@@ -788,31 +788,31 @@ plot(coex, "neato")

 z <- plot(coex, "neato")

 @

-The following functions are interfaces to those in BGL, they only calculate 

-the (x, y)-coordinates of the vertices in the graph.  The actual layout is 

-achieved with additional function, we provide an example on how to do so.

-

-Following functions are available:

-

-The \Rfunction{randomGraphLayout} function puts the vertices randomly 

-on a plane;

-

-The \Rfunction{circleLayout} function puts the vertices as vertices of 

-a regular polygon;

-

-The \Rfunction{kamadaKawaiSpringLayout} function is for connected, 

-undirected graphs, it treats the edges as springs and tries to minimize 

-the energy of the whole system;

-

-The \Rfunction{fruchtermanReingoldForceDirectedLayout} function is for 

-unweighted, undirected, possibly disconnected graphs, it treats the edges 

-as forces that pull vertices together, no-edges as forces that push 

-vertices apart, vertices move to a position as environment changes; 

-initial positions of the vertices are set randomly by calling 

-\Rfunction{randomGraphLayout}.  Notice that the choice of "width" and 

-"height" values has dramatic impact on the performance.

-

-<<Layoutdemo2>>=

+%The following functions are interfaces to those in BGL, they only calculate 

+%the (x, y)-coordinates of the vertices in the graph.  The actual layout is 

+%achieved with additional function, we provide an example on how to do so.

+%

+%Following functions are available:

+%

+%The \Rfunction{randomGraphLayout} function puts the vertices randomly 

+%on a plane;

+%

+%The \Rfunction{circleLayout} function puts the vertices as vertices of 

+%a regular polygon;

+%

+%The \Rfunction{kamadaKawaiSpringLayout} function is for connected, 

+%undirected graphs, it treats the edges as springs and tries to minimize 

+%the energy of the whole system;

+%

+%The \Rfunction{fruchtermanReingoldForceDirectedLayout} function is for 

+%unweighted, undirected, possibly disconnected graphs, it treats the edges 

+%as forces that pull vertices together, no-edges as forces that push 

+%vertices apart, vertices move to a position as environment changes; 

+%initial positions of the vertices are set randomly by calling 

+%\Rfunction{randomGraphLayout}.  Notice that the choice of "width" and 

+%"height" values has dramatic impact on the performance.

+

+<<Layoutdemo2,echo=FALSE,eval=FALSE>>=

 randomGraphLayout(coex)

 circleLayout(coex)

 kamadaKawaiSpringLayout(coex)

@@ -821,10 +821,10 @@ fruchtermanReingoldForceDirectedLayout(coex, 10, 10)

 Outputs are the (x, y)-coordinates of the vertices in the layout.

-If you want to draw the graphs based on the calculated coordinates, you need 

-an additional function.  The following is an example.

+%If you want to draw the graphs based on the calculated coordinates, you need 

+%an additional function.  The following is an example.

-<<Layoutdemo3>>=

+<<Layoutdemo3,echo=FALSE,eval=FALSE>>=

 crudeGraphPlot <- function(g, alg=circleLayout, ...) {

 #

 # the alg parameter is a function that computes the

@@ -848,33 +848,33 @@ crudeGraphPlot(coex)

 crudeGraphPlot(coex, alg=kamadaKawaiSpringLayout, col="green")

 @

-<<figlayout1, fig=TRUE, echo=false, results=hide, include=FALSE>>=

+<<figlayout1, fig=TRUE, echo=false, results=hide, include=FALSE,eval=FALSE>>=

 crudeGraphPlot(coex)

 @

-<<figlayout2, fig=TRUE, echo=false, results=hide, include=FALSE>>=

+<<figlayout2, fig=TRUE, echo=false, results=hide, include=FALSE,eval=FALSE>>=

 crudeGraphPlot(coex, alg=kamadaKawaiSpringLayout, col="green")

 @

-\begin{figure}[tp]

-\begin{center}

-\begin{tabular}{cc}

-\includegraphics[width=0.49\textwidth]{RBGL-figneato} &

-\includegraphics[width=0.49\textwidth]{RBGL-figlayout1} \\

-\includegraphics[width=0.49\textwidth]{RBGL-figlayout2} \\

-\end{tabular}

-\end{center}

-\caption{\label{fig:graphlayout}%

-a) plot(coex, neato).

-b) crudeGraphPlot(coex).

-c) crudeGraphPlot(coex, alg=kamadaKawaiSpringLayout, col="green"). }

-\end{figure}

-

-Call crudeGraphPlot(coex) gives the default circular layout on your graphics device.

-

-Call crudeGraphPlot(coex, alg=kamada.kawai.spring.layout, col="green") shows you the spring layout with green edges, see Figure~\ref{fig:graphlayout}.

-

-

+%\begin{figure}[tp]

+%\begin{center}

+%\begin{tabular}{cc}

+%\includegraphics[width=0.49\textwidth]{RBGL-figneato} &

+%\includegraphics[width=0.49\textwidth]{RBGL-figlayout1} \\

+%\includegraphics[width=0.49\textwidth]{RBGL-figlayout2} \\

+%\end{tabular}

+%\end{center}

+%\caption{\label{fig:graphlayout}%

+%a) plot(coex, neato).

+%b) crudeGraphPlot(coex).

+%c) crudeGraphPlot(coex, alg=kamadaKawaiSpringLayout, col="green"). }

+%\end{figure}

+%

+%Call crudeGraphPlot(coex) gives the default circular layout on your graphics device.

+%

+%Call crudeGraphPlot(coex, alg=kamada.kawai.spring.layout, col="green") shows you the spring layout with green edges, see Figure~\ref{fig:graphlayout}.

+%

+%

 \subsection{Isomorphism}

 The \Rfunction{isomorphism} function determines if two graphs are isomorphism,