BiDAG (version 2.1.4)

bidag2coda: Converting a single BiDAG chain to mcmc object

Description

This function converts a single object of one of the BiDAG classes, namely 'orderMCMC' or 'partitionMCMC' to an object of class 'mcmc'. This object can be further used for convergence and mixing diagnostics implemented in the package coda

Usage

bidag2coda(
  MCMCtrace,
  edges = FALSE,
  pdag = TRUE,
  p = 0.1,
  burnin = 0.2,
  window = 100,
  cumulative = FALSE
)

Value

Object of class mcmc from the package coda

Arguments

MCMCtrace

object of class orderMCMC or partitionMCMC

edges

logical, when FALSE (default), then only DAG score trace is extracted; when TRUE, a trace of posterior probabilities is extracted for every edge (based on the sampled DAGs defined by parameters 'window' and 'cumulative') resulting in up to n^2 trace vectors, where n is the number of nodes in the network

pdag

logical, when edges=TRUE, defines if the DAGs are converted to CPDAGs prior to computing posterior probabilities; ignored otherwise

p

numeric, between 0 and 1; defines the minimum probability for including posterior traces in the returned objects (for probabilities close to 0 PRSF diagnostics maybe too conservative)

burnin

numeric between 0 and 1, indicates the percentage of the samples which will be discarded as 'burn-in' of the MCMC chain; the rest of the samples will be used to calculate the posterior probabilities; 0.2 by default

window

integer, defines a number of DAG samples for averaging and computing edges' posterior probabilities; ignored when edges=FALSE

cumulative

logical, indicates if posterior probabilities should be calculated based on a cumulative sample of DAGs, where 25% of the first samples are discarded

Author

Polina Suter

Examples

if (FALSE) {
library(coda)
myscore<-scoreparameters("bde",Asia)
ordersample<-sampleBN(myscore,"order")
order_mcmc<-bidag2coda(ordersample)
par(mfrow=c(1,2))
densplot(order_mcmc)
traceplot(order_mcmc)
}