Package index

Overview

Package overview

causalDisco causalDisco-package

causalDisco: Causal Discovery in R

Causal Discovery Interface

High-level interface for running causal discovery.

disco()

Perform Causal Discovery

knowledge()

Define Background Knowledge

Causal Discovery Algorithms

Core search algorithms implemented or wrapped by causalDisco.

boss()

BOSS Algorithm for Causal Discovery

boss_fci()

BOSS-FCI Algorithm for Causal Discovery

fci()

FCI Algorithm for Causal Discovery

ges()

GES Algorithm for Causal Discovery

gfci()

GFCI Algorithm for Causal Discovery

grasp()

GRaSP Algorithm for Causal Discovery

grasp_fci()

GRaSP-FCI Algorithm for Causal Discovery

gs()

GS Algorithm for Causal Discovery

iamb() iamb_fdr() fast_iamb() inter_iamb()

IAMB Family of Causal Discovery Algorithms

pc()

PC Algorithm for Causal Discovery

sp_fci()

SP-FCI Algorithm for Causal Discovery

tfci()

TFCI Algorithm for Causal Discovery

tges()

TGES Algorithm for Causal Discovery

tpc()

TPC Algorithm for Causal Discovery

R6 Classes

BnlearnSearch

R6 Interface to bnlearn Search Algorithms

CausalDiscoSearch

R6 Interface to causalDisco Search Algorithms

PcalgSearch

R6 Interface to pcalg Search Algorithms

TetradSearch

R6 Interface to Tetrad Search Algorithms

Setup for Tetrad Engine

Functions for installing and verifying the Tetrad Java backend.

install_tetrad()

Install Tetrad GUI

verify_tetrad()

Check Tetrad Installation

causalDisco Algorithm Run Functions

Low-level functions that execute causalDisco search algorithms and detail their parameters.

tfci_run()

Run the TFCI Algorithm for Causal Discovery

tges_run()

Run the TGES Algorithm for Causal Discovery

tpc_run()

Run the TPC Algorithm for Causal Discovery

Tests for TPC

Test functions implemented for use in the TPC algorithm.

cor_test()

Test for Vanishing Partial Correlations

reg_test()

Regression-based Information Loss Test

Simulation

generate_dag_data()

Generate Synthetic Data from a Linear Gaussian DAG

sim_dag()

Simulate a Random DAG

Example Datasets

Small simulated datasets to illustrate causalDisco workflows.

cat_data

Simulated Categorical Data

cat_data_mcar

Simulated Categorical Data with MCAR

cat_ord_data

Simulated Ordered Categorical Data

mix_data

Simulated Mixed Data

num_data

Simulated Numerical Data

num_data_latent

Simulated Numerical Data with Latent Variable

tpc_example

Simulated Life-Course Data

Printing, Summarizing, and Plotting Objects

print(<Disco>)

Print a Disco Object

print(<Knowledge>)

Print a Knowledge Object

summary(<Disco>)

Summarize a Disco Object

summary(<Knowledge>)

Summarize a Knowledge Object

plot(<Disco>)

Plot a Disco Object

plot(<Knowledge>)

Plot a Knowledge Object

plot

Plot Method for causalDisco Objects

make_tikz()

Generate TikZ Code from a Causal Graph

Graph Metrics

confusion()

Confusion Matrix

evaluate()

Evaluate Causal Graph Estimates

f1_score()

F1 score

false_omission_rate()

False Omission Rate

fdr()

False Discovery Rate

g1_score()

G1 score

npv()

Negative Predictive Value

precision()

Precision

recall()

Recall

specificity()

Specificity

reexports shd hd aid

Objects exported from other packages

Knowledge helpers

add_exogenous() add_exo()

Add Exogenous Variables to Knowledge

add_tier()

Add a Tier to Knowledge

add_to_tier()

Add Variables to a Tier in Knowledge

add_vars()

Add Variables to Knowledge

remove_edge()

Remove an Edge from Knowledge

remove_tiers()

Remove Tiers from Knowledge

remove_vars()

Remove Variables from Knowledge

require_edge()

Add Required Edges to Knowledge

forbid_edge()

Add Forbidden Edges to Knowledge

get_tiers()

Get Tiers from Knowledge

reorder_tiers()

Reorder Tiers in Knowledge

seq_tiers()

Generate a Bundle of Tier–Variable Formulas

reposition_tier()

Move a Tier Relative to Another in Knowledge

convert_tiers_to_forbidden()

Convert Tiered Knowledge to Forbidden Knowledge

set_knowledge()

Set Background Knowledge to Disco Method

as_tetrad_knowledge()

Convert Knowledge to Tetrad Knowledge

as_bnlearn_knowledge()

Convert Knowledge to bnlearn Knowledge

as_pcalg_constraints()

Convert Knowledge to pcalg Knowledge

knowledge_to_caugi()

Convert Knowledge to Caugi

deparse_knowledge()

Deparse a Knowledge Object into Knowledge DSL Code

unfreeze()

Unfreeze a Knowledge Object.

`+`(<Knowledge>)

Merge Knowledge Objects

Extend causalDisco

Functions for extending causalDisco with new algorithms from the available engines.

distribute_engine_args()

Distribute and Validate Engine Arguments

new_disco_method()

Add a New causalDisco Method

register_tetrad_algorithm()

Register a New Tetrad Algorithm

reset_tetrad_alg_registry()

Reset the Tetrad Algorithm Registry