causalDisco (version 0.9.5)

probmat2amat: Convert a matrix of probabilities into an adjacency matrix

Description

Convert a matrix of probabilities into an adjacency matrix

Usage

probmat2amat(
  probmat,
  threshold,
  method = "cutoff",
  keep_vnames = TRUE,
  graph_criterion = "pdag",
  deletesym = FALSE
)

Value

A square matrix of probabilities (all entries in [0,1]).

Arguments

probmat

Square matrix of probabilities.

threshold

Value between 0 and 1. Any probabilities lower than this value will be set to 0 (no arrowhead).

method

Either "cutoff" or "bpco", see details.

keep_vnames

If TRUE, variable names (provided as rownames in the input probmat) will be preserved in the output.

graph_criterion

Which criterion to check if the output graph fulfills for the bpco method. Should be one of "dag", "pdag" or "cpdag" or NULL. Choosing NULL (the default) puts no further restrictions on the output. See isValidGraph for definitions.

deletesym

If TRUE, edges are deleted symmetrically in the bcpo method. This means that instead of removing arrowheads (setting singular elements to 0), the procedure removes full edges (setting both potential arrowheads for the given edge to zero). This only makes a difference if the graph may include undirected edges, which should be encoded as bidirected edges.

Details

Two methods for converting the probability matrix into an adjacency matrix are implemented. First, the cutoff-method (method = "cutoff") simply uses a threshold value and sets all values below that to zero in the outputted adjacency matrix. No checks are performed to ensure that the resulting matrix is a proper dag/pdag/cpdag adjacency matrix. Second, the backwards PC orientation method (method = "bpco") first uses a cutoff, and then sets further elements to zero until the resulting matrix can be converted into a proper adjacency matrix (using the graph criterion specified in the graph_criterion argument) by applying the PC algorithm orientation rules. See Petersen et al. 2022 for further details.

References

Petersen, Anne Helby, et al. "Causal discovery for observational sciences using supervised machine learning." arXiv preprint arXiv:2202.12813 (2022).

Examples

#Make random probability matrix that can be 
#converted into adjancency matrix
pmat <- matrix(runif(25, 0, 1), 5, 5)
diag(pmat) <- 0

#Convert to adjacency matrix using cutoff-method (threshold = 0.5)
probmat2amat(pmat, threshold = 0.5)

#Convert to adjacency matrix using BPCO-method (threshold = 0.5)
probmat2amat(pmat, threshold = 0.5, method = "bpco")