Graph: An undirected graph
In rdecision: Decision Analytic Modelling in Health Economics
Graph R Documentation
An undirected graph
Description
An R6 class to represent a graph (from discrete mathematics).
Details
Encapsulates and provides methods for computation and checking of
undirected graphs. Graphs are systems of vertices connected in pairs by
edges. A base class.
Value
A GML stream as a character vector.
Methods
Public methods
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Method new()
Create a new Graph object from sets of nodes
and edges.
Usage
Graph$new(V, E)
Arguments
VAn unordered set of Nodes, as a list.
EAn unordered set of Edges, as a list.
Returns
A Graph object.
Method order()
Return the order of the graph (number of vertices).
Usage
Graph$order()
Returns
Order of the graph (integer).
Method size()
Return the size of the graph (number of edges).
Usage
Graph$size()
Returns
Size of the graph (integer).
Method vertexes()
A list of all the Node objects in the graph.
Usage
Graph$vertexes()
Details
The list of Node objects is returned in the same order as their
indexes understood by vertex_index, vertex_at and
vertex_along, which is not necessarily the same order in which
they were supplied in the V argument to new.
Method vertex_along()
Sequence of vertex indices.
Usage
Graph$vertex_along()
Details
Similar to base::seq_along, this function provides
the indices of the vertices in the graph. It is intended for use by
graph algorithms which iterate vertices.
Returns
A numeric vector of indices from 1 to the order of the graph.
The vertex at index i is not guaranteed to be the same vertex at
V[[i]] of the argument V to new (i.e., the order in
which the vertices are stored internally within the class may differ
from the order in which they were supplied).
Method vertex_index()
Find the index of a vertex in the graph.
Usage
Graph$vertex_index(v)
Arguments
vA vertex, or list of vertexes.
Returns
Index of v. The index of vertex v is the one
used internally to the class object, which is not necessarily the same as
the order of vertices in the V argument of new. NA
if v is not a vertex, or is a vertex that is not in the graph.
Method vertex_at()
Find the vertex at a given index.
Usage
Graph$vertex_at(index, as_list = FALSE)
Arguments
indexIndex of vertex in the graph, as an integer, or vector of
integers.
as_listBoolean. If TRUE the method returns list of Nodes,
even if the length of index is 1.
Details
The inverse of function vertex_index. The function will
raise an abort signal if all the supplied indexes are not vertexes. The
function is vectorized, but for historical compatibility the return
object is a single Node if index is a scalar. The
return object can be guaranteed to be a list if as_list is set.
Returns
Node at index if index is a scalar, a list of Nodes
at the values of index if index is a vector, or an empty
list if index is an empty array.
Method has_vertex()
Test whether a vertex is an element of the graph.
Usage
Graph$has_vertex(v)
Arguments
vVertex, or list of vertices.
Returns
A logical scalar or logical vector the same length as v if v is
a vector, with TRUE if v is an element of V(G).
Method vertex_label()
Find label of vertexes at index i.
Usage
Graph$vertex_label(iv)
Arguments
ivIndex of vertex, or vector of indexes.
Returns
Label(s) of vertex at index i
Method edges()
A list of all the Edge objects in the graph.
Usage
Graph$edges()
Details
The list of Edge objects is returned in the same order as their
indexes understood by edge_index, edge_at and
edge_along, which is not necessarily the same order in which they
were supplied in the E argument to new.
Method edge_along()
Sequence of edge indices.
Usage
Graph$edge_along()
Details
Similar to base::seq_along, this function provides
the indices of the edges in the graph. It is intended for use by
graph algorithms which iterate edges. It is equivalent to
seq_along(g$edges()), where g is a graph.
Returns
A numeric vector of indices from 1 to the size of the graph.
The edge at index i is not guaranteed to be the same edge at
E[[i]] of the argument E to new (i.e., the order in
which the edges are stored internally within the class may differ
from the order in which they were supplied).
Method edge_index()
Find the index of an edge in a graph.
Usage
Graph$edge_index(e)
Arguments
eAn edge object, or list of edge objects.
Details
The index of edge e is the one used internally to the
class object, which is not necessarily the same as the
order of edges in the E argument of new.
Returns
Index of e. NA if e is not an edge, or is an
edge that is not in the graph.
Method edge_at()
Find the edge at a given index.
Usage
Graph$edge_at(index, as_list = FALSE)
Arguments
indexIndex of edge in the graph, as an integer, vector of
integers, or list of integers.
as_listBoolean. If TRUE the method returns list of Edges,
even if the length of index is 1.
Details
The inverse of function edge_index. The function will
raise an abort signal if the supplied index is not an edge. The
function is vectorized, but for historical compatibility the return
object is a single Edge if index is a scalar. The
return object can be guaranteed to be a list if as_list is set.
Returns
The edge, or list of edges, with the specified index.
Method has_edge()
Test whether an edge is an element of the graph.
Usage
Graph$has_edge(e)
Arguments
eEdge or list of edges.
Returns
Logical vector with each element TRUE if the corresponding
element of e is an element of E(G).
Method edge_label()
Find label of edge at index i
Usage
Graph$edge_label(ie)
Arguments
ieIndex of edge, or vector of indexes.
Returns
Label of edge at index i, or character vector with the labels at
indexes ie.
Method graph_adjacency_matrix()
Compute the adjacency matrix for the graph.
Usage
Graph$graph_adjacency_matrix(boolean = FALSE)
Arguments
booleanIf TRUE, the adjacency matrix is logical, each
cell is {FALSE, TRUE}.
Details
Each cell contains the
number of edges joining the two vertexes, with the convention of
self loops being counted twice, unless binary is TRUE when
cells are either 0 (not adjacent) or 1 (adjacent).
Returns
A square integer matrix with the number of rows and columns
equal to the order of the graph. The rows and columns are labelled
with the node labels, if all the nodes in the graph have unique labels,
or the node indices if not.
Method is_simple()
Is this a simple graph?
Usage
Graph$is_simple()
Details
A simple graph has no self loops or multi-edges.
Returns
TRUE if simple, FALSE if not.
Method is_connected()
Test whether the graph is connected.
Usage
Graph$is_connected()
Details
Graphs with no vertices are considered unconnected; graphs with
1 vertex are considered connected. Otherwise a graph is connected if all
nodes can be reached from an arbitrary starting point. Uses a depth first
search.
Returns
TRUE if connected, FALSE if not.
Method is_acyclic()
Checks for the presence of a cycle in the graph.
Usage
Graph$is_acyclic()
Details
Uses a depth-first search from each node to detect the
presence of back edges. A back edge is an edge from the current node
joining a previously detected (visited) node, that is not the parent
node of the current one.
Returns
TRUE if no cycles detected.
Method is_tree()
Compute whether the graph is connected and acyclic.
Usage
Graph$is_tree()
Returns
TRUE if the graph is a tree; FALSE if not.
Method degree()
The degree of a vertex in the graph.
Usage
Graph$degree(v)
Arguments
vThe subject node.
Details
The number of incident edges.
Returns
Degree of the vertex, integer.
Method neighbours()
Find the neighbours of a node.
Usage
Graph$neighbours(v)
Arguments
vThe subject node (scalar, not a list).
Details
A property of the graph, not the node. Does not include self,
even in the case of a loop to self.
Returns
A list of nodes which are joined to the subject.
Method as_DOT()
Export a representation of the graph in DOT format.
Usage
Graph$as_DOT(rankdir = "LR", width = 7, height = 7)
Arguments
rankdirOne of "LR" (default), "TB", "RL" or "BT".
widthof the drawing, in inches
heightof the drawing, in inches
Details
Writes the representation in the graphviz DOT language
(https://graphviz.org/doc/info/lang.html) for drawing with one
of the graphviz tools including dot (Gansner, 1993).
Returns
A character vector. Intended for passing to writeLines
for saving as a text file.
Method as_gml()
Exports the digraph as a Graph Modelling Language (GML)
stream.
Usage
Graph$as_gml()
Details
Intended to work with the igraph or DiagrammeR packages, which
are able to import GML files.
Method clone()
The objects of this class are cloneable with this method.
Usage
Graph$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Author(s)
Andrew Sims andrew.sims@newcastle.ac.uk
References
Gansner ER, Koutsofios E, North SC, Vo K-P. A technique for drawing
directed graphs. IEEE Transactions on Software Engineering,
1993;19:214–30, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1109/32.221135")}.
Gross JL, Yellen J, Zhang P. Handbook of Graph Theory. Second edition,
Chapman and Hall/CRC.; 2013, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1201/b16132")}
rdecision documentation built on April 3, 2025, 6:09 p.m.
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| Graph | R Documentation |
An undirected graph
Description
An R6 class to represent a graph (from discrete mathematics).
Details
Encapsulates and provides methods for computation and checking of undirected graphs. Graphs are systems of vertices connected in pairs by edges. A base class.
Value
A GML stream as a character vector.
Methods
Public methods
Method new()
Create a new Graph object from sets of nodes
and edges.
Usage
Graph$new(V, E)
Arguments
VAn unordered set of Nodes, as a list.
EAn unordered set of Edges, as a list.
Returns
A Graph object.
Method order()
Return the order of the graph (number of vertices).
Usage
Graph$order()
Returns
Order of the graph (integer).
Method size()
Return the size of the graph (number of edges).
Usage
Graph$size()
Returns
Size of the graph (integer).
Method vertexes()
A list of all the Node objects in the graph.
Usage
Graph$vertexes()
Details
The list of Node objects is returned in the same order as their
indexes understood by vertex_index, vertex_at and
vertex_along, which is not necessarily the same order in which
they were supplied in the V argument to new.
Method vertex_along()
Sequence of vertex indices.
Usage
Graph$vertex_along()
Details
Similar to base::seq_along, this function provides
the indices of the vertices in the graph. It is intended for use by
graph algorithms which iterate vertices.
Returns
A numeric vector of indices from 1 to the order of the graph.
The vertex at index i is not guaranteed to be the same vertex at
V[[i]] of the argument V to new (i.e., the order in
which the vertices are stored internally within the class may differ
from the order in which they were supplied).
Method vertex_index()
Find the index of a vertex in the graph.
Usage
Graph$vertex_index(v)
Arguments
vA vertex, or list of vertexes.
Returns
Index of v. The index of vertex v is the one
used internally to the class object, which is not necessarily the same as
the order of vertices in the V argument of new. NA
if v is not a vertex, or is a vertex that is not in the graph.
Method vertex_at()
Find the vertex at a given index.
Usage
Graph$vertex_at(index, as_list = FALSE)
Arguments
indexIndex of vertex in the graph, as an integer, or vector of integers.
as_listBoolean. If TRUE the method returns list of Nodes, even if the length of
indexis 1.
Details
The inverse of function vertex_index. The function will
raise an abort signal if all the supplied indexes are not vertexes. The
function is vectorized, but for historical compatibility the return
object is a single Node if index is a scalar. The
return object can be guaranteed to be a list if as_list is set.
Returns
Node at index if index is a scalar, a list of Nodes
at the values of index if index is a vector, or an empty
list if index is an empty array.
Method has_vertex()
Test whether a vertex is an element of the graph.
Usage
Graph$has_vertex(v)
Arguments
vVertex, or list of vertices.
Returns
A logical scalar or logical vector the same length as v if v is a vector, with TRUE if v is an element of V(G).
Method vertex_label()
Find label of vertexes at index i.
Usage
Graph$vertex_label(iv)
Arguments
ivIndex of vertex, or vector of indexes.
Returns
Label(s) of vertex at index i
Method edges()
A list of all the Edge objects in the graph.
Usage
Graph$edges()
Details
The list of Edge objects is returned in the same order as their
indexes understood by edge_index, edge_at and
edge_along, which is not necessarily the same order in which they
were supplied in the E argument to new.
Method edge_along()
Sequence of edge indices.
Usage
Graph$edge_along()
Details
Similar to base::seq_along, this function provides
the indices of the edges in the graph. It is intended for use by
graph algorithms which iterate edges. It is equivalent to
seq_along(g$edges()), where g is a graph.
Returns
A numeric vector of indices from 1 to the size of the graph.
The edge at index i is not guaranteed to be the same edge at
E[[i]] of the argument E to new (i.e., the order in
which the edges are stored internally within the class may differ
from the order in which they were supplied).
Method edge_index()
Find the index of an edge in a graph.
Usage
Graph$edge_index(e)
Arguments
eAn edge object, or list of edge objects.
Details
The index of edge e is the one used internally to the
class object, which is not necessarily the same as the
order of edges in the E argument of new.
Returns
Index of e. NA if e is not an edge, or is an
edge that is not in the graph.
Method edge_at()
Find the edge at a given index.
Usage
Graph$edge_at(index, as_list = FALSE)
Arguments
indexIndex of edge in the graph, as an integer, vector of integers, or list of integers.
as_listBoolean. If TRUE the method returns list of Edges, even if the length of
indexis 1.
Details
The inverse of function edge_index. The function will
raise an abort signal if the supplied index is not an edge. The
function is vectorized, but for historical compatibility the return
object is a single Edge if index is a scalar. The
return object can be guaranteed to be a list if as_list is set.
Returns
The edge, or list of edges, with the specified index.
Method has_edge()
Test whether an edge is an element of the graph.
Usage
Graph$has_edge(e)
Arguments
eEdge or list of edges.
Returns
Logical vector with each element TRUE if the corresponding
element of e is an element of E(G).
Method edge_label()
Find label of edge at index i
Usage
Graph$edge_label(ie)
Arguments
ieIndex of edge, or vector of indexes.
Returns
Label of edge at index i, or character vector with the labels at
indexes ie.
Method graph_adjacency_matrix()
Compute the adjacency matrix for the graph.
Usage
Graph$graph_adjacency_matrix(boolean = FALSE)
Arguments
booleanIf
TRUE, the adjacency matrix is logical, each cell is {FALSE,TRUE}.
Details
Each cell contains the
number of edges joining the two vertexes, with the convention of
self loops being counted twice, unless binary is TRUE when
cells are either 0 (not adjacent) or 1 (adjacent).
Returns
A square integer matrix with the number of rows and columns equal to the order of the graph. The rows and columns are labelled with the node labels, if all the nodes in the graph have unique labels, or the node indices if not.
Method is_simple()
Is this a simple graph?
Usage
Graph$is_simple()
Details
A simple graph has no self loops or multi-edges.
Returns
TRUE if simple, FALSE if not.
Method is_connected()
Test whether the graph is connected.
Usage
Graph$is_connected()
Details
Graphs with no vertices are considered unconnected; graphs with 1 vertex are considered connected. Otherwise a graph is connected if all nodes can be reached from an arbitrary starting point. Uses a depth first search.
Returns
TRUE if connected, FALSE if not.
Method is_acyclic()
Checks for the presence of a cycle in the graph.
Usage
Graph$is_acyclic()
Details
Uses a depth-first search from each node to detect the presence of back edges. A back edge is an edge from the current node joining a previously detected (visited) node, that is not the parent node of the current one.
Returns
TRUE if no cycles detected.
Method is_tree()
Compute whether the graph is connected and acyclic.
Usage
Graph$is_tree()
Returns
TRUE if the graph is a tree; FALSE if not.
Method degree()
The degree of a vertex in the graph.
Usage
Graph$degree(v)
Arguments
vThe subject node.
Details
The number of incident edges.
Returns
Degree of the vertex, integer.
Method neighbours()
Find the neighbours of a node.
Usage
Graph$neighbours(v)
Arguments
vThe subject node (scalar, not a list).
Details
A property of the graph, not the node. Does not include self, even in the case of a loop to self.
Returns
A list of nodes which are joined to the subject.
Method as_DOT()
Export a representation of the graph in DOT format.
Usage
Graph$as_DOT(rankdir = "LR", width = 7, height = 7)
Arguments
rankdirOne of "LR" (default), "TB", "RL" or "BT".
widthof the drawing, in inches
heightof the drawing, in inches
Details
Writes the representation in the graphviz DOT language
(https://graphviz.org/doc/info/lang.html) for drawing with one
of the graphviz tools including dot (Gansner, 1993).
Returns
A character vector. Intended for passing to writeLines
for saving as a text file.
Method as_gml()
Exports the digraph as a Graph Modelling Language (GML) stream.
Usage
Graph$as_gml()
Details
Intended to work with the igraph or DiagrammeR packages, which are able to import GML files.
Method clone()
The objects of this class are cloneable with this method.
Usage
Graph$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Author(s)
Andrew Sims andrew.sims@newcastle.ac.uk
References
Gansner ER, Koutsofios E, North SC, Vo K-P. A technique for drawing directed graphs. IEEE Transactions on Software Engineering, 1993;19:214–30, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1109/32.221135")}.
Gross JL, Yellen J, Zhang P. Handbook of Graph Theory. Second edition, Chapman and Hall/CRC.; 2013, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1201/b16132")}
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