caugi (version 1.1.0)

as_caugi: Convert to a caugi

Description

Convert an object to a caugi. The object can be a graphNEL, matrix, tidygraph, daggity, bn, or igraph.

Usage

as_caugi(
  x,
  class = c("DAG", "PDAG", "ADMG", "PAG", "UNKNOWN"),
  simple = TRUE,
  collapse = FALSE,
  collapse_to = "---",
  ...
)

Value

A caugi object.

Arguments

x

An object to convert to a caugi.

class

"DAG", "PDAG", "ADMG", "PAG", or "UNKNOWN". "PAG" is only supported for integer coded matrices. "ADMG" is for Acyclic Directed Mixed Graphs (with --> and <-> edges).

simple

logical. If TRUE (default) the graph will be simple (no multiple edges or self-loops).

collapse

logical. If TRUE collapse mutual directed edges to undirected edges. Default is FALSE.

collapse_to

Character string to use as the edge glyph when collapsing. Should be a registered symmetrical edge glyph. Default is "---".

...

Additional arguments passed to specific methods.

Details

For matrices, as_caugi assumes that the rows are the from nodes and the columns are the to nodes. Thus, for a graph, G: A --> B, we would have that G["A", "B"] == 1 and G["B", "A"] == 0. For PAGs, the integer codes are as follows (as used in pcalg):

• 0: no edge

• 1: circle (e.g., A o-o B or A o-- B)

• 2: arrowhead (e.g., A --> B or A o-> B)

• 3: tail (e.g., A o-- B or A --- B)

See Also

Other conversions: as_adjacency(), as_bnlearn(), as_dagitty(), as_igraph()

Examples

# igraph
ig <- igraph::graph_from_literal(A - +B, B - +C)
cg_ig <- as_caugi(ig, class = "DAG")

# graphNEL
gn <- graph::graphNEL(nodes = c("A", "B", "C"), edgemode = "directed")
gn <- graph::addEdge("A", "B", gn)
gn <- graph::addEdge("B", "C", gn)
cg_gn <- as_caugi(gn, class = "DAG")

# adjacency matrix
m <- matrix(0L, 3, 3, dimnames = list(LETTERS[1:3], LETTERS[1:3]))
m["A", "B"] <- 1L
m["B", "C"] <- 1L
cg_adj <- as_caugi(m, class = "DAG")

# bnlearn
bn <- bnlearn::model2network("[A][B|A][C|B]")
cg_bn <- as_caugi(bn, class = "DAG")

# dagitty
dg <- dagitty::dagitty("dag {
 A -> B
 B -> C
 }")
cg_dg <- as_caugi(dg, class = "DAG")

cg <- caugi(A %-->% B %-->% C, class = "DAG")

# check that all nodes are equal in all graph objects
for (cg_converted in list(cg_ig, cg_gn, cg_adj, cg_bn, cg_dg)) {
  stopifnot(identical(nodes(cg), nodes(cg_converted)))
  stopifnot(identical(edges(cg), edges(cg_converted)))
}

# collapse mutual edges
ig2 <- igraph::graph_from_literal(A - +B, B - +A, C - +D)
cg2 <- as_caugi(ig2, class = "PDAG", collapse = TRUE, collapse_to = "---")

# coded integer matrix for PAGs (pcalg style)
nm <- c("A", "B", "C", "D")
M <- matrix(0L, 4, 4, dimnames = list(nm, nm))

# A --> B
M["A", "B"] <- 2L # mark at B end
M["B", "A"] <- 3L # mark at A end

# A --- C
M["A", "C"] <- 3L
M["C", "A"] <- 3L

# B o-> C
M["B", "C"] <- 2L
M["C", "B"] <- 1L

# C o-o D
M["C", "D"] <- 1L
M["D", "C"] <- 1L

cg <- as_caugi(M, class = "PAG")