Parameterized Bayesian Networks, Abstract Classes

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Documentation for package ‘Peanut’ version 0.8-4

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A B C D F G I M O P Q R S T U W

Peanut-package Parameterized Bayesian Networks, Abstract Classes

-- A --

as.legal.name Checks to see if names are valid for objects in warehouse.
as.Pnet A Parameterized Bayesian network
as.Pnode A Parameterized Bayesian network node

-- B --

BuildAllTables Builds the conditional probability table for a Pnode
BuildNetManifest Builds a network manifest from a list of Pnets
BuildNodeManifest Builds a table describing a set of Pnodes
BuildTable Builds the conditional probability table for a Pnode

-- C --

calcExpTables Calculate expected tables for a parameterized network
calcPnetLLike Calculates the log likelihood for a set of data under a Pnet model
calcStat Key functions for the Statistics class
calcStat-method Class '"Statistic"'
ClearWarehouse A cache for Pnets or Pnodes
CompensatoryGadget Shiny gadget for editing parameterized nodes (PNodes)

-- D --

defaultAlphas Reshapes alpha or beta vector based on rule and parents
defaultBetas Reshapes alpha or beta vector based on rule and parents
DPCGadget Shiny gadget for editing parameterized nodes (PNodes)

-- F --

flattenStats Flattens a statistic list into a numeric or character vector.
flog.try Trys to execute an expression with errors logged.

-- G --

GEMfit Fits the parameters of a parameterized network using the GEM algorithm
GetPriorWeight Gets the weight to be associated with the prior table during EM learning

-- I --

is.legal.name Checks to see if names are valid for objects in warehouse.
is.Pnet A Parameterized Bayesian network
is.PnetWarehouse A cache for Pnets or Pnodes
is.Pnode A Parameterized Bayesian network node
is.PnodeWarehouse A cache for Pnets or Pnodes
is.valid A cache for Pnets or Pnodes
isPnodeContinuous Functions for handling continuous nodes.

-- M --

maxAllTableParams Find optimal parameters of Pnet or Pnode to match expected tables
maxCPTParam Find optimal parameters of Pnet or Pnode to match expected tables

-- O --

OffsetGadget Shiny gadget for editing parameterized nodes (PNodes)
Omega2Pnet Constructs a parameterized network from an Omega matrix.

-- P --

Peanut Parameterized Bayesian Networks, Abstract Classes
Pnet A Parameterized Bayesian network
Pnet-class Class '"Pnet"'
Pnet-method A Parameterized Bayesian network
Pnet2Omega Constructs an Omega matrix from a parameterized network.
Pnet2Qmat Makes an augmented Q-matrix from a collection of parameterized nets
PnetAdjoin Merges (or separates) two Pnets with common variables
PnetCompile Compiles a Parameterized Bayesian Network
PnetDescription Gets the title or comments associated with a parameterized network.
PnetDescription<- Gets the title or comments associated with a parameterized network.
PnetDetach Merges (or separates) two Pnets with common variables
PnetFindNode Finds nodes in a parameterized network.
PnetHub Returns the name of the hub net if this is a spoke net.
PnetHub<- Returns the name of the hub net if this is a spoke net.
PnetMakeStubNodes Creates (or removes) references to nodes in a network
PnetName Gets or Sets the name of a Netica network.
PnetName<- Gets or Sets the name of a Netica network.
PnetPathname Returns the path associated with a network.
PnetPathname<- Returns the path associated with a network.
PnetPnodes Returns a list of Pnodes associated with a Pnet
PnetPnodes<- Returns a list of Pnodes associated with a Pnet
PnetPriorWeight Gets the weight to be associated with the prior table during EM learning
PnetPriorWeight<- Gets the weight to be associated with the prior table during EM learning
PnetRemoveStubNodes Creates (or removes) references to nodes in a network
PnetSerialize Writes/restores network from a string.
PnetTitle Gets the title or comments associated with a parameterized network.
PnetTitle<- Gets the title or comments associated with a parameterized network.
PnetUnserialize Writes/restores network from a string.
PnetWarehouse Class '"PnetWarehouse"'
PnetWarehouse-class Class '"PnetWarehouse"'
Pnode A Parameterized Bayesian network node
Pnode-class Class '"Pnode"'
PnodeAlphas Access the combination function slope parameters for a Pnode
PnodeAlphas.default Access the combination function slope parameters for a Pnode
PnodeAlphas<- Access the combination function slope parameters for a Pnode
PnodeAlphas<-.default Access the combination function slope parameters for a Pnode
PnodeBetas Access the combination function slope parameters for a Pnode
PnodeBetas<- Access the combination function slope parameters for a Pnode
PnodeDescription Gets the title or Description associated with a parameterized node node.
PnodeDescription<- Gets the title or Description associated with a parameterized node node.
PnodeEAP Pnode Marginal Statistics
PnodeEvidence Accesses the value to which a given node has been instantiated.
PnodeEvidence<- Accesses the value to which a given node has been instantiated.
PnodeLabels Lists or changes the labels associated with a parameterize node.
PnodeLabels<- Lists or changes the labels associated with a parameterize node.
PnodeLink Accesses the link function associated with a Pnode
PnodeLink<- Accesses the link function associated with a Pnode
PnodeLinkScale Accesses the link function scale parameter associated with a Pnode
PnodeLinkScale<- Accesses the link function scale parameter associated with a Pnode
PnodeLnAlphas Access the combination function slope parameters for a Pnode
PnodeLnAlphas<- Access the combination function slope parameters for a Pnode
PnodeMargin Pnode Marginal Statistics
PnodeMedian Pnode Marginal Statistics
PnodeMode Pnode Marginal Statistics
PnodeName Gets or sets name of a parameterized node.
PnodeName<- Gets or sets name of a parameterized node.
PnodeNet Returns a list of Pnodes associated with a Pnet
PnodeNumParents Gets or sets the parents of a parameterized node.
PnodeNumStates Accessor for states of a parameterized node.
PnodeParentNames Gets or sets the parents of a parameterized node.
PnodeParents Gets or sets the parents of a parameterized node.
PnodeParents<- Gets or sets the parents of a parameterized node.
PnodeParentTvals Fetches a list of numeric variables corresponding to parent states
PnodePostWeight Fetches the posterior weight associated with a node
PnodePriorWeight Gets the weight to be associated with the prior table during EM learning
PnodePriorWeight<- Gets the weight to be associated with the prior table during EM learning
PnodeProbs Gets or sets the conditional probability table associated with a Netica node.
PnodeProbs<- Gets or sets the conditional probability table associated with a Netica node.
PnodeQ Accesses a state-wise Q-matrix associated with a Pnode
PnodeQ<- Accesses a state-wise Q-matrix associated with a Pnode
PnodeRules Accesses the combination rules for a Pnode
PnodeRules<- Accesses the combination rules for a Pnode
PnodeSD Pnode Marginal Statistics
PnodeStateBounds Functions for handling continuous nodes.
PnodeStateBounds<- Functions for handling continuous nodes.
PnodeStateDescriptions Accessors for the titles and descriptions associated with states of a parameterized node.
PnodeStateDescriptions<- Accessors for the titles and descriptions associated with states of a parameterized node.
PnodeStates Accessor for states of a parameterized node.
PnodeStates<- Accessor for states of a parameterized node.
PnodeStateTitles Accessors for the titles and descriptions associated with states of a parameterized node.
PnodeStateTitles<- Accessors for the titles and descriptions associated with states of a parameterized node.
PnodeStateValues Accesses the numeric values associated with the state of a parameterized node.
PnodeStateValues<- Accesses the numeric values associated with the state of a parameterized node.
PnodeTitle Gets the title or Description associated with a parameterized node node.
PnodeTitle<- Gets the title or Description associated with a parameterized node node.
PnodeWarehouse Class '"PnodeWarehouse"'
PnodeWarehouse-class Class '"PnodeWarehouse"'

-- Q --

Qmat2Pnet Makes or adjusts parameterized networks based on augmented Q-matrix

-- R --

RegressionGadget Shiny gadget for editing parameterized nodes (PNodes)

-- S --

show-method Class '"Statistic"'
Statistic Key functions for the Statistics class
Statistic-class Class '"Statistic"'
StatName Class '"Statistic"'
StatName-method Class '"Statistic"'

-- T --

topsort Topologically sorts the rows and columns of an Omega matrix

-- U --

unserializePnet Writes/restores network from a string.

-- W --

Warehouse A cache for Pnets or Pnodes
WarehouseCopy Copies and object in the warehouse
WarehouseCopy-method Copies and object in the warehouse
WarehouseData Manipulates the manifest for a warehouse
WarehouseFetch A cache for Pnets or Pnodes
WarehouseFree A cache for Pnets or Pnodes
WarehouseInventory Manipulates the manifest for a warehouse
WarehouseMake A cache for Pnets or Pnodes
WarehouseManifest Manipulates the manifest for a warehouse
WarehouseManifest<- Manipulates the manifest for a warehouse
WarehouseSave A cache for Pnets or Pnodes
WarehouseSupply A cache for Pnets or Pnodes
WarehouseSupply-method A cache for Pnets or Pnodes
WarehouseUnpack Writes/restores network from a string.