getGraph: Get the "graph" Part or Aspect of R Object

In pcalg: Methods for Graphical Models and Causal Inference

Get the "graph" Part or Aspect of R Object

Description

Get the graph part or “aspect” of an R object, notably from our pc(), skeleton(), fci(), etc, results.

Usage

getGraph(x)

Arguments

x	potentially any R object which can be interpreted as a graph (with nodes and edges).

Value

a graph object, i.e., one inheriting from (the virtual) class "graph", package graph.

Methods

signature(x = "ANY")

the default method just tries as(x, "graph"), so works when a coerce (S4) method is defined for x.

signature(x = "pcAlgo")

and

signature(x = "fciAlgo")

extract the graph part explicitly.

signature(x = "matrix")

interpret x as adjacency matrix and return the corresponding "graphAM" object.

For sparseMatrix methods, see the ‘Note’.

Note

For large graphs, it may be attractive to work with sparse matrices from the Matrix package. If desired, you can activate this by

 require(Matrix)
 setMethod("getGraph", "sparseMatrix", function(x) as(x, "graphNEL"))
 setMethod("getGraph", "Matrix",       function(x) as(x, "graphAM"))
  

Author(s)

Martin Maechler

See Also

fci, etc. The graph class description in package graph.

Examples

A <- rbind(c(0,1,0,0,1),
           c(0,0,0,1,1),
           c(1,0,0,1,0),
           c(1,0,0,0,1),
           c(0,0,0,1,0))
sum(A) # 9
getGraph(A) ## a graph with 5 nodes and  'sum(A)' edges

pcalg documentation built on Sept. 26, 2023, 9:06 a.m.