Add code blocks and author

README.md

@@ -1,3 +1,8 @@
+---
+author: Author I. Name
+---
+
+
 # Background
 
 This is a style guide to help formatting Markdown tutorials. Please add some background about the tutorial in this section, clearly explaining the question/problem and the type of analysis that the methods in the tutorial should be used for. In the next section please add a short description of all the programs or packages used in the tutorial. 
@@ -86,6 +91,35 @@ Use block-quotes for step-by-step instructions (this will produce a framed box o
 >
 > Nothing interesting will happen
 
+Use the code environment to add code blocks:
+```java
+public class HelloWorld {
+
+    public static void main(String[] args) {
+        // Prints "Hello, World" to the terminal window.
+        System.out.println("Hello, World");
+    }
+
+}
+```
+
+```xml
+\begin{lstlisting}[language=XML]
+	<BirthDeathSkylineModel spec="BirthDeathSkylineModel" id="birthDeath" tree="@tree" contemp="true">
+	      <parameter name="origin" id="origin" value ="100" lower="0."/>    
+	      <parameter name="R0" id="R0" value="2" lower="0." dimension ="10"/>
+	      <parameter name="becomeUninfectiousRate" id="becomeUninfectiousRate" value="1" lower="0." dimension ="10"/>
+	      <parameter name="samplingProportion" id="samplingProportion" value="0."/>
+	      <parameter name="rho" id="rho" value="1e-6" lower="0." upper="1."/>
+	</BirthDeathSkylineModel>
+```
+
+```R
+	> myString <- "Hello, World!"
+	> print (myString)
+	[1] "Hello, World!"
+```
+
 
 
 # Hyperlinks

main.tex

@@ -168,7 +168,35 @@ \section{Instructions}
 
 \end{framed}
 
-
+Use lstlisting boxes for inserting code in different languages:
+
+\begin{lstlisting}[language=java]
+public class HelloWorld {
+
+    public static void main(String[] args) {
+        // Prints "Hello, World" to the terminal window.
+        System.out.println("Hello, World");
+    }
+
+}
+\end{lstlisting}
+
+
+\begin{lstlisting}[language=XML]
+	<BirthDeathSkylineModel spec="BirthDeathSkylineModel" id="birthDeath" tree="@tree" contemp="true">
+	      <parameter name="origin" id="origin" value ="100" lower="0."/>    
+	      <parameter name="R0" id="R0" value="2" lower="0." dimension ="10"/>
+	      <parameter name="becomeUninfectiousRate" id="becomeUninfectiousRate" value="1" lower="0." dimension ="10"/>
+	      <parameter name="samplingProportion" id="samplingProportion" value="0."/>
+	      <parameter name="rho" id="rho" value="1e-6" lower="0." upper="1."/>
+	</BirthDeathSkylineModel>
+\end{lstlisting}
+
+\begin{lstlisting}[language=R]
+	> myString <- "Hello, World!"
+	> print (myString)
+	[1] "Hello, World!"
+\end{lstlisting}
 
 \bigskip
 \section{Hyperlinks}

preamble.tex

@@ -128,7 +128,28 @@
 \usepackage{placeins}
 \usepackage{epstopdf}
 
-\lstset{breaklines=true}
+
+
+\lstset{backgroundcolor=\color[rgb]{0.972,0.972,0.972},
+		tabsize=4,
+		rulecolor=,
+        basicstyle=\scriptsize,
+        upquote=true,
+        aboveskip={1.5\baselineskip},
+        columns=fixed,
+        showstringspaces=false,
+        extendedchars=true,
+        breaklines=true,
+        prebreak = \raisebox{0ex}[0ex][0ex]{\ensuremath{\hookleftarrow}},
+        frame=single,
+        showtabs=false,
+        showspaces=false,
+        showstringspaces=false,
+        identifierstyle=\ttfamily,
+        keywordstyle=\color[rgb]{0,0,1},
+        commentstyle=\color[rgb]{0.133,0.545,0.133},
+        stringstyle=\color[rgb]{0.627,0.126,0.941}
+}
 
 \definecolor{shadecolor}{RGB}{194,225,255}