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.

Author
Francesco Sambo [aut, cre], Alberto Franzin [aut]
Date of publication
2016-11-10 13:43:16
Maintainer
Francesco Sambo <francesco.sambo@unipd.it>
License
GPL (>= 2) | file LICENSE
Version
1.0.1

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.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.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.

Files in this package

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