rstringsplitbnlearn

Splitting a graphical network string in R

I have the following string derived from a Bayesian Network learning algorithm (like from bnlearn or deal packages):

[1] "[wst|af:bq:rloss_s:pre3][af|bq][d|wst:af:con:rloss_s][bq|con][con|af][rloss_s|af:con:pre3][pre3|af:con]"

The string defines the connection between variables and the direction of the connection. The first variable of each term in brackets ([...]) represents a node and all variables behind | represent the nodes that are connected in direction to the first node. These variables are sperated by :.

I would like to transform the string into a data.frame that represents the connection between each variable. It should look like this:

> data.frame(string_table)
      from      to
1       af     wst
2       bq     wst
3  rloss_s     wst
4     pre3     wst
5       bq      af
6      wst       d
7       af       d
8      con       d
9  rloss_s       d
10     con      bq
11      af     con
12      af rloss_s
13     con rloss_s
14    pre3 rloss_s
15      af    pre3
16     con    pre3
Solution

  • I would use the graph tools here rather than string manipulation. Here is an example to illustrate

    library(bnlearn)

d = clgaussian.test
m = hc(d)

    So you have the string / model

    bnlearn::modelstring(m)
#[1] "[A][B][C][H][D|A:H][F|B:C][E|B:D][G|A:D:E:F]"

    using bnlearn loop through to get the parents of each node

    stack(sapply(nodes(m), function(x) parents(m, x)))

    or use igraph on the adjacency matrix to get the edge list

    library(igraph)
as_edgelist(graph_from_adjacency_matrix(amat(m)))

    EDIT:

    Seems bnlearn has a function to extract the edges

    arcs(m)