# Bayesian Network Structure Learning from Data with Missing Values

## Documentation for package ‘bnstruct’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G H I J K L M N O P R S T U V W

## -- A --

add.observations<- | add further evidence to an existing list of observations of an 'InferenceEngine'.
add.observations<--method | add further evidence to an existing list of observations of an 'InferenceEngine'.
asia | load 'Asia' dataset.
asia_10000 | 'Asia' dataset.

## -- B --

belief.propagation | perform belief propagation.
belief.propagation,InferenceEngine | perform belief propagation.
belief.propagation-method | perform belief propagation.
BN | BN class definition.
bn | get the 'BN' object contained in an 'InferenceEngine'.
BN,BN-class | BN class definition.
bn,InferenceEngine | get the 'BN' object contained in an 'InferenceEngine'.
BN-class | BN class definition.
bn-method | get the 'BN' object contained in an 'InferenceEngine'.
bn<- | set the original 'BN' object contained in an 'InferenceEngine'.
bn<--method | set the original 'BN' object contained in an 'InferenceEngine'.
BNDataset | BNDataset class.
BNDataset,BNDataset-class | BNDataset class.
BNDataset-class | BNDataset class.
boot | get selected element of bootstrap list.
boot,BNDataset | get selected element of bootstrap list.
boot-method | get selected element of bootstrap list.
boots | get list of bootstrap samples of a 'BNDataset'.
boots,BNDataset | get list of bootstrap samples of a 'BNDataset'.
boots-method | get list of bootstrap samples of a 'BNDataset'.
boots<- | set list of bootstrap samples of a 'BNDataset'.
boots<--method | set list of bootstrap samples of a 'BNDataset'.
bootstrap | Perform bootstrap.
bootstrap,BNDataset | Perform bootstrap.
bootstrap-method | Perform bootstrap.
build.junction.tree | build a JunctionTree.
build.junction.tree,InferenceEngine | build a JunctionTree.
build.junction.tree-method | build a JunctionTree.

## -- C --

child | load 'Child' dataset.
child_NA_5000 | 'Child' dataset.
complete | Subset a 'BNDataset' to get only complete cases.
complete,BNDataset | Subset a 'BNDataset' to get only complete cases.
complete-method | Subset a 'BNDataset' to get only complete cases.
cpts | get the list of conditional probability tables of a 'BN'.
cpts,BN | get the list of conditional probability tables of a 'BN'.
cpts-method | get the list of conditional probability tables of a 'BN'.
cpts<- | set the list of conditional probability tables of a network.
cpts<--method | set the list of conditional probability tables of a network.

## -- D --

dag | get adjacency matrix of a network.
dag,BN | get adjacency matrix of a network.
dag-method | get adjacency matrix of a network.
dag.to.cpdag | convert a DAG to a CPDAG
dag<- | set adjacency matrix of an object.
dag<--method | set adjacency matrix of an object.
data.file | get data file of a 'BNDataset'.
data.file,BNDataset | get data file of a 'BNDataset'.
data.file-method | get data file of a 'BNDataset'.
data.file<- | set data file of a 'BNDataset'.
data.file<--method | set data file of a 'BNDataset'.
discreteness | get status (discrete or continuous) of the variables of an object.
discreteness,BN | get status (discrete or continuous) of the variables of an object.
discreteness,BNDataset | get status (discrete or continuous) of the variables of an object.
discreteness-method | get status (discrete or continuous) of the variables of an object.
discreteness<- | set status (discrete or continuous) of the variables of an object.
discreteness<--method | set status (discrete or continuous) of the variables of an object.

## -- E --

edge.dir.wpdag | counts the edges in a WPDAG with their directionality
em | expectation-maximization algorithm.
em,InferenceEngine,BNDataset | expectation-maximization algorithm.
em-method | expectation-maximization algorithm.

## -- G --

get.most.probable.values | compute the most probable values to be observed.
get.most.probable.values,BN | compute the most probable values to be observed.
get.most.probable.values,InferenceEngine | compute the most probable values to be observed.
get.most.probable.values-method | compute the most probable values to be observed.

## -- H --

has.boots | check whether a 'BNDataset' has bootstrap samples or not.
has.boots,BNDataset | check whether a 'BNDataset' has bootstrap samples or not.
has.boots-method | check whether a 'BNDataset' has bootstrap samples or not.
has.imputed.boots | check whether a 'BNDataset' has bootstrap samples from imputed data or not.
has.imputed.boots,BNDataset | check whether a 'BNDataset' has bootstrap samples from imputed data or not.
has.imputed.boots-method | check whether a 'BNDataset' has bootstrap samples from imputed data or not.
has.imputed.data | check if a BNDataset contains impited data.
has.imputed.data,BNDataset | check if a BNDataset contains impited data.
has.imputed.data-method | check if a BNDataset contains impited data.
has.raw.data | check if a BNDataset contains raw data.
has.raw.data,BNDataset | check if a BNDataset contains raw data.
has.raw.data-method | check if a BNDataset contains raw data.
header.file | get header file of a 'BNDataset'.
header.file,BNDataset | get header file of a 'BNDataset'.
header.file-method | get header file of a 'BNDataset'.
header.file<- | set header file of a 'BNDataset'.
header.file<--method | set header file of a 'BNDataset'.

## -- I --

imp.boots | get list of bootstrap samples from imputed data of a 'BNDataset'.
imp.boots,BNDataset | get list of bootstrap samples from imputed data of a 'BNDataset'.
imp.boots-method | get list of bootstrap samples from imputed data of a 'BNDataset'.
imp.boots<- | set list of bootstrap samples from imputed data of a 'BNDataset'.
imp.boots<--method | set list of bootstrap samples from imputed data of a 'BNDataset'.
impute | Impute a 'BNDataset' raw data with missing values.
impute,BNDataset | Impute a 'BNDataset' raw data with missing values.
impute-method | Impute a 'BNDataset' raw data with missing values.
imputed.data | get imputed data of a BNDataset.
imputed.data,BNDataset | get imputed data of a BNDataset.
imputed.data-method | get imputed data of a BNDataset.
imputed.data<- | add imputed data.
imputed.data<--method | add imputed data.
InferenceEngine | InferenceEngine class.
InferenceEngine,InferenceEngine-class | InferenceEngine class.
InferenceEngine-class | InferenceEngine class.
initialize-method | BN class definition.
initialize-method | BNDataset class.
initialize-method | InferenceEngine class.

## -- J --

jpts | get the list of joint probability tables compiled by an 'InferenceEngine'.
jpts,InferenceEngine | get the list of joint probability tables compiled by an 'InferenceEngine'.
jpts-method | get the list of joint probability tables compiled by an 'InferenceEngine'.
jpts<- | set the list of joint probability tables compiled by an 'InferenceEngine'.
jpts<--method | set the list of joint probability tables compiled by an 'InferenceEngine'.
jt.cliques | get the list of cliques of the junction tree of an 'InferenceEngine'.
jt.cliques,InferenceEngine | get the list of cliques of the junction tree of an 'InferenceEngine'.
jt.cliques-method | get the list of cliques of the junction tree of an 'InferenceEngine'.
jt.cliques<- | set the list of cliques of the junction tree of an 'InferenceEngine'.
jt.cliques<--method | set the list of cliques of the junction tree of an 'InferenceEngine'.
junction.tree | get the junction tree of an 'InferenceEngine'.
junction.tree,InferenceEngine | get the junction tree of an 'InferenceEngine'.
junction.tree-method | get the junction tree of an 'InferenceEngine'.
junction.tree<- | set the junction tree of an 'InferenceEngine'.
junction.tree<--method | set the junction tree of an 'InferenceEngine'.

## -- K --

knn.impute | Perform imputation of a data frame using k-NN.

## -- L --

layering | return the layering of the nodes.
layering,BN | return the layering of the nodes.
layering-method | return the layering of the nodes.
learn.dynamic.network | learn a dynamic network (structure and parameters) of a BN from a BNDataset.
learn.dynamic.network,BN | learn a dynamic network (structure and parameters) of a BN from a BNDataset.
learn.dynamic.network,BNDataset | learn a dynamic network (structure and parameters) of a BN from a BNDataset.
learn.dynamic.network-method | learn a dynamic network (structure and parameters) of a BN from a BNDataset.
learn.network | learn a network (structure and parameters) of a BN from a BNDataset.
learn.network,BN | learn a network (structure and parameters) of a BN from a BNDataset.
learn.network,BNDataset | learn a network (structure and parameters) of a BN from a BNDataset.
learn.network-method | learn a network (structure and parameters) of a BN from a BNDataset.
learn.params | learn the parameters of a BN.
learn.params,BN,BNDataset | learn the parameters of a BN.
learn.params-method | learn the parameters of a BN.
learn.structure | learn the structure of a network.
learn.structure,BN,BNDataset | learn the structure of a network.
learn.structure-method | learn the structure of a network.

## -- M --

marginals | compute the list of inferred marginals of a BN.
marginals,InferenceEngine | compute the list of inferred marginals of a BN.
marginals-method | compute the list of inferred marginals of a BN.

## -- N --

name | get name of an object.
name,BN | get name of an object.
name,BNDataset | get name of an object.
name-method | get name of an object.
name<- | set name of an object.
name<--method | set name of an object.
node.sizes | get size of the variables of an object.
node.sizes,BN | get size of the variables of an object.
node.sizes,BNDataset | get size of the variables of an object.
node.sizes-method | get size of the variables of an object.
node.sizes<- | set the size of variables of an object.
node.sizes<--method | set the size of variables of an object.
num.boots | get number of bootstrap samples of a 'BNDataset'.
num.boots,BNDataset | get number of bootstrap samples of a 'BNDataset'.
num.boots-method | get number of bootstrap samples of a 'BNDataset'.
num.boots<- | set number of bootstrap samples of a 'BNDataset'.
num.boots<--method | set number of bootstrap samples of a 'BNDataset'.
num.items | get number of items of a 'BNDataset'.
num.items,BNDataset | get number of items of a 'BNDataset'.
num.items-method | get number of items of a 'BNDataset'.
num.items<- | set number of items of a 'BNDataset'.
num.items<--method | set number of items of a 'BNDataset'.
num.nodes | get number of nodes of an object.
num.nodes,BN | get number of nodes of an object.
num.nodes,InferenceEngine | get number of nodes of an object.
num.nodes-method | get number of nodes of an object.
num.nodes<- | set number of nodes of an object.
num.nodes<--method | set number of nodes of an object.
num.time.steps | get number of time steps observed in a 'BN' or a 'BNDataset'.
num.time.steps,BN | get number of time steps observed in a 'BN' or a 'BNDataset'.
num.time.steps,BNDataset | get number of time steps observed in a 'BN' or a 'BNDataset'.
num.time.steps-method | get number of time steps observed in a 'BN' or a 'BNDataset'.
num.time.steps<- | set number of time steps of a 'BN' or a 'BNDataset'.
num.time.steps<--method | set number of time steps of a 'BN' or a 'BNDataset'.
num.variables | get number of variables of a 'BNDataset'.
num.variables,BNDataset | get number of variables of a 'BNDataset'.
num.variables-method | get number of variables of a 'BNDataset'.
num.variables<- | set number of variables of a 'BNDataset'.
num.variables<--method | set number of variables of a 'BNDataset'.

## -- O --

observations | get the list of observations of an 'InferenceEngine'.
observations,InferenceEngine | get the list of observations of an 'InferenceEngine'.
observations-method | get the list of observations of an 'InferenceEngine'.
observations<- | set the list of observations of an 'InferenceEngine'.
observations<--method | set the list of observations of an 'InferenceEngine'.

## -- P --

plot | plot a 'BN' as a picture.
plot,BN | plot a 'BN' as a picture.
plot.BN | plot a 'BN' as a picture.
plot.BN,BN | plot a 'BN' as a picture.
print | print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.
print,BN | print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.
print,BNDataset | print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.
print,InferenceEngine | print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.
print.BN | print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.
print.BN,BN | print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.
print.BNDataset | print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.
print.BNDataset,BNDataset | print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.
print.InferenceEngine | print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.
print.InferenceEngine,InferenceEngine | print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.

## -- R --

raw.data | get raw data of a BNDataset.
raw.data,BNDataset | get raw data of a BNDataset.
raw.data-method | get raw data of a BNDataset.
raw.data<- | add raw data.
raw.data<--method | add raw data.
read.bif | Read a network from a '.bif' file.
read.bif,character | Read a network from a '.bif' file.
read.bif-method | Read a network from a '.bif' file.
read.dataset | Read a dataset from file.
read.dataset,BNDataset,character,character | Read a dataset from file.
read.dataset-method | Read a dataset from file.
read.dsc | Read a network from a '.dsc' file.
read.dsc,character | Read a network from a '.dsc' file.
read.dsc-method | Read a network from a '.dsc' file.
read.net | Read a network from a '.net' file.
read.net,character | Read a network from a '.net' file.
read.net-method | Read a network from a '.net' file.

## -- S --

sample.dataset | sample a 'BNDataset' from a network of an inference engine.
sample.dataset,BN | sample a 'BNDataset' from a network of an inference engine.
sample.dataset,InferenceEngine | sample a 'BNDataset' from a network of an inference engine.
sample.dataset-method | sample a 'BNDataset' from a network of an inference engine.
sample.row | sample a row vector of values for a network.
sample.row,BN | sample a row vector of values for a network.
sample.row-method | sample a row vector of values for a network.
save.to.eps | save a 'BN' picture as '.eps' file.
save.to.eps,BN,character | save a 'BN' picture as '.eps' file.
save.to.eps-method | save a 'BN' picture as '.eps' file.
scoring.func | Read the scoring function used to learn the structure of a network.
scoring.func,BN | Read the scoring function used to learn the structure of a network.
scoring.func-method | Read the scoring function used to learn the structure of a network.
scoring.func<- | Set the scoring function used to learn the structure of a network.
scoring.func<--method | Set the scoring function used to learn the structure of a network.
shd | compute the Structural Hamming Distance between two adjacency matrices.
show | Show method for objects.
show-method | Show method for objects.
struct.algo | Read the algorithm used to learn the structure of a network.
struct.algo,BN | Read the algorithm used to learn the structure of a network.
struct.algo-method | Read the algorithm used to learn the structure of a network.
struct.algo<- | Set the algorithm used to learn the structure of a network.
struct.algo<--method | Set the algorithm used to learn the structure of a network.

## -- T --

test.updated.bn | check if an updated 'BN' is present in an 'InferenceEngine'.
test.updated.bn,InferenceEngine | check if an updated 'BN' is present in an 'InferenceEngine'.
test.updated.bn-method | check if an updated 'BN' is present in an 'InferenceEngine'.
tune.knn.impute | tune the parameter k of the knn algorithm used in imputation.

## -- U --

updated.bn | get the updated 'BN' object contained in an 'InferenceEngine'.
updated.bn,InferenceEngine | get the updated 'BN' object contained in an 'InferenceEngine'.
updated.bn-method | get the updated 'BN' object contained in an 'InferenceEngine'.
updated.bn<- | set the updated 'BN' object contained in an 'InferenceEngine'.
updated.bn<--method | set the updated 'BN' object contained in an 'InferenceEngine'.

## -- V --

variables | get variables of an object.
variables,BN | get variables of an object.
variables,BNDataset | get variables of an object.
variables-method | get variables of an object.
variables<- | set variables of an object.
variables<--method | set variables of an object.

## -- W --

wpdag | get the WPDAG of an object.
wpdag,BN | get the WPDAG of an object.
wpdag-method | get the WPDAG of an object.
wpdag.from.dag | Initialize a WPDAG from a DAG.
wpdag.from.dag,BN | Initialize a WPDAG from a DAG.
wpdag.from.dag-method | Initialize a WPDAG from a DAG.
wpdag<- | set WPDAG of the object.
wpdag<--method | set WPDAG of the object.
write.dsc | Write a network saving it in a '.dsc' file.
write.dsc,BN | Write a network saving it in a '.dsc' file.
write.dsc-method | Write a network saving it in a '.dsc' file.
write_xgmml | Write a network saving it in an 'XGMML' file.
write_xgmml,BN | Write a network saving it in an 'XGMML' file.
write_xgmml-method | Write a network saving it in an 'XGMML' file.