# R interface to Netica(R) Bayesian Network Engine

## Documentation for package ‘RNetica’ version 0.3-4

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

## Help Pages

A C D E F G H I J L M N O P R S T U W misc

RNetica-package | R interface to Netica(R) Bayesian Network Engine

## -- A --

AbsorbNodes | Delete a Netica nodes in a way that maintains the connectivity.
AddLink | Adds or removes a link between two nodes in a Netican network.
AdjoinNetwork | Links an evidence model network to a system model netwok.
as.CPA | Representation of a conditional probability table as an array.
as.CPF | Representation of a conditional probability table as a data frame.
as.IDname | Tests to see if a string is a valid as a Netica Identifier.

## -- C --

CaseFileDelimiter | Gets or sets special characters for case files.
CaseFileMissingCode | Gets or sets special characters for case files.
CaseFileStream | A stream of cases for reading/writing Netica findings to a file
CloseCaseStream | A stream of cases for reading/writing Netica findings
CompileNetwork | Builds the junction tree for a Netica Network
CopyNetworks | Makes copies of Netica networks.
CopyNodes | Copies or duplicates nodes in a Netica network.
CPA | Representation of a conditional probability table as an array.
CPF | Representation of a conditional probability table as a data frame.
CreateNetwork | Creates (destroys) a new Netica network.

## -- D --

DeleteLink | Adds or removes a link between two nodes in a Netican network.
DeleteNetwork | Creates (destroys) a new Netica network.
DeleteNodes | Creates (or destroys) a node in a Netica Bayesian network.
DeleteNodeTable | Deletes the conditional probability table of a Netica node.

## -- E --

EliminationOrder | Retrieves or sets the elimination order used in compiling a Netica network.
EliminationOrder<- | Retrieves or sets the elimination order used in compiling a Netica network.
EnterFindings | Enters findings for multiple nodes in a Netica network.
EnterNegativeFinding | Sets findings for a Netaca node to a list of ruled out values.
EVERY_STATE | Extracts portions of the conditional probability table of a Netica node.
Extract.NeticaNode | Extracts portions of the conditional probability table of a Netica node.

## -- F --

FadeCPT | Fades a Netica Conditional Probability Table
FindingsProbability | Finds the probability of the findings entered into a Netica network.

## -- G --

getCaseStreamDataFrameName | A stream of cases for reading/writing Netica from memory
getCaseStreamLastFreq | A stream of cases for reading/writing Netica findings
getCaseStreamLastId | A stream of cases for reading/writing Netica findings
getCaseStreamPath | A stream of cases for reading/writing Netica findings to a file
getCaseStreamPos | A stream of cases for reading/writing Netica findings
GetClique | Forces a collection of nodes in a Netica network to be in the same clique.
GetNamedNetworks | Finds a Netica network (if it exists) for the name.
GetNetworkAutoUpdate | Turns Netica automatic updating on or off for a network.
GetNetworkFileName | Reads or writes a Netica network from a file.
GetNthNetwork | Fetch a Netica network by its position in the Netica list.
GetRelatedNodes | Computes topological properities of a 'Netica' network.

## -- H --

HasNodeTable | Tests to see if a Netica node has a conditional probability table.

## -- I --

IDname | Tests to see if a string is a valid as a Netica Identifier.
is.active | Check to see if a Netica network or node object is still valid.
is.CaseFileStream | A stream of cases for reading/writing Netica findings to a file
is.CliqueNode | Forces a collection of nodes in a Netica network to be in the same clique.
is.continuous | Determines whether a Netica node is discrete or continuous.
is.CPA | Representation of a conditional probability table as an array.
is.CPF | Representation of a conditional probability table as a data frame.
is.discrete | Determines whether a Netica node is discrete or continuous.
is.IDname | Tests to see if a string is a valid as a Netica Identifier.
is.MemoryCaseStream | A stream of cases for reading/writing Netica from memory
is.NeticaBN | An object referencing a Bayesian network in Netica.
is.NeticaCaseStream | A stream of cases for reading/writing Netica findings
is.NeticaNode | An object referencing a node in a Netica Bayesian network.
is.NetworkCompiled | Builds the junction tree for a Netica Network
is.NodeRelated | Computes topological properities of a 'Netica' network.
IsBeliefUpdated | Returns the current marginal probability distribution associated with a node in a Netica network.
isCaseStreamOpen | A stream of cases for reading/writing Netica findings
IsNodeDeterministic | Determines if a node in a Netica Network is deterministic or not.

## -- J --

JointProbability | Calculates the joint probability over several network nodes.
JunctionTreeReport | Produces a report about the junction tree from a compiled Netica network.

## -- L --

LearnCases | Learn Conditional Probabilitiy Tables from a Netica Case Stream
LearnCPTs | Learn Conditional Probability Tables with Missing Data.
LearnFindings | Learn Netica conditional probabilities from findings.
LicenseKey | Starting and stopping the Netica shared library.

## -- M --

MakeCliqueNode | Forces a collection of nodes in a Netica network to be in the same clique.
MemoryCaseStream | A stream of cases for reading/writing Netica from memory
MemoryStreamContents | Access the contents of a MemoryCaseStream
MemoryStreamContents<- | Access the contents of a MemoryCaseStream
MostProbableConfig | Finds the configuration of the nodes most likel to have lead to observed findings.

## -- N --

NeticaBN | An object referencing a Bayesian network in Netica.
NeticaCaseStream | A stream of cases for reading/writing Netica findings
NeticaNode | An object referencing a node in a Netica Bayesian network.
NeticaVersion | Fetches the version number of Netica.
NetworkAllNodes | Finds nodes in a Netica network.
NetworkAllUserFields | Gets user definable fields associated with a Netica network.
NetworkComment | Gets the title or comments associated with a Netica network.
NetworkComment<- | Gets the title or comments associated with a Netica network.
NetworkCompiledSize | Produces a report about the junction tree from a compiled Netica network.
NetworkFindNode | Finds nodes in a Netica network.
NetworkFootprint | Returns a list of names of unconnected edges.
NetworkName | Gets or Sets the name of a Netica network.
NetworkName<- | Gets or Sets the name of a Netica network.
NetworkNodeSetColor | Returns or sets a display colour to use with a netica node.b
NetworkNodeSets | Returns a list of node sets associated with a Netica network.
NetworkNodesInSet | Returns a list of node labeled with the given node set in a Netica Network.
NetworkRedo | Undoes (redoes) a Netica operation on a network.
NetworkSetPriority | Changes the priority order of the node sets.
NetworkTitle | Gets the title or comments associated with a Netica network.
NetworkTitle<- | Gets the title or comments associated with a Netica network.
NetworkUndo | Undoes (redoes) a Netica operation on a network.
NetworkUserField | Gets user definable fields associated with a Netica network.
NetworkUserField<- | Gets user definable fields associated with a Netica network.
NewContinuousNode | Creates (or destroys) a node in a Netica Bayesian network.
NewDiscreteNode | Creates (or destroys) a node in a Netica Bayesian network.
NodeAllUserFields | Gets user definable fields associated with a Netica node.
NodeBeliefs | Returns the current marginal probability distribution associated with a node in a Netica network.
NodeChildren | Returns a list of the children of a node in a Netica network.
NodeDescription | Gets the title or Description associated with a Netica node.
NodeDescription<- | Gets the title or Description associated with a Netica node.
NodeExperience | Gets or sets the amount of experience associated with a node.
NodeExperience<- | Gets or sets the amount of experience associated with a node.
NodeFinding | Returns of sets the observed value associated with a Netica node.
NodeFinding<- | Returns of sets the observed value associated with a Netica node.
NodeInputNames | Associates names with incomming edges on a Netica node.
NodeInputNames<- | Associates names with incomming edges on a Netica node.
NodeKind | Gets or changes the kind of a node in a Netica network.
NodeKind<- | Gets or changes the kind of a node in a Netica network.
NodeLevels | Accesses the levels associated with a Netica node.
NodeLevels<- | Accesses the levels associated with a Netica node.
NodeLikelihood | Returns or sets the virtual evidence associated with a Netica node.
NodeLikelihood<- | Returns or sets the virtual evidence associated with a Netica node.
NodeName | Gets or set of a Netica node.
NodeName<- | Gets or set of a Netica node.
NodeNet | Finds which Netica network a node comes from.
NodeNumStates | Accessor for states of a Netica node.
NodeParents | Gets or sets the parents of a node in a Netica network.
NodeParents<- | Gets or sets the parents of a node in a Netica network.
NodeProbs | Gets or sets the conditional probability table associated with a Netica node.
NodeProbs<- | Gets or sets the conditional probability table associated with a Netica node.
NodeSets | Lists or changes the node sets associated with a Netica node.
NodeSets<- | Lists or changes the node sets associated with a Netica node.
NodeStateComments | Accessors for the titles and comments associated with states of Netica nodes.
NodeStateComments<- | Accessors for the titles and comments associated with states of Netica nodes.
NodeStates | Accessor for states of a Netica node.
NodeStates<- | Accessor for states of a Netica node.
NodeStateTitles | Accessors for the titles and comments associated with states of Netica nodes.
NodeStateTitles<- | Accessors for the titles and comments associated with states of Netica nodes.
NodeTitle | Gets the title or Description associated with a Netica node.
NodeTitle<- | Gets the title or Description associated with a Netica node.
NodeUserField | Gets user definable fields associated with a Netica node.
NodeUserField<- | Gets user definable fields associated with a Netica node.
NodeVisPos | Gets, sets the visual position of the node on the Netica display.
NodeVisPos<- | Gets, sets the visual position of the node on the Netica display.
NodeVisStyle | Gets/sets the nodes visual appearence in Netica.
NodeVisStyle<- | Gets/sets the nodes visual appearence in Netica.
normalize | Normalizes a conditional probability table.
normalize.array | Normalizes a conditional probability table.
normalize.CPA | Normalizes a conditional probability table.
normalize.CPF | Normalizes a conditional probability table.
normalize.data.frame | Normalizes a conditional probability table.
normalize.default | Normalizes a conditional probability table.
normalize.matrix | Normalizes a conditional probability table.

## -- O --

OpenCaseStream | A stream of cases for reading/writing Netica findings
Ops.NeticaBN | An object referencing a Bayesian network in Netica.
Ops.NeticaNode | An object referencing a node in a Netica Bayesian network.

## -- P --

ParentNames | Returns a list of the names of the states of the parents of a Netica node.
ParentStates | Returns a list of the names of the states of the parents of a Netica node.
print.NeticaBN | An object referencing a Bayesian network in Netica.
print.NeticaCaseStream | A stream of cases for reading/writing Netica findings
print.NeticaNode | An object referencing a node in a Netica Bayesian network.

## -- R --

read.CaseFile | Read or write data frame in Netica Case File format.
ReadFindings | Retrieves a record from a Netica Case Stream
ReadNetworks | Reads or writes a Netica network from a file.
RetractNetFindings | Clears any findings for a Netica node or network.
RetractNodeFinding | Clears any findings for a Netica node or network.
ReverseLink | Reverses a link in a Netica network.
RNetica | R interface to Netica(R) Bayesian Network Engine

## -- S --

SetNetworkAutoUpdate | Turns Netica automatic updating on or off for a network.
StartNetica | Starting and stopping the Netica shared library.
StopNetica | Starting and stopping the Netica shared library.

## -- T --

toString.NeticaBN | An object referencing a Bayesian network in Netica.
toString.NeticaCaseStream | A stream of cases for reading/writing Netica findings
toString.NeticaNode | An object referencing a node in a Netica Bayesian network.

## -- U --

UncompileNetwork | Builds the junction tree for a Netica Network

## -- W --

WithOpenCaseStream | Evaluate an expression and then close the Netica Case Stream.
WithoutAutoUpdate | Turns Netica automatic updating on or off for a network.
write.CaseFile | Read or write data frame in Netica Case File format.
WriteFindings | Appends the current findings to a Netica case file.
WriteNetworks | Reads or writes a Netica network from a file.

## -- misc --

[.NeticaNode | Extracts portions of the conditional probability table of a Netica node.
[<-.NeticaNode | Extracts portions of the conditional probability table of a Netica node.
[[.NeticaNode | Extracts portions of the conditional probability table of a Netica node.