Updates:

manuscript/02_probability.md

@@ -109,20 +109,20 @@ Answer: No, the events can simultaneously occur and so
 exclusive. To elaborate let:
 
 {$$}
- \begin{eqnarray*}
-     A_1 & = & \{\mbox{Person has sleep apnea}\} \\
-A_2 & = & \{\mbox{Person has RLS}\}
-   \end{eqnarray*}
+ \begin{aligned}
+     A_1 & = \{\mbox{Person has sleep apnea}\} \\
+A_2 & = \{\mbox{Person has RLS}\}
+   \end{aligned}
  {/$$}
 
 Then
 
 {$$}
- \begin{eqnarray*}
-     P(A_1 \cup A_2 ) & = & P(A_1) + P(A_2) - P(A_1 \cap
+ \begin{aligned}
+     P(A_1 \cup A_2 ) & = P(A_1) + P(A_2) - P(A_1 \cap
 A_2) \\
-    & = & 0.13 - \mbox{Probability of having both}
-   \end{eqnarray*}
+    & = 0.13 - \mbox{Probability of having both}
+   \end{aligned}
  {/$$}
 
 Given the scenario, it's likely that some fraction of the population has both.

manuscript/03_conditional.md

@@ -132,12 +132,12 @@ the specificity, {$$}P(- ~|~ D^c) =.985{/$$} and the prevalence
 {$$}P(D) = .001{/$$}.
 
 {$$}
-\begin{eqnarray*}
-P(D ~|~ +) & = &\frac{P(+~|~D)P(D)}{P(+~|~D)P(D) + P(+~|~D^c)P(D^c)}\\
- & = & \frac{P(+~|~D)P(D)}{P(+~|~D)P(D) + \{1-P(-~|~D^c)\}\{1 - P(D)\}} \\
- & = & \frac{.997\times .001}{.997 \times .001 + .015 \times .999}\\
- & = & .062
-\end{eqnarray*}
+\begin{aligned}
+P(D ~|~ +) & = \frac{P(+~|~D)P(D)}{P(+~|~D)P(D) + P(+~|~D^c)P(D^c)}\\
+ & = \frac{P(+~|~D)P(D)}{P(+~|~D)P(D) + \{1-P(-~|~D^c)\}\{1 - P(D)\}} \\
+ & = \frac{.997\times .001}{.997 \times .001 + .015 \times .999}\\
+ & = .062
+\end{aligned}
 {/$$}
 
 In this population a positive test result only suggests a 6% probability that

manuscript/LittleInferenceBook.Rmd

@@ -1,53 +1,57 @@
----
-output:
-  html_document:
-    toc: true
-    toc_depth: 2
-    includes:
-      before_body: frontmatter.html
----
-
-
-```{r book, results='asis', echo = FALSE}
-
-# Get list of .md files from the LeanPub configuration file
-chapters <- readLines(con = "Book.txt")
-
-# Set the encoding
-encoding <- "Latin1"
-
-# Output the content of every file
-invisible(
-  sapply(X = chapters, encoding = encoding,
-         FUN = function(file, encoding){
-           # Read in file contents
-           contents <- readLines(con = file, encoding = encoding)
-
-           # Replace with correct equation markers
-           contents <- gsub(pattern = "([{][$]{2}[}] *)|( *[{]/[$]{2}[}])",
-                            replacement = "$$",
-                            x = contents)
-
-           # Fix code blocks
-           contents <- paste(contents, collapse = "\n")
-           contents <- gsub(pattern = " ~ ", replacement = " \tilde ", x = contents)
-           contents <- gsub(pattern = paste0("\n[{](title ?= ?\"([^\"]*)\")?",
-                                             "[^~]*~~*[[:space:]]*",
-                                             "([^~]*)",
-                                             "~~*\n"),
-                            replacement = "\n**\\2**\n\n```\n\\3\n```\n\n",
-                            x = contents)
-           contents <- gsub(pattern = " \\tilde ", replacement = " ~ ", x = contents)
-
-           # Identify inline equations
-           contents <- gsub(pattern = "[$]{2}", replacement = "$", x = contents)
-           contents <- gsub(pattern = "(\n{2,})[$]([^$]*)[$]",
-                            replacement = "\\1$$\\2$$",
-                            x = contents)
-
-           # Output file contents
-           cat(contents, "\n\n", sep = "")
-         })
-)
-```
-
+---
+output:
+  pdf_document:
+    toc: true
+    includes:
+      in_header: title.tex
+  html_document:
+    toc: true
+    toc_depth: 2
+    includes:
+      before_body: frontmatter.html
+---
+
+
+```{r book, results='asis', echo = FALSE}
+
+# Get list of .md files from the LeanPub configuration file
+chapters <- readLines(con = "Book.txt")
+
+# Set the encoding
+encoding <- "Latin1"
+
+# Output the content of every file
+invisible(
+  sapply(X = chapters, encoding = encoding,
+         FUN = function(file, encoding){
+           # Read in file contents
+           contents <- readLines(con = file, encoding = encoding)
+
+           # Replace with correct equation markers
+           contents <- gsub(pattern = "([{][$]{2}[}] *)|( *[{]/[$]{2}[}])",
+                            replacement = "$$",
+                            x = contents)
+
+           # Fix code blocks
+           contents <- paste(contents, collapse = "\n")
+           contents <- gsub(pattern = " ~ ", replacement = " \tilde ", x = contents)
+           contents <- gsub(pattern = paste0("\n[{](title ?= ?\"([^\"]*)\")?",
+                                             "[^~]*~~*[[:space:]]*",
+                                             "([^~]*)",
+                                             "~~*\n"),
+                            replacement = "\n**\\2**\n\n```\n\\3\n```\n\n",
+                            x = contents)
+           contents <- gsub(pattern = " \\tilde ", replacement = " ~ ", x = contents)
+
+           # Identify inline equations
+           contents <- gsub(pattern = "[$]{2}", replacement = "$", x = contents)
+           contents <- gsub(pattern = "(\n{2,})[$]([^$]*)[$]",
+                            replacement = "\\1$$\\2$$",
+                            x = contents)
+
+           # Output file contents
+           cat(contents, "\n\n", sep = "")
+         })
+)
+```
+

manuscript/title.tex

@@ -0,0 +1,8 @@
+\usepackage{titling}
+\setlength{\droptitle}{-1in}
+\pretitle{%
+  \begin{center}
+  \LARGE
+  \includegraphics{images/title_page.png}\\[\bigskipamount]
+}
+\posttitle{\end{center}}