%\VignetteEngine{knitr::knitr} 
%\VignetteIndexEntry{gRbase-graphs: Graphs in the gRbase package}
%\VignetteDepends{gRbase}
%\VignetteKeyword{graphs}

\documentclass[11pt]{article}

%\usepackage[T1]{fontenc}
%\usepackage[latin1]{inputenc}
\usepackage{boxedminipage,color,a4wide,url}
%\usepackage[utf8]{inputenc}
%\usepackage{inputenx}

\def\code#1{\texttt{#1}}
\def\pkg#1{{\bf #1}}
\def\grbase{\pkg{gRbase}}
\def\graph{\pkg{graph}}
\def\rgraphviz{\pkg{Rgraphviz}}
\def\rbgl{\pkg{RBGL}}
\def\igraph{\pkg{igraph}}
\def\graphnel{\texttt{graphNEL}}
\def\R{\texttt{R}}

<<echo=FALSE>>=
require( gRbase )
prettyVersion <- packageDescription("gRbase")$Version
prettyDate <- format(Sys.Date())
@


\title{Graphs in the \grbase\ package}
\author{S{\o}ren H{\o}jsgaard}
\date{\pkg{gRbase} version \Sexpr{prettyVersion} as of \Sexpr{prettyDate}}

\begin{document}

%\SweaveInput{Rmarkup.STY}

%% \definecolor{darkred}{rgb}{.7,0,0}
%% \definecolor{midnightblue}{rgb}{0.098,0.098,0.439}
%% 
%% \DefineVerbatimEnvironment{Sinput}{Verbatim}{
%%   fontfamily=tt,
%%   %%fontseries=b,
%%   %% xleftmargin=2em,
%%   formatcom={\color{midnightblue}}
%% }
%% \DefineVerbatimEnvironment{Soutput}{Verbatim}{
%%   fontfamily=tt,
%%   %%fontseries=b,
%%   %% xleftmargin=2em,
%%   formatcom={\color{darkred}}
%% }
%% \DefineVerbatimEnvironment{Scode}{Verbatim}{
%%   fontfamily=tt,
%%   %%fontseries=b,
%%   %% xleftmargin=2em,
%%   formatcom={\color{blue}}
%% }
%% 
%%\fvset{listparameters={\setlength{\topsep}{-2pt}}}
%\renewenvironment{Schunk}{\linespread{.90}}{}


\maketitle


<<include=FALSE>>=
library(knitr)
opts_chunk$set(
               fig.path='fig/graph',tidy=FALSE, 
               fig.height=2
)
@

%\setkeys{Gin}{width=0.6\textwidth}

<<echo=FALSE, warning=FALSE>>=
dir.create("fig")
oopt <- options()
options("digits"=4, "width"=80, "prompt"="R> ", "continue"="  ")
options(useFancyQuotes="UTF-8")
@ %def


<<echo=F>>=
library(gRbase)
library(graph)
@

\tableofcontents

\parindent0pt\parskip5pt

\section{Introduction}
\label{sec:intro}

The packages \graph, \rbgl, \rgraphviz\ and
\igraph\ are extremely useful tools for graph operations, manipulation
and layout. The \grbase\ package adds some additional tools to these
fine packages. The most important tools are:

\begin{enumerate}
\item Undirected and directed acyclic graphs can be specified using
  formulae or an adjacency list using the functions \code{ug()} and
  \code{dag()}.

  This gives graphs represented in one of the following
  forms:\footnote{There is a fourth form: \igraph\ objects. These,
    however, will probably not be supported in the future.}
  \begin{itemize}
  \item A \graphnel\ object (the default),
  \item A dense adjacency matrix (a ``standard'' matrix in \R).
  \item A sparse adjacency matrix( a \code{dgCMatrix}
    from the \code{Matrix} package).
  \end{itemize}

\item Some graph algorithms are implemented in \grbase. These can be
  applied to graphs represented as \graphnel s and matrices. The most
  important algorithms are:
  \begin{itemize}
  \item \code{moralize()}, (moralize a directed acyclic graph)
  \item \code{mcs()},(maximum cardinality search for undirected graph)
  \item \code{triangulate()}, (triangulate undirected graph)
  \item \code{rip()}, (RIP ordering of cliques of triangulated undirected graph)
  \item \code{jTree()} (Create junction tree from triangualted
    undirected graph).
  \item \code{getCliques()}, (get the (maximal) cliques of an undirected graph)
  \item \code{minimalTriang()} (minimal triangulation of undirected
    graph)
  \item \code{mpd()} (maximal prime subgraph decomposition of
    undirected graph)
  \end{itemize}

  The general scheme is the following: For example, for maximum
  cardinality search there is a \code{mcs()} function and a
  \code{mcs.default()} method performs maximum cardinality search for
  graphs represented as \graphnel s and as sparse and dense matrices.
  The workhorse is the function \code{mcsMAT()} which takes a sparse
  or a dense matrix as input.
\end{enumerate}

\section{Graphs}
\label{sec:xxx}

Undirected graphs can be created by the \code{ug()} function and
directed acyclic graphs (DAGs) by the \code{dag()} function.
The graphs can be specified either using formulae or a list of
vectors; see examples below.

\subsection{Undirected graphs}


An undirected graph is created by the \code{ug()} function.
The following specifications are equivalent (notice that ``\code{:}''
and ``\code{*}'' can be used interchangably):


%% @
%% <<print=F>>=
%% ug11 <- ug( ~a:b:c + c:d + d:e + a:e + f:g )
%% ug12 <- ug( c("a","b","c"),c("c","d"),c("d","e"),c("a","e"),c("f","g") )
%% ug13 <- ug(~a:b:c, ~c:d, ~d:e + a:e + f:g)
%% ug14 <- ugList( list(c("a","b","c"),c("c","d"),c("d","e"),c("a","e"),c("f","g")) )
%% @ %def



%% Default is to return a \code{graphNEL} object (for which there is a
%% plot method):


%% @
%% <<>>=
%% ug11
%% @ %def




%% @
%% <<>>=
%% plot( ug11 )
%% @ %def




%% A representation as a dense adjacency matrix can be
%% obtained with:
%% @
%% <<print=F>>=
%% ug11m <- ug(~a*b*c + c*d + d*e + a*e + f*g, result="matrix"); ug11m
%% @ %def


%% A representation as a sparse adjacency matrix is obtained with
%% @
%% <<print=F>>=
%% ug11M <- ug(~a*b*c + c*d + d*e + a*e + f*g, result="dgCMatrix"); ug11M
%% @ %def


<<>>=
uG11 <- ug( ~a:b + b:c:d)
uG12 <- ug( c("a", "b"), c("b", "c", "d") )
uG13 <- ug( list( c("a", "b"), c("b", "c", "d") ) )
@ %def


Default is to return a \code{graphNEL} object (for which there is a
plot method):

<<>>=
uG11
nodes(uG11)
str( edges(uG11) )
plot( uG11 )
@ %def

Matrix representations are obtained with:
<<>>=
uG11m <- ug( ~a:b + b:c:d, result="matrix")
uG11M <- ug( ~a:b + b:c:d, result="dgCMatrix")
@ %def

\subsection{Directed acyclic graphs (DAGs)}

A directed acyclic graph is created by the \code{dag()} function.
The
following specifications are equivalent (notice that ``\code{:}''
and ``\code{*}'' can be used interchangably):

<<>>=
daG11 <- dag( ~a:b + b:c:d)
daG12 <- dag( c("a", "b"), c("b", "c", "d") )
daG13 <- dag( list( c("a", "b"), c("b", "c", "d") ) )
@ %def


%% <<print=F>>=
%% daG11 <- dag(~a + b:a + c:a:b + d:c:e + e:a + g:f)
%% daG12 <- dag("a", c("b","a"), c("c","a","b"), c("d","c","e"),
%%              c("e","a"),c("g","f"))
%% daG13 <- dag(~a, ~b:a,  ~c:a:b, ~d:c:e, ~e:a, ~g:f)
%% dag14 <- dagList(list( "a", c("b","a"), c("c","a","b"), c("d","c","e"),
%%                       c("e","a"),c("g","f") ))
%% @

The syntax rules are that \texttt{\~{ }a} (and \code{"a"}) means that ``a'' has no parents while
\texttt{\~{ }c:a:b} (and \code{c("c","a","b")}) means that ``c'' has parents ``a'' and
``b''.
<<>>=
daG11
nodes( daG11 )
str( edges( daG11 ) )
plot( daG11 )
@ %def


Matrix representations are obtained with:
<<>>=
daG11m <- dag( ~a:b + b:c:d, result="matrix")
daG11M <- dag( ~a:b + b:c:d, result="dgCMatrix")
@ %def





\subsection{Other types of graphs}
\label{sec:other-types-graphs}

The \code{dag()} function allows for creation of directed
graphs which are not DAGs. Consider
<<>>=
d1.bi <- dag(~a:b + b:a)
edgemode( d1.bi )
str( edges(d1.bi) )
@ %def
This graph is not DAG because there is an edge from \code{a} to
\code{b} and from \code{b} to \code{a}; i.e., the edge is bidirected.
Likewise we may create:
<<>>=
d2.cyc <- dag(~a:b + b:c + c:a)
@ %def

<<>>=
par(mfrow=c(1,2)); plot(d1.bi); plot(d2.cyc)
@ %def

Notice: Supplying \code{dag()} with \code{forceCheck=TRUE} forces \code{dag()}
to check if the graph is acyclic:
<<results='markup', eval=F>>=
dag(~a:b + b:c + c:a, forceCheck=TRUE)
@ %def

\subsection{Graph properties}
\label{sec:graph-properties}

%% The \graphnel\ objects are very convenient to work with because there
%% are many different methods for such objects, for example:
%% @
%% <<>>=
%% str( graph::nodes( uG11 ) )
%% str( graph::edges( uG11 ) )
%% graph::edgeMatrix( uG11 )
%% @ %def
%% and
%% @
%% <<>>=
%% str( RBGL::maxClique( uG11 ) )
%% @ %def



\subsection{Adjacency matrices}
\label{sec:adjacency-matrices}

Graphs in the \graph\ package (i.e.\ \graphnel\ objects) are represented as adjacency
lists. However, there is a substantial overhead (in terms of computing time) for
such objects. The graph algorithms in \grbase\ are mostly based on a representation
as sparse adjacency matrices (which leads to faster code).

A non-zero value at entry $(i,j)$ in an adjacency matrix $A$ for a
graph means that there is an edge from $i$ to $j$. If also $(j,i)$ is
non-zero then there is also an edge from $j$ to $i$. In this case we
may think of a bidirected edge between $i$ and $j$ or we may think of
the edge as being undirected. We do not distinguish between undirected
and bidirected edges in the \grbase\ package. Put differently, in
\grbase, edges are either directed or undirected/bidirected. In
contrast, with \graphnel\ objects one can work with three types of
edges: undirected, directed and bidirected edges.

\begin{itemize}
\item \code{is.UG()} checks if the adjacency
matrix is symmetric (If applied to a graphNEL, the adjacency matrix is
created and checked for symmetry.)

\item \code{is.TUG()} checks if the graph is undirected and
triangulated (also called chordal) by checking if the adjacency matrix is
symmetric and the vertices can be given a perfect ordering using
maximum cardinality seach.

\item \code{is.DG()} checks if a graph is directed, i.e., that
there are no undirected edges. This is done by computing the
elementwise product of A and the transpose of A; if there are no
non--zero entries in this product then the graph is directed.

\item  \code{is.DAG()} will
return \code{TRUE} if all edges are directed and if there are no
cycles in the graph. (This is checked by checking if the vertices in
the graph can be given a topological ordering which is based on
identifying an undirected edge with a bidrected edge).

\end{itemize}

Notice a special case, namely if the graph has no edges at all (such
that the adjacency matrix consists only of zeros). Such a graph is
both undirected, triangulated, directed and directed acyclic.


Consider these examples (where \code{isDirected()} is a method from
the \graph\ package):

%% @
%% <<>>=
%% properties <- function(x){
%%     c(is.UG=is.UG(x), is.TUG=is.TUG(x), is.DG=is.DG(x), is.DAG=is.DAG(x),
%%       isD=graph::isDirected(x))
%% }
%% properties( uG11 )
%% properties( daG11 )
%% properties( d1.bi )
%% properties( d2.cyc )
%% @ %def


\subsection{Graph coercion}
\label{sec:graph-coercion}


Graphs can be coerced between differente representations using
\code{as()}; for example:
<<>>=
mat <- as(uG11, "matrix")
Mat <- as(mat, "dgCMatrix")
NEL <- as(Mat, "graphNEL")
@ %def

%% <<>>=
%% (mat <- as(uG11, "matrix"))
%% (Mat <- as(mat, "dgCMatrix"))
%% (NEL <- as(Mat, "graphNEL"))
%% @ %def
%% 

Faster (generally) coercion can be obtained with
<<>>=
mat <- coerceGraph(uG11, "matrix")
Mat <- coerceGraph(uG11, "dgCMatrix")
NEL <- coerceGraph(mat, "graphNEL")
@ %def
and, at a lower level,
<<>>=
mat <- graphNEL2M(uG11, result="matrix")
Mat <- graphNEL2M(uG11, result="dgCMatrix")
NEL <- M2graphNEL(mat)
@ %def

We also have
<<>>=
str( M2adjList(mat) )
@ %def


%% <<>>=
%% if( require(microbenchmark) ){
%%   microbenchmark(as(uG11, "matrix"), coerceGraph(uG11, "matrix"), graphNEL2M(uG11),
%%                  as(uG11, "dgCMatrix"), coerceGraph(uG11, "dgCMatrix"),
%%                  graphNEL2M(uG11, result="Matrix"),
%%                  as(mat, "graphNEL"), coerceGraph(mat, "graphNEL"), M2graphNEL(mat), 
%%                  times=10)
%% }
%% @ %def
%% 





\section{Advanced graph operations}
\label{sec:advanc-graph-oper}

\subsection{Moralization}
\label{sec:moralization}

%% @
%% <<>>=
%% apropos("^moralize\\.")
%% @ %def


A moralized directed acyclic graph is obtained with

<<>>=
daG11.mor <- moralize(daG11)
@ %def

<<>>=
par(mfrow=c(1,2)); plot(daG11); plot(daG11.mor)
@ %def

We can work with a matrix representation too. Default is that the
output representation is the same as the input representation, but
this can be changed:
<<>>=
moralize( daG11m, result="dgCMatrix" )
@ %def




\subsection{Topological sort - is a directed graph a DAG?}
\label{sec:topological-sort}

A topological ordering of a directed graph is a linear ordering of its
vertices such that, for every edge ($u \rightarrow v$), $u$ comes before $v$ in the
ordering. A topological ordering is possible if and only if the graph
has no directed cycles, that is, if it is a directed acyclic graph
(DAG). Any DAG has at least one topological ordering.
<<>>=
topoSort(daG11)
topoSort(daG11m)
topoSort(daG11M)
@ %def


The following graph has a cycle and hence a topological ordering can
not be made:
<<>>=
topoSort(dag(~a:b + b:c + c:a))
@ %def

Likewise for an undirected graph (recall that we regard an undirected
edge as a bidirected edge):
<<>>=
topoSort( ug( ~a:b ) )
@ %def


\subsection{Getting the cliques of an undirected graph}
\label{sec:getting-cliques}

In graph theory, a clique is often a complete subset of a graph. A
maximal clique is a clique which can not be enlarged. In statistics
(and that is the convention we follow here) a clique is usually
understood to be a maximal clique.
Finding the cliques of a general graph is an NP--complete
problem. Finding the cliques of triangulated graph is linear in the
number of cliques.

<<>>=
str( getCliques(uG11) )
str( getCliques(uG11m) )
str( getCliques(uG11M) )
@ %def

For \graphnel\ objects one may also use the \code{maxClique()} function
in \rbgl, but \code{getCliques()} applies also to matrices and it is
substantially faster.
%% 
%% <<>>=
%% if (require(microbenchmark)){
%%     microbenchmark(
%%         RBGL::maxClique( uG11 ), getCliques( uG11 ), 
%%         getCliques( uG11m ), getCliques( uG11M ),
%%         times=10)}
%% @ %def
%% 



\subsection{Perfect ordering and maximum cardinality search}
\label{sec:maxim-card-search}

An undirected graph is triangulated (or chordal) if it has no
cycles of length $\ge 4$ without a chord. This is equivalent to that the
vertices can be given a perfect ordering. A perfect ordering (if it
exists) can be obtained with Maximum
Cardinality Search. If \code{character(0)} is returned the graph is not
triangulated. Otherwise a perfect ordering of the nodes is returned.

<<>>=
mcs(uG11)
mcs(uG11m)
mcs(uG11M)
@ %def

In some applications it is convenient to retain control over the
ordering (if it exists). For example:
<<>>=
mcs(uG11, root=c("a","c"))
@ %def
The desired ordering (specified by \code{root}) is followed as far as
possible (here only to the first variable \code{"a"}). Notice the
output when applying \code{mcs()} to a directed
graph:\footnote{Perhaps better to signal an error.}
<<>>=
mcs( daG11 )
mcs( as(daG11, "matrix") )
@ %def

\subsection{Triangulation}
\label{sec:triangulation}

Any undirected graph can be triangulated by adding edges to the graph,
so called fill-ins:

<<>>=
uG <- ug( ~a:b:c + c:d + d:e + a:e + f:g )
mcs(uG)
(tuG  <- triangulate(uG))
mcs(tuG)
@

<< >>= 
(tuG  <- triangulate(uG))
@



<<>>=
par(mfrow=c(1,2)); plot(uG); plot(tuG)
@ %def

\subsection{RIP ordering / junction tree}
\label{sec:rip-ordering-}

A RIP--ordering of the cliques of a triangulated graph can be obtained
as:

<<>>=
rp <- rip(tuG); rp
@ %def

<<>>=
plot( rp )
@ %def

There is more information in a RIP-object:
<< >>= 
names(rp)
rp$nodes
rp$host
rp$children
str(rp$separators)
@

The \code{host} component tells for each node, a clique in which the node can be found


%% See also:
%% @
%% <<>>=
%% str( rp )
%% @ %def



The function \code{jTree} takes an undirected graph as input;
triangulates it if it is not already so and then finds a RIP--ordering.

\subsection{Minimal triangulation and maximum prime subgraph decomposition}
\label{sec:minim-triang-maxim}

A triangulation is minimal if no fill-ins can be removed without
breaking the property that the graph is triangulated. (A related
concept is the minimum triangulation, which is the the graph with the
smallest number of fill-ins. The minimum triangulation is unique, but
finding the minimum triangulation is NP-hard.)

For example, this graph has two 4--cycles:
<<>>=
g1 <- ug(~a:b + b:c + c:d + d:e + e:f + a:f + b:e)
g1mt <- minimalTriang(g1) # A minimal triangulation
@ %def

<<>>=
par(mfrow = c(1,2)); plot(g1); plot(g1mt)
@ %def

The following graph is also a triangulation of \code{g1}, and from
this a minimal triangulation can be obtained:
<<>>=
g2 <- ug(~a:b:e:f + b:c:d:e)
g1mt2 <- minimalTriang(g1, tobject=g2)
@ %def

<<>>=
par(mfrow = c(1,2)); plot(g2); plot(g1mt2)
@ %def

The junction tree of a maximum prime subgraph decomposition is obtained with:
<<>>=
mm <- mpd( g1 ); mm
@ %def

<<>>=
par(mfrow = c(1,2))
plot(subGraph(mm$cliques[[1]], g1))
plot(subGraph(mm$cliques[[2]], g1))
@ %def


\section{Time and space considerations}
\label{sec:time-space}

\subsection{Time}
\label{sec:time}


It is worth noticing that working with graphs representated as
\code{graphNEL} objects can be somewhat slower than working with graphs
represented as adjacency matrices.
Consider finding the cliques of an undirected graph
represented as a \graphnel\ object or as a matrix:

<<>>=
if(require(microbenchmark)){
    microbenchmark(
        RBGL::maxClique(uG11),
        getCliques(uG11),
        getCliques(uG11m),
        getCliques(uG11M),
        times=10) }
@ %def


\subsection{Space}
\label{sec:space}


The \graphnel\ representation is -- at least -- in
principle more economic in terms of space requirements than the
adjacency matrix representation (because the adjacency matrix
representation uses a $0$ to represent a ``missing edge''. The sparse
matrix representation is clearly only superior to the standard matrix
representation if the graph is sparse:

<<>>=
V <- 1:300
M <- 1:10
## Sparse graph
##
g1 <- randomGraph(V, M, 0.05)
length(edgeList(g1))
s <- c(NEL=object.size(g1), 
       dense=object.size(as(g1, "matrix")),
       sparse=object.size(as(g1, "dgCMatrix")))
s / max(s)
## More dense graph
##
g1 <- randomGraph(V, M, 0.5)
length(edgeList(g1))
s <- c(NEL=object.size(g1), 
       dense=object.size(as(g1, "matrix")),
       sparse=object.size(as(g1, "dgCMatrix")))
s / max(s)
@ %def


\section{Graph queries}

The \graph\ and \rbgl\ packages implement various graph operations for
\code{graphNEL} objects. See the documentation for these packages.
The \grbase\ implements a few additional functions, see
Section~\ref{sec:intro}. An additional function in \grbase\ for graph
operations is \code{querygraph()}. This function is intended as a wrapper for the
various graph operations available in \grbase, \graph\ and
\rbgl. There are two main virtues of \code{querygraph()}: 1)
\code{querygraph()} operates on any of the three graph representations
described above\footnote{Actually not quite yet, but it will be so in
  the future.}  and 2) \code{querygraph()} provides a unified
interface to the graph operations. The general syntax is
<<>>=
args(querygraph)
@ %def




<<echo=FALSE>>=
#rm(print.list)
options("width"=85)
@ %def


\end{document}




% \RecustomVerbatimEnvironment{Sinput}{Verbatim}%
% {fontsize=\scriptsize,frame=single,framerule=1pt,
%   rulecolor=\color{red},   fillcolor=\color{yellow} }
% \RecustomVerbatimEnvironment{Soutput}{Verbatim}%
% {fontsize=\scriptsize, frame=single,framerule=0.1pt}


% "MAXCLIQUE",
% "cliques",
% "connectedComp",
% "concomp",
% "separates",
% "adj",
% "cl",
% "ne",
% "is.triangulated",
% "subgraph",
% "an",
% "pa",
% "ch",
% "nodes",
% "edges",
% "is.complete",
% "simplicialNodes",
% "is.simplicial",
% "ancestralSet",
% "ancestralGraph"






% \section{Operations on undirected graphs}
% \label{sec:xxx}


% \subsection{Simple operations}
% \label{sec:xxx}

% Simple operations on undirected graphs are:

% @
% <<>>=
% nodes(ug1)
% edges(ug1)
% @ %def



% Many features of a graph are obtained by asking queries using the
% \code{queryg} function:

% \subsubsection{Nodes}
% <<>>=
% queryg(ug1, "nodes")
% @ %def


% \subsubsection{Edges}
% @
% <<>>=
% queryg(ug1, "edges")
% @ %def


% \subsubsection{Cliques}
% @
% <<>>=
% queryg(ug1, "cliques")
% @ %def

% \subsubsection{Connected components}
% @
% <<>>=
% queryg(ug1, "concomp")
% @ %def


% \subsubsection{Closure}
% @
% <<>>=
% queryg(ug1, "cl", "c")
% @ %def

% \subsubsection{Adjacencies}
% \label{sec:xxx}
% @
% <<>>=
% queryg(ug1, "adj", "c")
% @ %def


% \subsubsection{Simplicial nodes}
% Nodes whose boundary is complete.

% @
% <<>>=
% queryg(ug1, "simplicialNodes")
% @ %def



% \subsubsection{Is complete}
% Is the graph complete?

% @
% <<>>=
% queryg(ug1, "is.complete")
% @ %def


% \subsubsection{Is simplical}
% Is a node/set simplical?

% @
% <<>>=
% queryg(ug1, "is.simplicial", "a")
% queryg(ug1, "is.simplicial", c("a","b","d"))
% @ %def

% \subsubsection{Is triangulated}

% @
% <<>>=
% queryg(ug1, "is.triangulated")
% @ %def


% \subsubsection{Is $A$ and $B$ separated by $S$}

% @
% <<>>=
% queryg(ug1, "separates", c("a","b"), c("d","f"), "c")
% queryg(ug1, "separates", c("a","b"), c("d","f"), c("c","e"))
% @ %def


% \subsubsection{Subgraph}
% @
% <<>>=
% queryg(ug1, "subgraph", c("a","b","c","f"))
% plot(queryg(ug1, "subgraph", c("a","b","c","f")))
% @ %def




% \subsection{Triangulation and Maximum Cardinality Search}
% \label{sec:xxx}







% % \section{Directed acyclic graphs}
% % \label{sec:dags}

% % A directed acyclic graph can be specified as:
% % <<>>=
% % dag1 <- dag(~a, ~b+a,  ~c+a, ~d+b+c, ~e+c)
% % dag1 <- dag("a", c("b","a"), c("c","a"), c("d","b","c"), c("e","c"))
% % nodes(dag1)
% % edges(dag1)
% % vpav(dag1)
% % @
% % Here \code{"a"} means that ``a'' has no parents, while
% % \code{c("d","b","c")} means that ``d'' has parents ``b'' and ``c''.

% % Graphs are displayed with \code{plot}:
% % @
% % <<>>=
% % plot(dag1)
% % @ %def



% \section{Operations on directed acyclic graphs}
% \label{sec:xxx}


% \subsection{Simple operations}
% \label{sec:xxx}

% Simple operations on directed acyclic graphs are:

% @
% <<>>=
% nodes(dag1)
% edges(dag1)
% vpav(dag1)
% @ %def

% \subsection{Graph queries}

% Many features of a graph are obtained by asking queries using the
% \code{queryg} function as above:


% \subsubsection{Parents}
% @
% <<>>=
% queryg(dag1, "pa", "d")
% @ %def


% \subsubsection{Children}
% @
% <<>>=
% queryg(dag1, "ch", "c")
% @ %def


% \subsubsection{Ancestral set}
% @
% <<>>=
% queryg(dag1, "ancestralSet", c("b","e"))
% @ %def

% \subsubsection{Ancestral graph}

% @
% <<>>=
% queryg(dag1, "ancestralGraph", c("b","e"))
% @ %def

% \subsubsection{Subgraph}
% @
% <<>>=
% queryg(dag1, "subgraph", c("a","b","c","f"))
% plot(queryg(dag1, "subgraph", c("a","b","c","f")))
% @ %def




% \subsection{Moralization}
% \label{sec:moralize}

% <<>>=
% moralize(dag1)
% plot(moralize(dag1))
% @




