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################################################################
# function:
# boundary takes two parameters:
# graph is the original graph from which the subgraph will be created
# subgraph either the subgraph or the nodes of the subgraph
# boundary returns a list of length equal to the number of nodes in the
# subgraph. Each element is a list of the nodes in graph
#
# created by: Elizabeth Whalen
# last updated: Feb 15, 2003, RG
################################################################
boundary<-function(subgraph, graph)
{
if ( !is(graph, "graph") )
stop("'graph' must be an object of type graph")
if( is(subgraph, "graph") )
snodes <- nodes(subgraph)
else if( is.character(subgraph) )
snodes <- subgraph
else
stop("'subgraph' type incorrect")
if( any( !(snodes %in% nodes(graph)) ) )
stop("some nodes not in graph")
subE <- inEdges(graph)[snodes]
lapply(subE, function(x) x[!(x %in% snodes)] )
}
##check to see if any edges are duplicated, as we often don't have
##good ways to deal with that
duplicatedEdges <- function(graph) {
if( !is(graph, "graphNEL") )
stop("only graphNEL supported")
for(e in graph@edgeL)
if( any(duplicated(e$edges)) )
return(TRUE)
return(FALSE)
}
ugraphOld <- function()
{
.Defunct("ugraph")
}
setMethod("ugraph", "graph",
function(graph) {
if (!isDirected(graph))
return(graph)
eMat <- edgeMatrix(graph)
## add recip edges
eMat <- cbind(eMat, eMat[c(2, 1), ])
## put into graphNEL edgeL format
eL <- lapply(split(as.vector(eMat[2, ]), as.vector(eMat[1, ])),
function(x) list(edges=unique(x)))
theNodes <- nodes(graph)
## some nodes may be missing
names(eL) <- theNodes[as.integer(names(eL))]
## add empty edge list for nodes with no edges
noEdgeNodes <- theNodes[!(theNodes %in% names(eL))]
noEdges <- lapply(noEdgeNodes,
function(x) list(edges=numeric(0)))
names(noEdges) <- noEdgeNodes
## FIXME: should we skip standard initialize for speed?
## need to copy over at least the nodeData...
graphNEL(nodes=theNodes, edgeL=c(eL, noEdges),
edgemode="undirected")
})
setMethod("edgeMatrix", c("graphNEL", "ANY"),
function(object, duplicates=FALSE) {
## Return a 2 row numeric matrix (from, to, weight)
ed <- object@edgeL
##reorder to the same order as nodes
ed <- ed[nodes(object)]
nN <- length(ed)
eds<-lapply(ed, function(x) x$edges)
elem <- listLen(eds)
from <- rep(seq_len(nN), elem)
to <- unlist(eds, use.names=FALSE)
ans <- rbind(from, to)
##we duplicate edges in undirected graphNEL
##so here we remove them
if( edgemode(object) == "undirected" && !duplicates) {
swap <- from>to
ans[1,swap]<-to[swap]
ans[2,swap]<-from[swap]
t1 <- paste(ans[1,], ans[2,], sep="+")
ans <- ans[ ,!duplicated(t1), drop=FALSE]
}
ans
})
setMethod("edgeMatrix", c("clusterGraph", "ANY"),
function(object, duplicates) {
cls<-object@clusters
nd <- nodes(object)
ans <- numeric(0)
for(cl in cls) {
idx <- match(cl, nd)
nn <- length(idx)
v1 <- rep(idx[-nn], (nn-1):1)
v2 <- numeric(0)
for( i in 2:nn)
v2 <- c(v2, i:nn)
v2 <- idx[v2]
ta <- rbind(v1, v2)
if( is.matrix(ans) )
ans <- cbind(ans, rbind(v1, v2))
else
ans <- rbind(v1, v2)
}
dimnames(ans) <- list(c("from", "to"), NULL)
ans
})
setMethod("edgeMatrix", c("distGraph", "ANY"),
function(object, duplicates) {
## Return a 2 row numeric matrix (from, to, weight)
ed <- edges(object)
##reorder to the same order as nodes
NODES <- nodes(object)
ed <- ed[NODES]
nN <- length(ed)
elem <- listLen(ed)
from <- rep(seq_len(nN), elem)
to <- match(unlist(ed), NODES)
ans <- rbind(from, to)
##we duplicate edges in undirected graphNEL
##so here we remove them
##FIXME: see graphNEL for a speedup of this part
if( edgemode(object) == "undirected" && !duplicates) {
t1 <- apply(ans, 2, function(x) {paste(sort(x),
collapse="+")})
ans <- ans[ ,!duplicated(t1), drop=FALSE]
}
ans
})
setMethod("edgeMatrix", "graphAM",
function(object, duplicates=FALSE) {
to <- apply(object@adjMat, 1, function(x) which(x != 0))
from <- rep(seq_len(numNodes(object)), listLen(to))
to <- unlist(to, use.names=FALSE)
ans <- rbind(from=from, to=to)
## we duplicate edges in undirected graphs
## so here we remove them
if (!isDirected(object) && !duplicates) {
swap <- from > to
ans[1, swap] <- to[swap]
ans[2, swap] <- from[swap]
t1 <- paste(ans[1, ], ans[2, ], sep="+")
ans <- ans[ , !duplicated(t1), drop=FALSE]
}
ans
})
##it seems to me that we might want the edge weights for
##a given edgeMatrix and that that would be much better done
##in the edgeMatrix function
##we are presuming that eM has integer offsets in it
##eWV <- function(g, eM, sep=ifelse(edgemode(g)=="directed", "->",
## "--"))
##{
## unE <- unique(eM[1,])
## edL <- g@edgeL
## eE <- lapply(edL, function(x) x$edges)
## eW <- lapply(edL, function(x) {
## ans = x$weights
## ed = length(x$edges)
## if( is.null(ans) && ed > 0 )
## ans = rep(1, ed)
## ans})
##
## nr <- listLen(eE)
## ##now we can subset -
## eMn <- paste(rep((1:length(nr))[unE],nr[unE]), unlist(eE[unE]), sep=sep)
## eWv <- unlist(eW[unE])
## dE <- paste(eM[1,], eM[2,], sep=sep)
## wh<-match(dE, eMn)
## if(any(is.na(wh)) )
## stop("edges in supplied edgematrix not found")
## ans <-eWv[wh]
## names(ans) <- eMn[wh]
## ans
##}
#eWV <- function(g, eM, sep=ifelse(edgemode(g)=="directed", "->",
# "--"))
#{
# edL <- g@edgeL
# ##fix up the edgeweights so we really find them
# eW <- lapply(edL, function(x) {
# ans = x$weights
# ed = length(x$edges)
# if( is.null(ans) && ed > 0 )
# ans = rep(1, ed)
# if( length(ans) > 0 )
# names(ans) = x$edges
# ans})
#
# a1 <- apply(eM, 2,
# function(x) eW[[x[1]]][as.character(x[2])])
# names(a1) <- paste(eM[1,], eM[2,], sep=sep)
# return(a1)
#}
eWV <- function (g, eM, sep = ifelse(edgemode(g) == "directed", "->",
"--"), useNNames = FALSE)
{
# returns vector of weights. default has names equal to node
# indices, but useNNames can be set to put node names as names
# of corresponding weights
#
n <- nodes(g)
from <- n[eM["from", ]]
to <- n[eM["to", ]]
eW <- tryCatch(edgeData(g, from=from, to=to, attr="weight"),
error=function(e) {
edgeDataDefaults(g, "weight") <- 1L
edgeData(g, from=from, to=to, attr="weight")
})
eW <- unlist(eW)
if (!useNNames)
nms <- paste(eM["from", ], eM["to", ], sep=sep)
else
nms <- paste(from, to, sep=sep)
names(eW) <- nms
eW
}
pathWeights <- function (g, p, eM = NULL)
{
#
# a path is a vector of names of adjacent nodes
# we form the vector of steps through the path
# (pairs of adjacent nodes) and attach the weights
# for each step. no checking is done to verify
# that the path p exists in g
#
if (length(p) < 2)
stop("'p' has length < 2")
if (is.null(eM))
eM <- edgeMatrix(g)
wv <- eWV(g, eM, useNNames = TRUE)
sep <- ifelse(edgemode(g) == "undirected", "--", "->")
pcomps <- cbind(p[-length(p)], p[-1])
if (edgemode(g) == "undirected") pcomps <- rbind(pcomps, pcomps[,c(2,1)]) # don't know node order in wv labels
inds <- apply(pcomps, 1, function(x) paste(x[1], x[2], sep = sep))
tmp <- wv[inds]
tmp[!is.na(tmp)]
}
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