Milo Milo - 2 months ago 14
R Question

How to create weighted adjacency list/matrix from edge list?

My problem is very simple: I need to create an adjacency list/matrix from a list of edges.

I have an edge list stored in a csv document with column1 = node1 and column2 = node2 and I would like to convert this to a weighted adjacency list or a weighted adjacency matrix.

To be more precise, here's how the data looks like -where the numbers are simply node ids:

node1,node2
551,548
510,512
548,553
505,504
510,512
552,543
512,510
512,510
551,548
548,543
543,547
543,548
548,543
548,542


Any tips on how to achieve the conversion from this to a weighted adjacency list/matrix?
This is how I resolved to do it previously, without success (courtesy of Dai Shizuka):

dat=read.csv(file.choose(),header=TRUE) # choose an edgelist in .csv file format
el=as.matrix(dat) # coerces the data into a two-column matrix format that igraph likes
el[,1]=as.character(el[,1])
el[,2]=as.character(el[,2])
g=graph.edgelist(el,directed=FALSE) # turns the edgelist into a 'graph object'


Thank you!

Answer

This response uses base R only. The result is a standard matrix used to represent the adjacency matrix.

 el  <- cbind(a=1:5, b=5:1) #edgelist (a=origin, b=destination)
 mat <- matrix(0, 5, 5)
 mat[el] <- 1
 mat
 #    [,1] [,2] [,3] [,4] [,5]
 #[1,]    0    0    0    0    1
 #[2,]    0    0    0    1    0
 #[3,]    0    0    1    0    0
 #[4,]    0    1    0    0    0
 #[5,]    1    0    0    0    0

Here mat is your adjacency matrix defined from edgelist el, which is a simple cbind of the vectors 1:5 and 5:1.

If your edgelist includes weights, then you need a slightly different solution.

el <- cbind(a=1:5, b=5:1, c=c(3,1,2,1,1)) # edgelist (a=origin, b=destination, c=weight)
mat<-matrix(0, 5, 5)
for(i in 1:NROW(el)) mat[ el[i,1], el[i,2] ] <- el[i,3]  # SEE UPDATE
mat
#     [,1] [,2] [,3] [,4] [,5]
#[1,]    0    0    0    0    3
#[2,]    0    0    0    1    0
#[3,]    0    0    2    0    0
#[4,]    0    1    0    0    0
#[5,]    1    0    0    0    0

UPDATE

Some time later I realized that the for loop (3rd line) in the previous weighted edgelist example is unnecessary. You can replace it with the following vectorized operation:

mat[el[,1:2]] <- el[,3]
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