IDA_parallel: Estimate Total Causal Effects using the IDA_parallel...

In ParallelPC: Paralellised Versions of Constraint Based Causal Discovery Algorithms

Description

This is the parallelised version of the IDA (stable) algorithm in the pcalg package.

Usage

IDA_parallel(datacsv, cause, effect, pcmethod, alpha, num.cores,
  mem.efficient = FALSE)

Arguments

datacsv	The dataset in csv format.
cause	The number of integer positions of the cause variables in the dataset.
effect	The number of integer positions of the target variables in the dataset.
pcmethod	Character string specifying method; the default, "parallel", will use the parallelised method for learning the skeleton of the graph, see skeleton_parallel.
alpha	significance level (number in (0; 1) for the individual conditional independence tests.
num.cores	The numbers of cores CPU to run the algorithm
mem.efficient	If TRUE, uses less amount of memory at any time point while running the algorithm

Value

A matrix that shows the causal effects (minimum of all possible effects) of the causes (columns) on the effects (rows)

References

Marloes H Maathuis, Markus Kalisch, Peter Buhlmann, et al. Estimating high-dimensional intervention effects from observational data. The Annals of Statistics, 37(6A):3133-3164,2009.

Examples

##########################################
## Using IDA_parallel without mem.efficeient
##########################################
library(bnlearn)
library(pcalg)
library(parallel)
data("gmI")
datacsv <- cov(gmI$x)
IDA_parallel(datacsv,1:2,3:4,"parallel",0.01, 2)

##########################################
## Using IDA_parallel with mem.efficeient
##########################################
library(bnlearn)
library(pcalg)
library(parallel)
data("gmI")
datacsv <- cov(gmI$x)
IDA_parallel(datacsv,1:2,3:4,"parallel",0.01, 2, TRUE)

Example output

Attaching package: 'bnlearn'

The following object is masked from 'package:stats':

    sigma


Attaching package: 'pcalg'

The following objects are masked from 'package:bnlearn':

    dsep, pdag2dag, shd, skeleton

n=7,p=7
Num CI Tests= 23 0 ,Total CI Tests= 23 ,Total Time= 0.133 
           [,1]       [,2]
[1,] -0.5962528  0.6407872
[2,] -0.2720181 -0.1364605
sh: 1: egrep: Permission denied
n=7,p=7
Num CI Tests= 23 0 ,Total CI Tests= 23 ,Total Time= 0.001 
           [,1]       [,2]
[1,] -0.5962528  0.6407872
[2,] -0.2720181 -0.1364605

ParallelPC documentation built on May 2, 2019, 9:14 a.m.