Graph from Sparse Adjacency Matrix

By Andrew Collier

I spent a decent chunk of my morning trying to figure out how to construct a sparse adjacency matrix for use with graph.adjacency(). I’d have thought that this would be rather straight forward, but I tripped over a few subtle issues with the Matrix package. My biggest problem (which in retrospect seems rather trivial) was that elements in my adjacency matrix were occupied by the pipe symbol.

> adjacency[1:10,1:10]
10 x 10 sparse Matrix of class 'ngCMatrix'
                         
 [1,] . . . . . | . . . .
 [2,] . . . . . . . | . .
 [3,] . . . . . . . . . .
 [4,] . . . . . . . . . .
 [5,] . . . . | . . . . .
 [6,] . . . . . . . . . .
 [7,] . . . . . . . . . .
 [8,] . . . . . . . . . .
 [9,] . . . . . . . . . .
[10,] . | . . . . . . . .

Of course, the error message I was encountering didn’t point me to this fact. No, that would have been far too simple! The solution is highlighted in the sample code below: you need to specify the symbol used for the occupied sites in the sparse matrix.

> library(Matrix)

>

> set.seed(1)

>

> edges = data.frame(i = 1:20, j = sample(1:20, 20, replace = TRUE))

>

> adjacency = sparseMatrix(i = as.integer(edges$i),

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