# Bayesian Inference for Directed Acyclic Graphs

## Documentation for package ‘BiDAG’ version 2.1.3

- DESCRIPTION file.

## Help Pages

Asia | Asia dataset
Asiamat | Asiamat
bidag2coda | Converting a single BiDAG chain to mcmc object
bidag2codalist | Converting multiple BiDAG chains to mcmc.list
Boston | Boston housing data
compact2full | Deriving an adjecency matrix of a full DBN
compareDAGs | Comparing two graphs
compareDBNs | Comparing two DBNs
connectedSubGraph | Deriving connected subgraph
DAGscore | Calculating the BGe/BDe score of a single DAG
DBNdata | Simulated data set from a 2-step dynamic Bayesian network
DBNmat | An adjacency matrix of a dynamic Bayesian network
DBNscore | Calculating the BGe/BDe score of a single DBN
DBNunrolled | An unrolled adjacency matrix of a dynamic Bayesian network
edgep | Estimating posterior probabilities of single edges
full2compact | Deriving a compact adjacency matrix of a DBN
getDAG | Extracting adjacency matrix (DAG) from MCMC object
getMCMCscore | Extracting score from MCMC object
getRuntime | Extracting runtime
getSpace | Extracting scorespace from MCMC object
getSubGraph | Deriving subgraph
getTrace | Extracting trace from MCMC object
graph2m | Deriving an adjacency matrix of a graph
gsim | A simulated data set from a Gaussian continuous Bayesian network
gsim100 | A simulated data set from a Gaussian continuous Bayesian network
gsimmat | An adjacency matrix of a simulated dataset
interactions | interactions dataset
iterativeMCMC | Structure learning with an iterative order MCMC algorithm on an expanded search space
iterativeMCMC class | iterativeMCMC class structure
itercomp | Performance assessment of iterative MCMC scheme against a known Bayesian network
kirc | kirc dataset
kirp | kirp dataset
learnBN | Bayesian network structure learning
m2graph | Deriving a graph from an adjacancy matrix
mapping | mapping dataset
modelp | Estimating a graph corresponding to a posterior probability threshold
orderMCMC | Structure learning with the order MCMC algorithm
orderMCMC class | orderMCMC class structure
partitionMCMC | DAG structure sampling with partition MCMC
partitionMCMC class | partitionMCMC class structure
plot.iterativeMCMC | Structure learning with an iterative order MCMC algorithm on an expanded search space
plot.itercomp | Performance assessment of iterative MCMC scheme against a known Bayesian network
plot.orderMCMC | Structure learning with the order MCMC algorithm
plot.partitionMCMC | DAG structure sampling with partition MCMC
plot.samplecomp | Performance assessment of sampling algorithms against a known Bayesian network
plot2in1 | Highlighting similarities between two graphs
plotDBN | Plotting a DBN
plotdiffs | Plotting difference between two graphs
plotdiffsDBN | Plotting difference between two DBNs
plotpcor | Comparing posterior probabilitites of single edges
plotpedges | Plotting posterior probabilities of single edges
print.iterativeMCMC | Structure learning with an iterative order MCMC algorithm on an expanded search space
print.itercomp | Performance assessment of iterative MCMC scheme against a known Bayesian network
print.orderMCMC | Structure learning with the order MCMC algorithm
print.partitionMCMC | DAG structure sampling with partition MCMC
print.samplecomp | Performance assessment of sampling algorithms against a known Bayesian network
print.scoreparameters | Initializing score object
print.scorespace | Prints 'scorespace' object
sampleBN | Bayesian network structure sampling from the posterior distribution
samplecomp | Performance assessment of sampling algorithms against a known Bayesian network
scoreagainstDAG | Calculating the score of a sample against a DAG
scoreagainstDBN | Score against DBN
scoreparameters | Initializing score object
scorespace | Prints 'scorespace' object
scorespace class | scorespace class structure
string2mat | Deriving interactions matrix
summary.iterativeMCMC | Structure learning with an iterative order MCMC algorithm on an expanded search space
summary.itercomp | Performance assessment of iterative MCMC scheme against a known Bayesian network
summary.orderMCMC | Structure learning with the order MCMC algorithm
summary.partitionMCMC | DAG structure sampling with partition MCMC
summary.samplecomp | Performance assessment of sampling algorithms against a known Bayesian network
summary.scoreparameters | Initializing score object
summary.scorespace | Prints 'scorespace' object