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```
# return the arcs in the graph.
arcs = function(x) {
# check x's class.
check.bn.or.fit(x)
if (is(x, "bn"))
x$arcs
else
fit2arcs(x)
}#ARCS
# rebuild the network structure using a new set fo arcs.
"arcs<-" = function(x, check.cycles = TRUE, check.illegal = TRUE, debug = FALSE,
value) {
# check x's class.
check.bn(x)
# a set of arcs is needed.
if (missing(value))
stop("no arc specified.")
# check logical arguments.
check.logical(check.cycles)
check.logical(check.illegal)
check.logical(debug)
# sanitize the set of arcs.
value = check.arcs(value, nodes = names(x$nodes))
# check whether the the graph contains directed cycles.
if (check.cycles)
if (!is.acyclic(nodes = names(x$nodes), arcs = value, debug = debug,
directed = TRUE))
stop("the specified network contains cycles.")
# check whether any arc is illegal.
if (check.illegal) {
illegal = which.listed(value, x$learning$illegal)
if (any(illegal)) {
illegal = apply(value[illegal, , drop = FALSE], 1,
function(x) { paste(" (", x[1], ", ", x[2], ")", sep = "") })
stop("the following arcs are not valid due to the parametric assumptions of the network:",
illegal, ".")
}#THEN
}#THEN
# update the arcs of the network.
x$arcs = value
# update the network structure.
x$nodes = cache.structure(names(x$nodes), arcs = x$arcs, debug = debug)
return(x)
}#ARCS<-
# return the directed arcs in the graph.
directed.arcs = function(x) {
# check x's class.
check.bn.or.fit(x)
if (is(x, "bn"))
x$arcs[which.directed(x$arcs, names(x$nodes)), , drop = FALSE]
else
fit2arcs(x)
}#DIRECTED.ARCS
# return the undirected arcs in the graph.
undirected.arcs = function(x) {
# check x's class.
check.bn.or.fit(x)
if (is(x, "bn"))
x$arcs[which.undirected(x$arcs, names(x$nodes)), , drop = FALSE]
else
matrix(character(0), nrow = 0, ncol = 2,
dimnames = list(NULL, c("from", "to")))
}#UNDIRECTED.ARCS
# return the arcs pointing to a particular node.
incoming.arcs = function(x, node) {
# check x's class.
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
arcs = directed.arcs(x)
arcs[arcs[, "to"] == node, , drop = FALSE]
}#INCOMING.ARCS
# return the arcs originating from a particular node.
outgoing.arcs = function(x, node) {
# check x's class.
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
arcs = directed.arcs(x)
arcs[arcs[, "from"] == node, , drop = FALSE]
}#OUTGOING.ARCS
# return the arcs incident on a particular node.
incident.arcs = function(x, node) {
# check x's class.
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
arcs = arcs(x)
arcs[(arcs[, "from"] == node) | (arcs[, "to"] == node), , drop = FALSE]
}#INCIDENT.ARCS
# return compelled arcs.
compelled.arcs = function(x) {
# check x's class.
check.bn.or.fit(x)
if (is(x, "bn.fit"))
x = cpdag(bn.net(x))
else
x = cpdag(x)
return(directed.arcs(x))
}#COMPELLED.ARCS
# return reversible arcs.
reversible.arcs = function(x) {
# check x's class.
check.bn.or.fit(x)
if (is(x, "bn.fit"))
cp = cpdag(bn.net(x))
else
cp = cpdag(x)
return(x$arcs[which.listed(x$arcs, undirected.arcs(cp)), ])
}#REVERSIBLE.ARCS
# return the number of arcs in the graph.
narcs = function(x) {
# check x's class.
check.bn.or.fit(x)
narcs.backend(x)
}#NARCS
# set an arc direction manually.
set.arc = function(x, from, to, check.cycles = TRUE, check.illegal = TRUE,
debug = FALSE) {
arc.operations(x = x, from = from, to = to, op = "set",
check.cycles = check.cycles, check.illegal = check.illegal, debug = debug)
}#SET.ARC
# remove an arc from the graph.
drop.arc = function(x, from, to, debug = FALSE) {
arc.operations(x = x, from = from, to = to, op = "drop",
check.cycles = FALSE, check.illegal = FALSE, debug = debug)
}#DROP.ARC
# reverse an arc in the graph.
reverse.arc = function(x, from, to, check.cycles = TRUE, check.illegal = TRUE,
debug = FALSE) {
arc.operations(x = x, from = from, to = to, op = "reverse",
check.cycles = check.cycles, check.illegal = check.illegal, debug = debug)
}#REVERSE.ARC
# set an undirected arc.
set.edge = function(x, from, to, check.cycles = TRUE, check.illegal = TRUE,
debug = FALSE) {
arc.operations(x = x, from = from, to = to, op = "seted",
check.cycles = check.cycles, check.illegal = check.illegal, debug = debug)
}#SET.EDGE
# remove an arc from the graph.
drop.edge = function(x, from, to, debug = FALSE) {
arc.operations(x = x, from = from, to = to, op = "droped",
check.cycles = FALSE, check.illegal = FALSE, debug = debug)
}#DROP.EDGE
```

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