Description Usage Arguments Details Value Author(s) References See Also Examples
Transform a Partial Ancestral Graph (PAG) into a valid
Maximal Ancestral Graph (MAG) that belongs to the Markov equivalence class
represented by the given PAG, with no additional edges into node x
.
1 
amat.pag 
Adjacency matrix of type amat.pag 
x 
(integer) position in adjacency matrix of node in the PAG into which no additional edges are oriented. 
max.chordal 
Positive integer: graph paths larger than

verbose 
Logical; if true, some output is produced during computation. 
This function converts a PAG (adjacency matrix) to a valid MAG (adjacency matrix) that belongs to the Markov equivalence class represented by the given PAG. Note that we assume that there are no selection variables, meaning that the edges in the PAG can be of the following types: >, <>, o>, and oo. In a first step, it uses the Arrowhead Augmentation of Zhang (2006), i.e., any o> edge is oriented into >. Afterwards, it orients each chordal component into a valid DAG without orienting any additional edges into x.
This function is used in the Generalized Backdoor Criterion
backdoor
with type="pag"
, see Maathuis and Colombo
(2015) for details.
The output is an adjacency matrix of type amat.pag representing a valid MAG that belongs to the Markov equivalence class represented by the given PAG.
Diego Colombo, Markus Kalisch and Martin Maechler.
M.H. Maathuis and D. Colombo (2015). A generalized backdoor criterion. Annals of Statistics 43 10601088.
Zhang, J. (2006). Causal Inference and Reasoning in Causally Insufficient Systems. Ph. D. thesis, Carnegie Mellon University.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18  ## create the graph
set.seed(78)
p < 12
g < randomDAG(p, prob = 0.4)
## Compute the true covariance and then correlation matrix of g:
true.corr < cov2cor(trueCov(g))
## define nodes 2 and 6 to be latent variables
L < c(2,6)
## Find PAG
## As dependence "oracle", we use the true correlation matrix in
## gaussCItest() with a large "virtual sample size" and a large alpha:
true.pag < dag2pag(suffStat = list(C= true.corr, n= 10^9),
indepTest= gaussCItest, graph=g, L=L, alpha= 0.9999)
## find a valid MAG such that no additional edges are directed into
(amat.mag < pag2magAM(true.pag@amat, 4)) # > the adj.matrix of the MAG

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