R: nel2igraph and PN.amalgamation - igraph not correctly produced - r

Question

I encounter a problem with the package shp2graph. I want to use the function PN.amalgamation which works fine (see below). Afterwards, I would like to create an igraph object. Here the code fails to do that.
I can create igraph objects just fine with every non-amalgamated shp2graph object.
Here my sample code, which largely is a copy paste from the description of the package shp2graph:
library(igraph)
library(shp2graph)
data(ORN)
rtNEL<-readshpnw(ORN.nt, ELComputed=TRUE)
res.sl<-SL.extraction(rtNEL[[2]],rtNEL[[3]])
res.me<-ME.simplification(res.sl[[1]],res.sl[[2]],DegreeL=res.sl[[4]])
res.pn<-PN.amalgamation(res.me[[1]],res.me[[2]],DegreeL=res.me[[4]])
ptcoords<-Nodes.coordinates(res.pn[[1]])
plot(ORN.nt)
points(ptcoords, col="green")
plot(ORN.nt)
points(Nodes.coordinates(rtNEL[[2]]), col="red")
# igraph created from amalgamation is wrong
test <- nel2igraph(nodelist= res.pn[[1]], edgelist=res.pn[[2]], Directed = TRUE)
plot(test,vertex.size=1,edge.width=1,edge.arrow.size=0,vertex.label=NA)
# res.me is one step before amalgamation
test <- nel2igraph(nodelist= res.me[[1]], edgelist=res.me[[2]], Directed = TRUE)
plot(test,vertex.size=1,edge.width=1,edge.arrow.size=0,vertex.label=NA)
Any help is appreciated.

Answer 1

I have found that the bug lies somehow in the interaction with the igraph package. The issue is that the labels of the nodes create by PN.amalgamation are not continuous anymore; some are missing, since we deleted them. However, igraph somehow still tries to create them and gives then the following warning:
For anyone having the same trouble here a work-around, which re-indeces the labels.
Create your own nel2igraph function:
nel2igraph_corr <- function (nodelist, edgelist, weight = NULL, eadf = NULL, Directed = FALSE)
{
nodes <- nodelist[, 1]
Ne <- length(edgelist[, 1])
Nn <- length(nodes)
for (i in 1:Nn) {
kk <- nodelist[i,][[1]]
edgelist[which(edgelist[,c(2)]==kk),2] <- i
edgelist[which(edgelist[,c(3)]==kk),3] <- i
nodelist[i,][[1]] <- i
}
if (!is.null(weight)) {
if (length(weight) != Ne && is.numeric(weight))
stop("Please give right edge weight, which must be numeric and the same length as edges elment")
}
if (!is.null(eadf)) {
if (length(eadf[, 1]) != Ne)
stop("The eadf must be numeric and the same length as edges elment")
}
gr <- graph.edgelist(unique(edgelist[, c(2, 3)]), directed = T)
gr <- set.vertex.attribute(gr, "x", V(gr), Nodes.coordinates(nodelist)[,1])
gr <- set.vertex.attribute(gr, "y", V(gr), Nodes.coordinates(nodelist)[,
2])
gr.es <- E(gr)
if (!is.null(weight))
gr <- set.edge.attribute(gr, "weight", gr.es, weight)
if (!is.null(eadf)) {
eanms <- colnames(eadf)
n <- length(eanms)
for (i in 1:n) gr <- set.edge.attribute(gr, eanms[i],
gr.es, eadf[, i])
}
gr
}