causalDisco (version 1.0.1)

ges: GES Algorithm for Causal Discovery

Description

Run the GES algorithm for causal discovery using one of several engines.

Usage

ges(engine = c("tetrad", "pcalg"), score, ...)

Value

A function that takes a single argument data (a data frame). When called, this function returns a list containing:

• knowledge A Knowledge object with the background knowledge used in the causal discovery algorithm. See knowledge() for how to construct it.

• caugi A caugi::caugi object (of class PDAG) representing the learned causal graph from the causal discovery algorithm.

Arguments

engine

Character; which engine to use. Must be one of:

"tetrad"

Tetrad Java library.

"pcalg"

pcalg R package.

score

Character; name of the scoring function to use.

...

Additional arguments passed to the chosen engine (e.g. score and algorithm parameters).

Recommendation

While it is possible to call the function returned directly with a data frame, we recommend using disco(). This provides a consistent interface and handles knowledge integration.

Details

For specific details on the supported scores, and parameters for each engine, see:

• TetradSearch for Tetrad (note, Tetrad refers to it as "fges"),

• PcalgSearch for pcalg.

See Also

Other causal discovery algorithms: boss(), boss_fci(), fci(), gfci(), grasp(), grasp_fci(), gs(), iamb-family, pc(), sp_fci(), tfci(), tges(), tpc()

Examples

data(tpc_example)

#### Using pcalg engine ####
# Recommended path using disco()
ges_pcalg <- ges(engine = "pcalg", score = "sem_bic")
disco(tpc_example, ges_pcalg)

# or using ges_pcalg directly
ges_pcalg(tpc_example)

# With all algorithm arguments specified
ges_pcalg <- ges(
  engine = "pcalg",
  score = "sem_bic",
  adaptive = "vstructures",
  phase = "forward",
  iterate = FALSE,
  maxDegree = 3,
  verbose = FALSE
)
disco(tpc_example, ges_pcalg)


#### Using tetrad engine with tier knowledge ####
# Requires Tetrad to be installed
if (verify_tetrad()$installed && verify_tetrad()$java_ok) {
  kn <- knowledge(
    tpc_example,
    tier(
      child ~ tidyselect::starts_with("child"),
      youth ~ tidyselect::starts_with("youth"),
      oldage ~ tidyselect::starts_with("oldage")
    )
  )

  # Recommended path using disco()
  ges_tetrad <- ges(engine = "tetrad", score = "sem_bic")
  disco(tpc_example, ges_tetrad, knowledge = kn)

  # or using ges_tetrad directly
  ges_tetrad <- ges_tetrad |> set_knowledge(kn)
  ges_tetrad(tpc_example)
}

# With all algorithm arguments specified
if (verify_tetrad()$installed && verify_tetrad()$java_ok) {
  ges_tetrad <- ges(
    engine = "tetrad",
    score = "ebic",
    symmetric_first_step = TRUE,
    max_degree = 3,
    parallelized = TRUE,
    faithfulness_assumed = TRUE
  )
  disco(tpc_example, ges_tetrad)
}