Bayesian Network Structure Learning from Data with Missing Values


[Up] [Top]

Documentation for package ‘bnstruct’ version 1.0.11

Help Pages

A B C D E G H I J K L M N O P Q 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.
asia_2_layers load a two-layers dataset derived from the '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.
interventions get the list of interventions of an 'InferenceEngine'.
interventions,InferenceEngine get the list of interventions of an 'InferenceEngine'.
interventions-method get the list of interventions of an 'InferenceEngine'.
interventions<- set the list of interventions for an 'InferenceEngine'.
interventions<--method set the list of interventions for an 'InferenceEngine'.

-- 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'.

-- Q --

quantiles get the list of quantiles of an object.
quantiles,BN get the list of quantiles of an object.
quantiles,BNDataset get the list of quantiles of an object.
quantiles-method get the list of quantiles of an object.
quantiles<- set the list of quantiles of an object.
quantiles<--method set the list of quantiles of an object.

-- 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.