bidag2coda: Converting a single BiDAG chain to mcmc object

In BiDAG: Bayesian Inference for Directed Acyclic Graphs

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
)

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

Value

Object of class mcmc from the package coda

Author(s)

Polina Suter

Examples

## Not run: 
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)

## End(Not run)

BiDAG documentation built on May 31, 2023, 6:46 p.m.