read.graph: Read and write a graph-object

In andrewzm/INLA: Functions which allow to perform full Bayesian analysis of latent Gaussian models using Integrated Nested Laplace Approximaxion

Description

Reads a graph-object to a file and write graph-object to file

Usage

inla.read.graph(..., size.only = FALSE)
inla.write.graph(graph, filename = "graph.dat", mode = c("binary", "ascii"), ...)

## S3 method for class 'inla.graph'
summary(object, ...)
## S3 method for class 'inla.graph'
plot(x, y, ...)
## S3 method for class 'inla.graph.summary'
print(x, ...)

Arguments

filename	The filename of the graph.
graph	An inla.graph-object, a (sparse) symmetric matrix, a filename containing the graph, or a list or collection of characters and/or numbers defining the graph.
mode	The mode of the file; ascii-file or a (gzip-compressed) binary. Default value depends on the inla.option internal.binary.mode which is default TRUE; see inla.setOption.
object	An inla.graph -object
x	An inla.graph -object
y	Not used
size.only	Only read the size of the graph
...	Additional arguments. In inla.read.graph, then it is the graph definition (object, character, filename), plus extra arguments. In inla.write.graph it is extra arguments to inla.read.graph.

Value

The output of inla.read.graph, is an inla.graph object, with elements

n	is the size of the graph
nnbs	is a vector with the number of neigbours
nbs	is a list-list with the neigbours
cc	list with connected component information (this entry can be auto-generated; see below) idis a vector with the connected component id for each node (starting from 1) nis the number of connected components nodesis a list-list of nodes belonging to each connected component

The connected component information, can be generated from the rest of the graph-structure, using graph = inla.add.graph.cc(graph) if you manually construct the inla.graph-object. Methods implemented for inla.graph are summary and plot. The method plot require the libraries Rgraphviz and graph from the Bioconductor-project, see http://www.bioconductor.org.

Author(s)

Havard Rue [e-mail]

See Also

inla.spy

Examples

## a graph on a file
cat("3 1 1 2 2 1 1 3 0\n", file="g.dat")
g = inla.read.graph("g.dat")
## writing an inla.graph-object to file
g.file = inla.write.graph(g, mode="binary")
## re-reading it from that file
gg = inla.read.graph(g.file)
summary(g)
plot(g)
inla.spy(g)
## when defining the graph directly in the call, we can use a mix of character and numbers
g = inla.read.graph(c(3, 1, "1 2 2 1 1 3", 0))
inla.spy(c(3, 1, "1 2 2 1 1 3 0"))
inla.spy(c(3, 1, "1 2 2 1 1 3 0"),  reordering=3:1)
inla.write.graph(c(3, 1, "1 2 2 1 1 3 0"))

andrewzm/INLA documentation built on May 10, 2019, 11:12 a.m.