gRbase (version 1.7-5)

ug: Create undirected and directed graphs

Description

These functions are wrappers for creation of graphs as implemented by graphNEL objects in the graph package.

Usage

ug(..., result="NEL")
dag(..., result="NEL", forceCheck=FALSE)
ugList(x, result="NEL")
dagList(x, result="NEL", forceCheck=FALSE)

Arguments

...

A generating class for a graph, see examples below

x

A list containing a generating class for a graph, see examples below

forceCheck

Logical determining if it should be checked if the graph is acyclical. Yes, one can specify graphs with cycles using the dag() function.

result

The format of the graph. The possible choices are "NEL" (for a graphNEL object), "matrix" (for an adjacency matrix), "igraph" (for an igraph object), "Matrix" (for a sparse matrix).

Value

• Functions ug(), dag(), ugList() and dagList() can return a graphNEL object, a sparse or dense adjacency matrix or an igraph object.

Examples

## The following specifications of undirected graphs are equivalent:
uG1 <- ug(~a:b, ~a:c, ~b:c ~c:d)
uG2 <- ug(c("a","b"), c("a","c"), c("b","c"), c("c","d"))
uG3 <- ug(~a:b:c, ~c:d)
uG4 <- ug(c("a","b","c"), c("c","d"))
uG5 <- ug(~a:b:c + c:d)

graph::edges(uG1)
graph::nodes(uG1)

## The following specifications of directed acyclig graphs are equivalent:
daG1 <- dag(~a:b:c, ~b:c, ~c:d)
daG2 <- dag(c("a","b","c"), c("b","c"), c("c","d"))
daG3 <- dag(~a:b:c + b:c + c:d)

graph::edges(daG1)
graph::nodes(daG2)

## dag() allows to specify directed graphs with cycles:
daG4 <- dag(~a:b+b:c+c:a) # A directed graph but with cycles
## A check for acyclicity can be done with
## daG5 <- dag(~a:b+b:c+c:a, forceCheck=TRUE) 

## A check for acyclicity is provided by topoSort
topoSort( daG3 )
topoSort( daG4 )

## Different representations
uG6 <- ug(~a:b:c + c:d, result="graphNEL")  # default
uG6
uG7 <- ug(~a:b:c + c:d, result="NEL")       # same
uG7
uG8 <- ug(~a:b:c + c:d, result="matrix")    # dense matrix
uG8
uG9 <- ug(~a:b:c + c:d, result="dgCMatrix") # sparse matrix
uG9