PC (pcalg)

Module name

pcalg_pc

Package

pcalg

Version

2.7-8

Language

R

Docs

here

Paper

Spirtes and Glymour[1]

Graph type

CPDAG, CG

MCMC

No

Edge constraints

Yes

Data type

C, D

Data missingness

Intervention type

Docker

bpimages/pcalg:2.7-8

PC

The Peter and Clark (PC) algorithm Spirtes and Glymour[1], is a constraint based method consisting of two main steps. The first step is called the adjacency search and amounts to finding the undirected skeleton of the DAG. The second step amounts to estimating a CPDAG.

Some fields described

  • edgeConstraints Name of the JSON file containing background knowledge

Example JSON

[
  {
    "id": "pc-gaussCItest",
    "alpha": [
      0.001,
      0.01,
      0.05,
      0.1
    ],
    "NAdelete": true,
    "mmax": "Inf",
    "u2pd": "relaxed",
    "skelmethod": "stable",
    "conservative": false,
    "majrule": false,
    "solveconfl": false,
    "numCores": 1,
    "verbose": false,
    "indepTest": "gaussCItest",
    "timeout": null,
    "edgeConstraints": "edgeConstraints.json"
  },
  {
    "id": "pc-binCItest",
    "alpha": [
      0.01,
      0.05,
      0.1
    ],
    "NAdelete": true,
    "mmax": "Inf",
    "u2pd": "relaxed",
    "skelmethod": "stable",
    "conservative": false,
    "majrule": false,
    "solveconfl": false,
    "numCores": 1,
    "verbose": false,
    "indepTest": "binCItest",
    "timeout": null,
    "edgeConstraints": "edgeConstraints.json"
  }
]