Convert Knowledge to pcalg Knowledge

pcalg only supports undirected (symmetric) background constraints:

• fixed_gaps - forbidding edges (zeros enforced)

• fixed_edges - requiring edges (ones enforced)

Usage

as_pcalg_constraints(kn, labels = kn$vars$var, directed_as_undirected = FALSE)

Arguments

kn

A knowledge object. Must have no tier information.

labels

Character vector of all variable names, in the exact order of your data columns. Every variable referenced by an edge in kn must appear here.

directed_as_undirected

Logical (default FALSE). If FALSE, we require that every edge in kn has its mirror-image present as well, and will error if any are missing. If TRUE, we automatically mirror every directed edge into an undirected constraint.

Value

A list with two elements, each an n × n logical matrix corresponding to pcalg fixed_gaps and fixed_edges arguments.

Details

This function takes a knowledge object (with only forbidden/required edges, no tiers) and returns the two logical matrices in the exact variable order you supply.

Errors

• If the Knowledge object contains tiered knowledge.

• If directed_as_undirected = FALSE and any edge lacks its symmetrical counterpart. This can only hold for forbidden edges.

See also

Other knowledge functions: +.Knowledge(), add_exogenous(), add_tier(), add_to_tier(), add_vars(), as_bnlearn_knowledge(), as_tetrad_knowledge(), convert_tiers_to_forbidden(), deparse_knowledge(), forbid_edge(), get_tiers(), knowledge(), knowledge_to_caugi(), remove_edge(), remove_tiers(), remove_vars(), reorder_tiers(), reposition_tier(), require_edge(), seq_tiers(), unfreeze()

Examples

# pcalg supports undirected constraints; build a tierless knowledge and convert
data(tpc_example)

kn <- knowledge(
  tpc_example,
  child_x1 %!-->% youth_x3,
  youth_x3 %!-->% child_x1
)

pc_constraints <- as_pcalg_constraints(kn, directed_as_undirected = FALSE)
print(pc_constraints)
#> $fixed_gaps
#>           child_x1 child_x2 oldage_x5 oldage_x6 youth_x3 youth_x4
#> child_x1     FALSE    FALSE     FALSE     FALSE     TRUE    FALSE
#> child_x2     FALSE    FALSE     FALSE     FALSE    FALSE    FALSE
#> oldage_x5    FALSE    FALSE     FALSE     FALSE    FALSE    FALSE
#> oldage_x6    FALSE    FALSE     FALSE     FALSE    FALSE    FALSE
#> youth_x3      TRUE    FALSE     FALSE     FALSE    FALSE    FALSE
#> youth_x4     FALSE    FALSE     FALSE     FALSE    FALSE    FALSE
#> 
#> $fixed_edges
#>           child_x1 child_x2 oldage_x5 oldage_x6 youth_x3 youth_x4
#> child_x1     FALSE    FALSE     FALSE     FALSE    FALSE    FALSE
#> child_x2     FALSE    FALSE     FALSE     FALSE    FALSE    FALSE
#> oldage_x5    FALSE    FALSE     FALSE     FALSE    FALSE    FALSE
#> oldage_x6    FALSE    FALSE     FALSE     FALSE    FALSE    FALSE
#> youth_x3     FALSE    FALSE     FALSE     FALSE    FALSE    FALSE
#> youth_x4     FALSE    FALSE     FALSE     FALSE    FALSE    FALSE
#> 

# error paths
# using tiers
kn <- knowledge(
  tpc_example,
  tier(
    child ~ starts_with("child"),
    youth ~ starts_with("youth"),
    oldage ~ starts_with("old")
  ),
  child_x1 %-->% youth_x3
)

try(as_pcalg_constraints(kn), silent = TRUE) # fails due to tiers

# using directed knowledge
kn <- knowledge(
  tpc_example,
  child_x1 %!-->% youth_x3
)

try(as_pcalg_constraints(kn), silent = TRUE) # fails due to directed knowledge