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R/frontend-nodes.R
In bnlearn: Bayesian Network Structure Learning, Parameter Learning and Inference
Defines functions
rename.nodes
remove.node
add.node
out.degree
in.degree
isolated.nodes
descendants
ancestors
spouses
children
parents
nbr
mb
Documented in
add.node
ancestors
children
descendants
in.degree
isolated.nodes
mb
nbr
out.degree
parents
remove.node
rename.nodes
spouses
# return the markov blanket of a node.
mb = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
if (is(x, "bn"))
x$nodes[[node]]$mb
else
mb.fitted(x, node)
}#MB
# return the neighbourhood of a node.
nbr = function(x, node, max.dist = 1) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# a maximum distance between 1 (at least) and the number of nodes (at most).
if (!is.positive.integer(max.dist))
stop("the maximum distance must be a positive integer.")
nnodes = length(.nodes(x))
if (max.dist > nnodes) {
warning("the maximum distance has been reduced to the number of nodes.")
max.dist = nnodes
}#THEN
if (is(x, "bn"))
get = function(node) x$nodes[[node]]$nbr
else
get = function(node) c(x[[node]]$parents, x[[node]]$children)
node.set = get(node)
# expand the neighbourhood if needed.
if (max.dist >= 2) {
new.nodes = node.set
for (dist in seq(2, max.dist)) {
# expand the neighbourhood...
new.nodes = sapply(new.nodes, get, USE.NAMES = FALSE)
# ... remove already-visited nodes...
new.nodes = setdiff(unlist(new.nodes), c(node.set, node))
# ... and update the return value.
node.set = unique(c(node.set, new.nodes))
# we have already included all the nodes, nothing more to do.
if (length(node.set) == nnodes)
break
}#FOR
}#THEN
return(node.set)
}#NBR
# get the parents of a node.
parents = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
if (is(x, "bn"))
x$nodes[[node]]$parents
else
x[[node]]$parents
}#PARENTS
# add one or more parents to a node.
"parents<-" = function(x, node, debug = FALSE, value) {
check.bn(x)
check.logical(debug)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# at least one parent node is needed.
if (missing(value))
stop("no parent specified.")
# node must be a valid node label.
if (!any(value %in% names(x$nodes)))
stop("node not present in the graph.")
# remove duplicate labels from value.
value = unique(value)
# drop the parents which are not listed for inclusion.
to.be.dropped = x$nodes[[node]]$parents[x$nodes[[node]]$parents %!in% value]
# add only the nodes that were not already there.
to.be.added = value[value %!in% x$nodes[[node]]$parents]
if (debug) {
cat("* resetting the parents of node", node, ".\n")
cat(" > old parents: '", x$nodes[[node]]$parents, "'\n")
cat(" > new parents: '", value, "'\n")
cat(" > to be really dropped: '", to.be.dropped, "'\n")
cat(" > to be really added: '", to.be.added, "'\n")
}#THEN
# dropping!
for (p in to.be.dropped) {
x = arc.operations(x = x, from = p, to = node, op = "drop",
check.cycles = FALSE, check.illegal = FALSE, update = FALSE,
debug = debug)
}#FOR
# adding!
for (p in to.be.added) {
x = arc.operations(x = x, from = p, to = node, op = "set",
check.cycles = TRUE, check.illegal = TRUE, update = FALSE,
debug = debug)
}#FOR
# update the network structure.
x$nodes = cache.structure(names(x$nodes), arcs = x$arcs, debug = debug)
return(x)
}#PARENTS<-
# get the children of a node.
children = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
if (is(x, "bn"))
x$nodes[[node]]$children
else
x[[node]]$children
}#CHILDREN
# add one or more children to a node.
"children<-" = function(x, node, debug = FALSE, value) {
check.bn(x)
check.logical(debug)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# a node is needed.
if (missing(value))
stop("no children specified.")
# node must be a valid node label.
if (!any(value %in% names(x$nodes)))
stop("node not present in the graph.")
# remove duplicate labels from value.
value = unique(value)
# drop the parents which are not listed for inclusion.
to.be.dropped = x$nodes[[node]]$children[x$nodes[[node]]$children %!in% value]
# add only the nodes that were not already there.
to.be.added = value[value %!in% x$nodes[[node]]$children]
if (debug) {
cat("* resetting the children of node", node, ".\n")
cat(" > old children: '", x$nodes[[node]]$children, "'\n")
cat(" > new children: '", value, "'\n")
cat(" > to be really dropped: '", to.be.dropped, "'\n")
cat(" > to be really added: '", to.be.added, "'\n")
}#THEN
# dropping!
for (child in to.be.dropped) {
x = arc.operations(x = x, from = node, to = child, op = "drop",
check.cycles = FALSE, check.illegal = FALSE, update = FALSE,
debug = debug)
}#FOR
# adding!
for (child in to.be.added) {
x = arc.operations(x = x, from = node, to = child, op = "set",
check.cycles = TRUE, check.illegal = TRUE, update = FALSE,
debug = debug)
}#FOR
# update the network structure.
x$nodes = cache.structure(names(x$nodes), arcs = x$arcs, debug = debug)
return(x)
}#CHILDREN<-
# get the spouses of a node.
spouses = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
chld = children(x, node)
sp = unique(unlist(lapply(chld, parents, x = x)))
return(setdiff(as.character(sp), node))
}#SPOUSES
# get the ancestors of a node.
ancestors = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# the first element is the node itself, which is not its own ancestor.
return(topological.ordering(x, start = node, reverse = TRUE)[-1])
}#ANCESTORS
# get the descendants of a node.
descendants = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# the first element is the node itself, which is not its own ancestor.
return(topological.ordering(x, start = node)[-1])
}#DESCENDANTS
# get the isolated nodes in the network.
isolated.nodes = function(x) {
check.bn.or.fit(x)
# isolated nodes have degree equal to zero.
isolated = (sapply(nodes(x), .degree, x = x) == 0)
return(names(which(isolated)))
}#ISOLATED.NODES
# get the in-degree of a node.
in.degree = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
if (is(x, "bn"))
length(x$nodes[[node]]$parents)
else
length(x[[node]]$parents)
}#IN.DEGREE
# get the out-degree of a node.
out.degree = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
if (is(x, "bn"))
length(x$nodes[[node]]$children)
else
length(x[[node]]$children)
}#OUT.DEGREE
# add a node to a network structure.
add.node = function(x, node) {
check.bn(x)
# a valid node (that is not already in the graph) is needed.
if (!is.string(node))
stop("'node' should be a single character string.")
if (node %in% names(x$nodes))
stop("node ", node, " is already present in the graph.")
# add the node, without adding arcs.
x$nodes[[node]] = list(mb = character(0), nbr = character(0),
parents = character(0), children = character(0))
return(x)
}#ADD.NODE
# remove a node from a network structure.
remove.node = function(x, node) {
check.bn(x)
# the resulting graphs should have at least one node.
if (length(x$nodes) == 1)
stop("trying to remove the only node in the graph.")
# a valid node (that is already in the graph) is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# removing a single node is a special case of creating a subgraph.
subgraph.backend(x = x, nodes = setdiff(names(x$nodes), node),
preserve.learning = TRUE)
}#REMOVE.NODE
# rename the nodes of a network structure.
rename.nodes = function(x, names) {
.relabel(x, value = names)
}#RENAME.NODES
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bnlearn documentation built on Aug. 21, 2025, 5:42 p.m.
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Defines functions rename.nodes remove.node add.node out.degree in.degree isolated.nodes descendants ancestors spouses children parents nbr mb
Documented in add.node ancestors children descendants in.degree isolated.nodes mb nbr out.degree parents remove.node rename.nodes spouses
# return the markov blanket of a node.
mb = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
if (is(x, "bn"))
x$nodes[[node]]$mb
else
mb.fitted(x, node)
}#MB
# return the neighbourhood of a node.
nbr = function(x, node, max.dist = 1) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# a maximum distance between 1 (at least) and the number of nodes (at most).
if (!is.positive.integer(max.dist))
stop("the maximum distance must be a positive integer.")
nnodes = length(.nodes(x))
if (max.dist > nnodes) {
warning("the maximum distance has been reduced to the number of nodes.")
max.dist = nnodes
}#THEN
if (is(x, "bn"))
get = function(node) x$nodes[[node]]$nbr
else
get = function(node) c(x[[node]]$parents, x[[node]]$children)
node.set = get(node)
# expand the neighbourhood if needed.
if (max.dist >= 2) {
new.nodes = node.set
for (dist in seq(2, max.dist)) {
# expand the neighbourhood...
new.nodes = sapply(new.nodes, get, USE.NAMES = FALSE)
# ... remove already-visited nodes...
new.nodes = setdiff(unlist(new.nodes), c(node.set, node))
# ... and update the return value.
node.set = unique(c(node.set, new.nodes))
# we have already included all the nodes, nothing more to do.
if (length(node.set) == nnodes)
break
}#FOR
}#THEN
return(node.set)
}#NBR
# get the parents of a node.
parents = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
if (is(x, "bn"))
x$nodes[[node]]$parents
else
x[[node]]$parents
}#PARENTS
# add one or more parents to a node.
"parents<-" = function(x, node, debug = FALSE, value) {
check.bn(x)
check.logical(debug)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# at least one parent node is needed.
if (missing(value))
stop("no parent specified.")
# node must be a valid node label.
if (!any(value %in% names(x$nodes)))
stop("node not present in the graph.")
# remove duplicate labels from value.
value = unique(value)
# drop the parents which are not listed for inclusion.
to.be.dropped = x$nodes[[node]]$parents[x$nodes[[node]]$parents %!in% value]
# add only the nodes that were not already there.
to.be.added = value[value %!in% x$nodes[[node]]$parents]
if (debug) {
cat("* resetting the parents of node", node, ".\n")
cat(" > old parents: '", x$nodes[[node]]$parents, "'\n")
cat(" > new parents: '", value, "'\n")
cat(" > to be really dropped: '", to.be.dropped, "'\n")
cat(" > to be really added: '", to.be.added, "'\n")
}#THEN
# dropping!
for (p in to.be.dropped) {
x = arc.operations(x = x, from = p, to = node, op = "drop",
check.cycles = FALSE, check.illegal = FALSE, update = FALSE,
debug = debug)
}#FOR
# adding!
for (p in to.be.added) {
x = arc.operations(x = x, from = p, to = node, op = "set",
check.cycles = TRUE, check.illegal = TRUE, update = FALSE,
debug = debug)
}#FOR
# update the network structure.
x$nodes = cache.structure(names(x$nodes), arcs = x$arcs, debug = debug)
return(x)
}#PARENTS<-
# get the children of a node.
children = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
if (is(x, "bn"))
x$nodes[[node]]$children
else
x[[node]]$children
}#CHILDREN
# add one or more children to a node.
"children<-" = function(x, node, debug = FALSE, value) {
check.bn(x)
check.logical(debug)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# a node is needed.
if (missing(value))
stop("no children specified.")
# node must be a valid node label.
if (!any(value %in% names(x$nodes)))
stop("node not present in the graph.")
# remove duplicate labels from value.
value = unique(value)
# drop the parents which are not listed for inclusion.
to.be.dropped = x$nodes[[node]]$children[x$nodes[[node]]$children %!in% value]
# add only the nodes that were not already there.
to.be.added = value[value %!in% x$nodes[[node]]$children]
if (debug) {
cat("* resetting the children of node", node, ".\n")
cat(" > old children: '", x$nodes[[node]]$children, "'\n")
cat(" > new children: '", value, "'\n")
cat(" > to be really dropped: '", to.be.dropped, "'\n")
cat(" > to be really added: '", to.be.added, "'\n")
}#THEN
# dropping!
for (child in to.be.dropped) {
x = arc.operations(x = x, from = node, to = child, op = "drop",
check.cycles = FALSE, check.illegal = FALSE, update = FALSE,
debug = debug)
}#FOR
# adding!
for (child in to.be.added) {
x = arc.operations(x = x, from = node, to = child, op = "set",
check.cycles = TRUE, check.illegal = TRUE, update = FALSE,
debug = debug)
}#FOR
# update the network structure.
x$nodes = cache.structure(names(x$nodes), arcs = x$arcs, debug = debug)
return(x)
}#CHILDREN<-
# get the spouses of a node.
spouses = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
chld = children(x, node)
sp = unique(unlist(lapply(chld, parents, x = x)))
return(setdiff(as.character(sp), node))
}#SPOUSES
# get the ancestors of a node.
ancestors = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# the first element is the node itself, which is not its own ancestor.
return(topological.ordering(x, start = node, reverse = TRUE)[-1])
}#ANCESTORS
# get the descendants of a node.
descendants = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# the first element is the node itself, which is not its own ancestor.
return(topological.ordering(x, start = node)[-1])
}#DESCENDANTS
# get the isolated nodes in the network.
isolated.nodes = function(x) {
check.bn.or.fit(x)
# isolated nodes have degree equal to zero.
isolated = (sapply(nodes(x), .degree, x = x) == 0)
return(names(which(isolated)))
}#ISOLATED.NODES
# get the in-degree of a node.
in.degree = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
if (is(x, "bn"))
length(x$nodes[[node]]$parents)
else
length(x[[node]]$parents)
}#IN.DEGREE
# get the out-degree of a node.
out.degree = function(x, node) {
check.bn.or.fit(x)
# a valid node is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
if (is(x, "bn"))
length(x$nodes[[node]]$children)
else
length(x[[node]]$children)
}#OUT.DEGREE
# add a node to a network structure.
add.node = function(x, node) {
check.bn(x)
# a valid node (that is not already in the graph) is needed.
if (!is.string(node))
stop("'node' should be a single character string.")
if (node %in% names(x$nodes))
stop("node ", node, " is already present in the graph.")
# add the node, without adding arcs.
x$nodes[[node]] = list(mb = character(0), nbr = character(0),
parents = character(0), children = character(0))
return(x)
}#ADD.NODE
# remove a node from a network structure.
remove.node = function(x, node) {
check.bn(x)
# the resulting graphs should have at least one node.
if (length(x$nodes) == 1)
stop("trying to remove the only node in the graph.")
# a valid node (that is already in the graph) is needed.
check.nodes(nodes = node, graph = x, max.nodes = 1)
# removing a single node is a special case of creating a subgraph.
subgraph.backend(x = x, nodes = setdiff(names(x$nodes), node),
preserve.learning = TRUE)
}#REMOVE.NODE
# rename the nodes of a network structure.
rename.nodes = function(x, names) {
.relabel(x, value = names)
}#RENAME.NODES
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