAML-like code after the first slide such as
+`transition: rotate`
+- You can specify it in a slide-by-slide basis
+
+Here's the option "linear"
+===
+transition: linear
+
+- Just put `transition: linear` right after the slide creation (three equal signs or more in a row)
+- Tansition options
+ - http://www.rstudio.com/ide/docs/presentations/slide_transitions_and_navigation
+
+Hierarchical organization
+===
+type: section
+- If you want a hierarchical organization structure, just add a `type: typename` option after the slide
+- This changes the default appearance
+ - http://www.rstudio.com/ide/docs/presentations/slide_transitions_and_navigation
+- This is of type `section`
+
+Here's a subsection
+===
+type: subsection
+
+Two columns
+===
+- Do whatever for column one
+- Then put `***` on a line by itself with blank lines before and after
+
+***
+
+- Then do whatever for column two
+
+
+Changing the slide font
+==========================================================
+font-import: http://fonts.googleapis.com/css?family=Risque
+font-family: 'Risque'
+
+- Add a `font-family: fontname` option after the slide
+ - http://www.rstudio.com/ide/docs/presentations/customizing_fonts_and_appearance
+- Specified in the same way as css font families
+ - http://www.w3schools.com/cssref/css_websafe_fonts.asp
+- Use `font-import: url` to import fonts
+- Important caveats
+ - Fonts must be present on the system that you're presenting on, or it will go to a fallback font
+ - You have to be connected to the internet to use an imported font (so don't rely on this for offline presentations)
+- This is the `Risque`
+ - http://fonts.googleapis.com/css?family=Risque
+
+Really changing things
+===
+- If you know html5 and CSS well, then you can basically change whatever you want
+- A css file with the same names as your presentation will be autoimported
+- You can use `css: file.css` to import a css file
+- You have to create named classes and then use `class: classname` to get slide-specific style control from your css
+ - (Or you can apply then within a `<span>`)
+- Ultimately, you have an html file, that you can edit as you wish
+ - This should be viewed as a last resort, as the whole point is to have reproducible presentations, but may be the easiest way to get the exact style control you want for a final product
+
+Slidify versus R Studio Presenter
+===
+**Slidify**
+- Flexible control from the R MD file
+- Under rapid ongoing development
+- Large user base
+- Lots and lots of styles and options
+- Steeper learning curve
+- More command-line oriented
+
+***
+**R Studio Presenter**
+- Embedded in R Studio
+- More GUI oriented
+- Very easy to get started
+- Smaller set of easy styles and options
+- Default styles look very nice
+- Ultimately as flexible as slidify with a little CSS and HTML knowledge
+
diff --git a/09_DevelopingDataProducts/rStudioPresent/index.md b/09_DevelopingDataProducts/rStudioPresent/index.md
index 399fb071a..b998542ae 100644
--- a/09_DevelopingDataProducts/rStudioPresent/index.md
+++ b/09_DevelopingDataProducts/rStudioPresent/index.md
@@ -1,132 +1,132 @@
-RStudio Presenter
-===
-author: Brian Caffo, Jeff Leek Roger Peng
-date: April 24 2014
-transition: rotate
-
-<small>
-Department of Biostatistics
-Bloomberg School of Public Health
-Johns Hopkins University
-Coursera Data Science Specialization
-</small>
-
-
-RStudio Presentation
-===
-- RStudio created a presentation authoring tool within their
-development environment.
-- If you are familiar with slidify, you will also be familiar with this tool
- - Code is authored in a generalized markdown format that allows for code chunks
- - The output is an html5 presentation
- - The file index for the presenter file is .Rpres, which gets converted to an .md file and then to an html file if desired
- - There's a preview tool in RStudio and GUIs for publishing to Rpubs or viewing/creating an html file
-
-Authoring content
-===
-- This is a fairly complete guide
- - http://www.rstudio.com/ide/docs/presentations/overview
-- Quick start is
- - `file` then `New File` then `R Presentation`
- - (`alt-f` then `f` then `p` if you want key strokes)
- - Use basically the same R markdown format for authoring as slidify/knitr
- - Single quotes for inline code
- - Tripple qutoes for block code
- - Same options for code evaluation, caching, hiding etcetera
-
-Compiling and tools
-===
-- R Studio auto formats and runs the code when you save the document
-- Mathjax JS library is loaded by default so that `$x^2$` yields $x^2$
-- Slide navigation button on the preview; clicking on the notepad icon takes you to that slide in the deck
-- Clicking on `more` yields options for
- - Clearning the knitr cache
- - Viewing in a browser (creates a temporay html file in `AppData/local/temp` for me)
- - Create a html file to save where you want)
-- A refresh button
-- A zoom button that brings up a full window
-
-Visuals
-===
-transition: linear
-
-- R Studio has made it easy to get some cool html5 effects, like cube transitions
-with simple options in YAML-like code after the first slide such as
-`transition: rotate`
-- You can specify it in a slide-by-slide basis
-
-Here's the option "linear"
-===
-transition: linear
-
-- Just put `transition: linear` right after the slide creation (three equal signs or more in a row)
-- Tansition options
- - http://www.rstudio.com/ide/docs/presentations/slide_transitions_and_navigation
-
-Hierarchical organization
-===
-type: section
-- If you want a hierarchical organization structure, just add a `type: typename` option after the slide
-- This changes the default appearance
- - http://www.rstudio.com/ide/docs/presentations/slide_transitions_and_navigation
-- This is of type `section`
-
-Here's a subsection
-===
-type: subsection
-
-Two columns
-===
-- Do whatever for column one
-- Then put `***` on a line by itself with blank lines before and after
-
-***
-
-- Then do whatever for column two
-
-
-Changing the slide font
-==========================================================
-font-import: http://fonts.googleapis.com/css?family=Risque
-font-family: 'Risque'
-
-- Add a `font-family: fontname` option after the slide
- - http://www.rstudio.com/ide/docs/presentations/customizing_fonts_and_appearance
-- Specified in the same way as css font families
- - http://www.w3schools.com/cssref/css_websafe_fonts.asp
-- Use `font-import: url` to import fonts
-- Important caveats
- - Fonts must be present on the system that you're presenting on, or it will go to a fallback font
- - You have to be connected to the internet to use an imported font (so don't rely on this for offline presentations)
-- This is the `Risque`
- - http://fonts.googleapis.com/css?family=Risque
-
-Really changing things
-===
-- If you know html5 and CSS well, then you can basically change whatever you want
-- A css file with the same names as your presentation will be autoimported
-- You can use `css: file.css` to import a css file
-- You have to create named classes and then use `class: classname` to get slide-specific style control from your css
- - (Or you can apply then within a `<span>`)
-- Ultimately, you have an html file, that you can edit as you wish
- - This should be viewed as a last resort, as the whole point is to have reproducible presentations, but may be the easiest way to get the exact style control you want for a final product
-
-Slidify versus R Studio Presenter
-===
-**Slidify**
-- Flexible control from the R MD file
-- Under rapid ongoing development
-- Large user base
-- Lots and lots of styles and options
-- Steeper learning curve
-- More command-line oriented
-
-***
-**R Studio Presenter**
-- Embedded in R Studio
-- More GUI oriented
-- Very easy to get started
-- Smaller set of easy styles and options
-- Default styles look very nice
-- Ultimately as flexible as slidify with a little CSS and HTML knowledge
-
+RStudio Presenter
+===
+author: Brian Caffo, Jeff Leek Roger Peng
+date: May 21 2014
+transition: rotate
+
+<small>
+Department of Biostatistics
+Bloomberg School of Public Health
+Johns Hopkins University
+Coursera Data Science Specialization
+</small>
+
+
+RStudio Presentation
+===
+- RStudio created a presentation authoring tool within their
+development environment.
+- If you are familiar with slidify, you will also be familiar with this tool
+ - Code is authored in a generalized markdown format that allows for code chunks
+ - The output is an html5 presentation
+ - The file index for the presenter file is .Rpres, which gets converted to an .md file and then to an html file if desired
+ - There's a preview tool in RStudio and GUIs for publishing to Rpubs or viewing/creating an html file
+
+Authoring content
+===
+- This is a fairly complete guide
+ - http://www.rstudio.com/ide/docs/presentations/overview
+- Quick start is
+ - `file` then `New File` then `R Presentation`
+ - (`alt-f` then `f` then `p` if you want key strokes)
+ - Use basically the same R markdown format for authoring as slidify/knitr
+ - Single quotes for inline code
+ - Tripple qutoes for block code
+ - Same options for code evaluation, caching, hiding etcetera
+
+Compiling and tools
+===
+- R Studio auto formats and runs the code when you save the document
+- Mathjax JS library is loaded by default so that `$x^2$` yields $x^2$
+- Slide navigation button on the preview; clicking on the notepad icon takes you to that slide in the deck
+- Clicking on `more` yields options for
+ - Clearning the knitr cache
+ - Viewing in a browser (creates a temporay html file in `AppData/local/temp` for me)
+ - Create a html file to save where you want)
+- A refresh button
+- A zoom button that brings up a full window
+
+Visuals
+===
+transition: linear
+
+- R Studio has made it easy to get some cool html5 effects, like cube transitions
+with simple options in YAML-like code after the first slide such as
+`transition: rotate`
+- You can specify it in a slide-by-slide basis
+
+Here's the option "linear"
+===
+transition: linear
+
+- Just put `transition: linear` right after the slide creation (three equal signs or more in a row)
+- Tansition options
+ - http://www.rstudio.com/ide/docs/presentations/slide_transitions_and_navigation
+
+Hierarchical organization
+===
+type: section
+- If you want a hierarchical organization structure, just add a `type: typename` option after the slide
+- This changes the default appearance
+ - http://www.rstudio.com/ide/docs/presentations/slide_transitions_and_navigation
+- This is of type `section`
+
+Here's a subsection
+===
+type: subsection
+
+Two columns
+===
+- Do whatever for column one
+- Then put `***` on a line by itself with blank lines before and after
+
+***
+
+- Then do whatever for column two
+
+
+Changing the slide font
+==========================================================
+font-import: http://fonts.googleapis.com/css?family=Risque
+font-family: 'Risque'
+
+- Add a `font-family: fontname` option after the slide
+ - http://www.rstudio.com/ide/docs/presentations/customizing_fonts_and_appearance
+- Specified in the same way as css font families
+ - http://www.w3schools.com/cssref/css_websafe_fonts.asp
+- Use `font-import: url` to import fonts
+- Important caveats
+ - Fonts must be present on the system that you're presenting on, or it will go to a fallback font
+ - You have to be connected to the internet to use an imported font (so don't rely on this for offline presentations)
+- This is the `Risque`
+ - http://fonts.googleapis.com/css?family=Risque
+
+Really changing things
+===
+- If you know html5 and CSS well, then you can basically change whatever you want
+- A css file with the same names as your presentation will be autoimported
+- You can use `css: file.css` to import a css file
+- You have to create named classes and then use `class: classname` to get slide-specific style control from your css
+ - (Or you can apply then within a `<span>`)
+- Ultimately, you have an html file, that you can edit as you wish
+ - This should be viewed as a last resort, as the whole point is to have reproducible presentations, but may be the easiest way to get the exact style control you want for a final product
+
+Slidify versus R Studio Presenter
+===
+**Slidify**
+- Flexible control from the R MD file
+- Under rapid ongoing development
+- Large user base
+- Lots and lots of styles and options
+- Steeper learning curve
+- More command-line oriented
+
+***
+**R Studio Presenter**
+- Embedded in R Studio
+- More GUI oriented
+- Very easy to get started
+- Smaller set of easy styles and options
+- Default styles look very nice
+- Ultimately as flexible as slidify with a little CSS and HTML knowledge
+