Read and write a graph-object

Construct a graph-object from a file or a matrix; write graph-object to file

inla.read.graph(..., size.only = FALSE)

inla.write.graph(
  graph,
  filename = "graph.dat",
  mode = c("binary", "ascii"),
  ...
)

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

# S3 method for class 'inla.graph'
summary(object, ...)

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

Arguments

...

Additional arguments. In inla.read.graph, then it is the graph definition (object, matrix, character, filename), plus extra arguments. In inla.write.graph it is extra arguments to inla.read.graph.

size.only

Only read the size of the graph

graph

An inla.graph-object, a (sparse) symmetric matrix, a filename containing the graph, a list or collection of characters and/or numbers defining the graph, or a neighbours list with class nb (see spdep::card and spdep::poly2nb for for details of nb and an example a function returning an nb object

filename

The filename of the graph.

mode

The mode of the file; 'ascii' for ascii-file or 'binary' for a binary-file (default).

x

An inla.graph -object

y

Not used

object

An inla.graph -object

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

  • 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

  • meanis a factor with one level for each connected component of size larger than one, otherwise NA

Methods implemented for inla.graph are summary and plot. The method plot require the libraries Rgraphviz and graph from the Bioconductor-project, see https://www.bioconductor.org.

See also

inla.spy()

Author

Havard Rue hrue@r-inla.org

Examples


## a graph from a file
g.file1 <- tempfile() # E.g. "g.dat"
cat("3 1 1 2 2 1 1 3 0\n", file = g.file1)
g = inla.read.graph(g.file1)
## writing an inla.graph-object to file
g.file2 = inla.write.graph(g, mode="binary", filename = tempfile())
## re-reading it from that file
gg = inla.read.graph(g.file2)
summary(g)
#> 	n =  3 
#> 	ncc =  2 
#> 	nnbs = (names)  0 1 
#> 	       (count)  1 2 
summary(gg)
#> 	n =  3 
#> 	ncc =  2 
#> 	nnbs = (names)  0 1 
#> 	       (count)  1 2 

if (FALSE) { # \dontrun{
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"))

## building a graph from adjacency matrix
adjacent = matrix(0, nrow = 4, ncol = 4)
adjacent[1,4] = adjacent[4,1] = 1
adjacent[2,4] = adjacent[4,2] = 1
adjacent[2,3] = adjacent[3,2] = 1
adjacent[3,4] = adjacent[4,3] = 1
g = inla.read.graph(adjacent)
plot(g)
summary(g)
} # }