bnstruct: Bayesian Network Structure Learning from Data with Missing Values

Bayesian Network Structure Learning from Data with Missing Values. The package implements the Silander-Myllymaki complete search, the Max-Min Parents-and-Children, the Hill-Climbing, the Max-Min Hill-climbing heuristic searches, and the Structural Expectation-Maximization algorithm. Available scoring functions are BDeu, AIC, BIC. The package also implements methods for generating and using bootstrap samples, imputed data, inference.

Install the latest version of this package by entering the following in R:
install.packages("bnstruct")
AuthorFrancesco Sambo [aut, cre], Alberto Franzin [aut]
Date of publication2016-12-13 15:33:34
MaintainerFrancesco Sambo <francesco.sambo@unipd.it>
LicenseGPL (>= 2) | file LICENSE
Version1.0.2

View on CRAN

Man pages

add.observations-set: add further evidence to an existing list of observations of...

asia: load 'Asia' dataset.

asia_10000: 'Asia' dataset.

belief.propagation: perform belief propagation.

BN-class: BN class definition.

BNDataset-class: BNDataset class.

bn-method: get the 'BN' object contained in an 'InferenceEngine'.

bn-set: set the original 'BN' object contained in an...

boot: get selected element of bootstrap list.

boots: get list of bootstrap samples of a 'BNDataset'.

boots-set: set list of bootstrap samples of a 'BNDataset'.

bootstrap: Perform bootstrap.

build.junction.tree: build a JunctionTree.

child: load 'Child' dataset.

child_NA_5000: 'Child' dataset.

complete: Subset a 'BNDataset' to get only complete cases.

cpts: get the list of conditional probability tables of a 'BN'.

cpts-set: set the list of conditional probability tables of a network.

dag: get adjacency matrix of a network.

dag-set: set adjacency matrix of an object.

dag.to.cpdag: convert a DAG to a CPDAG

data.file: get data file of a 'BNDataset'.

data.file-set: set data file of a 'BNDataset'.

discreteness: get status (discrete or continuous) of the variables of an...

discreteness-set: set status (discrete or continuous) of the variables of an...

em: expectation-maximization algorithm.

get.most.probable.values: compute the most probable values to be observed.

has.boots: check whether a 'BNDataset' has bootstrap samples or not.

has.imputed.boots: check whether a 'BNDataset' has bootstrap samples from...

has.imputed.data: check if a BNDataset contains impited data.

has.raw.data: check if a BNDataset contains raw data.

header.file: get header file of a 'BNDataset'.

header.file-set: set header file of a 'BNDataset'.

imp.boots: get list of bootstrap samples from imputed data of a...

imp.boots-set: set list of bootstrap samples from imputed data of a...

impute: Impute a 'BNDataset' raw data with missing values.

imputed.data: get imputed data of a BNDataset.

imputed.data-set: add imputed data.

InferenceEngine-class: InferenceEngine class.

jpts: get the list of joint probability tables compiled by an...

jpts-set: set the list of joint probability tables compiled by an...

jt.cliques: get the list of cliques of the junction tree of an...

jt.cliques-set: set the list of cliques of the junction tree of an...

junction.tree: get the junction tree of an 'InferenceEngine'.

junction.tree-set: set the junction tree of an 'InferenceEngine'.

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

layering: return the layering of the nodes.

learn.dynamic.network: learn a dynamic network (structure and parameters) of a BN...

learn.network: learn a network (structure and parameters) of a BN from a...

learn.params: learn the parameters of a BN.

learn.structure: learn the structure of a network.

marginals: compute the list of inferred marginals of a BN.

name: get name of an object.

name-set: set name of an object.

node.sizes: get size of the variables of an object.

node.sizes-set: set the size of variables of an object.

num.boots: get number of bootstrap samples of a 'BNDataset'.

num.boots-set: set number of bootstrap samples of a 'BNDataset'.

num.items: get number of items of a 'BNDataset'.

num.items-set: set number of items of a 'BNDataset'.

num.nodes: get number of nodes of an object.

num.nodes-set: 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-set: set number of time steps of a 'BN' or a 'BNDataset'.

num.variables: get number of variables of a 'BNDataset'.

num.variables-set: set number of variables of a 'BNDataset'.

observations: get the list of observations of an 'InferenceEngine'.

observations-set: set the list of observations of an 'InferenceEngine'.

plot: plot a 'BN' as a picture.

print: print an object to 'stdout'.

raw.data: get raw data of a BNDataset.

raw.data-set: add raw data.

read.bif: Read a network from a '.bif' file.

read.dataset: Read a dataset from file.

read.dsc: Read a network from a '.dsc' file.

read.net: Read a network from a '.net' file.

sample.dataset: sample a 'BNDataset' from a network of an inference engine.

sample.row: sample a row vector of values for a network.

save.to.eps: save a 'BN' picture as '.eps' file.

scoring.func: Read the scoring function used to learn the structure of a...

scoring.func-set: Set the scoring function used to learn the structure of a...

shd: compute the Structural Hamming Distance between two adjacency...

show: Show method for objects.

struct.algo: Read the algorithm used to learn the structure of a network.

struct.algo-set: Set the algorithm used to learn the structure of a network.

test.updated.bn: check if an updated 'BN' is present in an 'InferenceEngine'.

tune.knn.impute: tune the parameter k of the knn algorithm used in imputation.

updated.bn-method: get the updated 'BN' object contained in an...

updated.bn-set: set the updated 'BN' object contained in an...

variables: get variables of an object.

variables-set: set variables of an object.

wpdag: get the WPDAG of an object.

wpdag.from.dag: Initialize a WPDAG from a DAG.

wpdag-set: set WPDAG of the object.

write.dsc: Write a network saving it in a '.dsc' file.

write_xgmml: Write a network saving it in an 'XGMML' file.

Functions

add.observations<- Man page
add.observations<-,InferenceEngine-method Man page
asia Man page
asia_10000 Man page
belief.propagation Man page
belief.propagation,InferenceEngine Man page
belief.propagation,InferenceEngine-method Man page
bn Man page
bn<- Man page
BN Man page
BN,BN-class Man page
BN-class Man page
BNDataset Man page
BNDataset,BNDataset-class Man page
BNDataset-class Man page
bn,InferenceEngine Man page
bn<-,InferenceEngine-method Man page
bn,InferenceEngine-method Man page
boot Man page
boot,BNDataset Man page
boot,BNDataset,numeric-method Man page
boots Man page
boots<- Man page
boots,BNDataset Man page
boots<-,BNDataset-method Man page
boots,BNDataset-method Man page
bootstrap Man page
bootstrap,BNDataset Man page
bootstrap,BNDataset-method Man page
build.junction.tree Man page
build.junction.tree,InferenceEngine Man page
build.junction.tree,InferenceEngine-method Man page
child Man page
child_NA_5000 Man page
complete Man page
complete,BNDataset Man page
complete,BNDataset-method Man page
cpts Man page
cpts<- Man page
cpts,BN Man page
cpts<-,BN-method Man page
cpts,BN-method Man page
dag Man page
dag<- Man page
dag,BN Man page
dag<-,BN-method Man page
dag,BN-method Man page
dag.to.cpdag Man page
data.file Man page
data.file<- Man page
data.file,BNDataset Man page
data.file<-,BNDataset-method Man page
data.file,BNDataset-method Man page
discreteness Man page
discreteness<- Man page
discreteness,BN Man page
discreteness,BNDataset Man page
discreteness<-,BNDataset-method Man page
discreteness,BNDataset-method Man page
discreteness<-,BN-method Man page
discreteness,BN-method Man page
em Man page
em,InferenceEngine,BNDataset Man page
em,InferenceEngine,BNDataset-method Man page
get.most.probable.values Man page
get.most.probable.values,BN Man page
get.most.probable.values,BN-method Man page
get.most.probable.values,InferenceEngine Man page
get.most.probable.values,InferenceEngine-method Man page
has.boots Man page
has.boots,BNDataset Man page
has.boots,BNDataset-method Man page
has.imputed.boots Man page
has.imputed.boots,BNDataset Man page
has.imputed.boots,BNDataset-method Man page
has.imputed.data Man page
has.imputed.data,BNDataset Man page
has.imputed.data,BNDataset-method Man page
has.raw.data Man page
has.raw.data,BNDataset Man page
has.raw.data,BNDataset-method Man page
header.file Man page
header.file<- Man page
header.file,BNDataset Man page
header.file<-,BNDataset-method Man page
header.file,BNDataset-method Man page
imp.boots Man page
imp.boots<- Man page
imp.boots,BNDataset Man page
imp.boots<-,BNDataset-method Man page
imp.boots,BNDataset-method Man page
impute Man page
impute,BNDataset Man page
impute,BNDataset-method Man page
imputed.data Man page
imputed.data<- Man page
imputed.data,BNDataset Man page
imputed.data<-,BNDataset-method Man page
imputed.data,BNDataset-method Man page
InferenceEngine Man page
InferenceEngine-class Man page
InferenceEngine,InferenceEngine-class Man page
initialize,BNDataset-method Man page
initialize,BN-method Man page
initialize,InferenceEngine-method Man page
jpts Man page
jpts<- Man page
jpts,InferenceEngine Man page
jpts<-,InferenceEngine-method Man page
jpts,InferenceEngine-method Man page
jt.cliques Man page
jt.cliques<- Man page
jt.cliques,InferenceEngine Man page
jt.cliques<-,InferenceEngine-method Man page
jt.cliques,InferenceEngine-method Man page
junction.tree Man page
junction.tree<- Man page
junction.tree,InferenceEngine Man page
junction.tree<-,InferenceEngine-method Man page
junction.tree,InferenceEngine-method Man page
knn.impute Man page
layering Man page
layering,BN Man page
layering,BN-method Man page
learn.dynamic.network Man page
learn.dynamic.network,BN Man page
learn.dynamic.network,BNDataset Man page
learn.dynamic.network,BNDataset-method Man page
learn.dynamic.network,BN-method Man page
learn.network Man page
learn.network,BN Man page
learn.network,BNDataset Man page
learn.network,BNDataset-method Man page
learn.network,BN-method Man page
learn.params Man page
learn.params,BN,BNDataset Man page
learn.params,BN,BNDataset-method Man page
learn.structure Man page
learn.structure,BN,BNDataset Man page
learn.structure,BN,BNDataset-method Man page
marginals Man page
marginals,InferenceEngine Man page
marginals,InferenceEngine-method Man page
name Man page
name<- Man page
name,BN Man page
name,BNDataset Man page
name<-,BNDataset-method Man page
name,BNDataset-method Man page
name<-,BN-method Man page
name,BN-method Man page
node.sizes Man page
node.sizes<- Man page
node.sizes,BN Man page
node.sizes,BNDataset Man page
node.sizes<-,BNDataset-method Man page
node.sizes,BNDataset-method Man page
node.sizes<-,BN-method Man page
node.sizes,BN-method Man page
num.boots Man page
num.boots<- Man page
num.boots,BNDataset Man page
num.boots<-,BNDataset-method Man page
num.boots,BNDataset-method Man page
num.items Man page
num.items<- Man page
num.items,BNDataset Man page
num.items<-,BNDataset-method Man page
num.items,BNDataset-method Man page
num.nodes Man page
num.nodes<- Man page
num.nodes,BN Man page
num.nodes<-,BN-method Man page
num.nodes,BN-method Man page
num.nodes,InferenceEngine Man page
num.nodes<-,InferenceEngine-method Man page
num.nodes,InferenceEngine-method Man page
num.time.steps Man page
num.time.steps<- Man page
num.time.steps,BN Man page
num.time.steps,BNDataset Man page
num.time.steps<-,BNDataset-method Man page
num.time.steps,BNDataset-method Man page
num.time.steps<-,BN-method Man page
num.time.steps,BN-method Man page
num.variables Man page
num.variables<- Man page
num.variables,BNDataset Man page
num.variables<-,BNDataset-method Man page
num.variables,BNDataset-method Man page
observations Man page
observations<- Man page
observations,InferenceEngine Man page
observations<-,InferenceEngine-method Man page
observations,InferenceEngine-method Man page
plot Man page
plot,BN Man page
plot.BN Man page
plot.BN,BN Man page
print Man page
print,BN Man page
print,BNDataset Man page
print,BNDataset-method Man page
print,BN-method Man page
print,InferenceEngine Man page
print,InferenceEngine-method Man page
raw.data Man page
raw.data<- Man page
raw.data,BNDataset Man page
raw.data<-,BNDataset-method Man page
raw.data,BNDataset-method Man page
read.bif Man page
read.bif,character Man page
read.bif,character-method Man page
read.dataset Man page
read.dataset,BNDataset,character,character Man page
read.dataset,BNDataset,character,character-method Man page
read.dsc Man page
read.dsc,character Man page
read.dsc,character-method Man page
read.net Man page
read.net,character Man page
read.net,character-method Man page
sample.dataset Man page
sample.dataset,BN Man page
sample.dataset,BN-method Man page
sample.dataset,InferenceEngine Man page
sample.dataset,InferenceEngine-method Man page
sample.row Man page
sample.row,BN Man page
sample.row,BN-method Man page
save.to.eps Man page
save.to.eps,BN,character Man page
save.to.eps,BN,character-method Man page
scoring.func Man page
scoring.func<- Man page
scoring.func,BN Man page
scoring.func<-,BN-method Man page
scoring.func,BN-method Man page
shd Man page
show Man page
show,AllTheClasses-method Man page
show,BNDataset-method Man page
show,BN-method Man page
show,InferenceEngine-method Man page
struct.algo Man page
struct.algo<- Man page
struct.algo,BN Man page
struct.algo<-,BN-method Man page
struct.algo,BN-method Man page
test.updated.bn Man page
test.updated.bn,InferenceEngine Man page
test.updated.bn,InferenceEngine-method Man page
tune.knn.impute Man page
updated.bn Man page
updated.bn<- Man page
updated.bn,InferenceEngine Man page
updated.bn<-,InferenceEngine-method Man page
updated.bn,InferenceEngine-method Man page
variables Man page
variables<- Man page
variables,BN Man page
variables,BNDataset Man page
variables<-,BNDataset-method Man page
variables,BNDataset-method Man page
variables<-,BN-method Man page
variables,BN-method Man page
wpdag Man page
wpdag<- Man page
wpdag,BN Man page
wpdag<-,BN-method Man page
wpdag,BN-method Man page
wpdag.from.dag Man page
wpdag.from.dag,BN Man page
wpdag.from.dag,BN-method Man page
write.dsc Man page
write.dsc,BN Man page
write.dsc,BN-method Man page
write_xgmml Man page
write_xgmml,BN Man page
write_xgmml,BN-method Man page

Files

inst
inst/examples
inst/examples/test_bp_child.R inst/examples/dbn.R inst/examples/naivebayes.R inst/examples/test_bp_asia.R
inst/scripts
inst/scripts/bnstruct.cmdline.R
inst/extdata
inst/extdata/asia_10000.data
inst/extdata/asia_2_layers.data
inst/extdata/asia_2_layers.header
inst/extdata/Child_data_na_5000.header
inst/extdata/Child_data_na_5000.data
inst/extdata/asia_10000.header
inst/doc
inst/doc/bnstruct.Rnw
inst/doc/bnstruct-manual.pdf
inst/doc/bnstruct.R
inst/doc/bnstruct.pdf
tests
tests/testthat.R
tests/testthat
tests/testthat/test_sl.R
src
src/util.c
src/mmhcfast.c
src/impfast.h
src/mmhcfast.h
src/impfast.c
src/util.h
src/smfast.h
src/smfast.c
NAMESPACE
data
data/asia_10000.rda
data/child_NA_5000.rda
R
R/AllClasses.R R/AllGenerics.R R/learn-methods.R R/buildJunctionTree-methods.R R/InferenceEngine-methods.R R/cpdag.R R/io.R R/beliefPropagation-methods.R R/BNDataset-methods.R R/boot.bn.R R/init.R R/mmhc.R R/sm.R R/BN-methods.R R/util.R R/imputation.R R/JunctionTree-methods.R R/em.R R/sem.R R/datasets.R R/io-methods.R
vignettes
vignettes/alarm_crosses_1000.eps
vignettes/childtest-1.pdf
vignettes/bnstruct.Rnw
vignettes/bibtex.bib
vignettes/nb.pdf
vignettes/hepar2_crosses_1000.eps
vignettes/child_crosses_1000.eps
vignettes/asiatest-1.pdf
vignettes/andes_crosses.eps
vignettes/childtest-2.pdf
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/raw.data-set.Rd man/sample.dataset.Rd man/num.time.steps.Rd man/cpts.Rd man/em.Rd man/name-set.Rd man/test.updated.bn.Rd man/bootstrap.Rd man/show.Rd man/jt.cliques.Rd man/complete.Rd man/observations.Rd man/num.time.steps-set.Rd man/learn.network.Rd man/write.dsc.Rd man/bn-method.Rd man/sample.row.Rd man/write_xgmml.Rd man/child_NA_5000.Rd man/struct.algo-set.Rd man/discreteness-set.Rd man/node.sizes.Rd man/jpts.Rd man/header.file.Rd man/read.dsc.Rd man/wpdag.Rd man/struct.algo.Rd man/num.boots.Rd man/variables-set.Rd man/header.file-set.Rd man/updated.bn-method.Rd man/has.raw.data.Rd man/marginals.Rd man/save.to.eps.Rd man/knn.impute.Rd man/get.most.probable.values.Rd man/read.bif.Rd man/bn-set.Rd man/variables.Rd man/imp.boots-set.Rd man/dag.to.cpdag.Rd man/has.boots.Rd man/shd.Rd man/InferenceEngine-class.Rd man/learn.structure.Rd man/add.observations-set.Rd man/updated.bn-set.Rd man/imp.boots.Rd man/layering.Rd man/num.nodes-set.Rd man/num.variables-set.Rd man/name.Rd man/data.file-set.Rd man/jpts-set.Rd man/discreteness.Rd man/boots-set.Rd man/wpdag.from.dag.Rd man/raw.data.Rd man/dag-set.Rd man/observations-set.Rd man/junction.tree-set.Rd man/belief.propagation.Rd man/boot.Rd man/dag.Rd man/data.file.Rd man/num.nodes.Rd man/impute.Rd man/cpts-set.Rd man/num.boots-set.Rd man/BNDataset-class.Rd man/scoring.func-set.Rd man/build.junction.tree.Rd man/num.items-set.Rd man/child.Rd man/jt.cliques-set.Rd man/node.sizes-set.Rd man/learn.dynamic.network.Rd man/wpdag-set.Rd man/BN-class.Rd man/has.imputed.boots.Rd man/read.net.Rd man/print.Rd man/num.variables.Rd man/asia_10000.Rd man/imputed.data.Rd man/asia.Rd man/plot.Rd man/tune.knn.impute.Rd man/read.dataset.Rd man/learn.params.Rd man/imputed.data-set.Rd man/num.items.Rd man/boots.Rd man/scoring.func.Rd man/has.imputed.data.Rd man/junction.tree.Rd
LICENSE

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All documentation is copyright its authors; we didn't write any of that.