HydeNet: Hybrid Bayesian Networks Using R and JAGS

Facilities for easy implementation of hybrid Bayesian networks using R. Bayesian networks are directed acyclic graphs representing joint probability distributions, where each node represents a random variable and each edge represents conditionality. The full joint distribution is therefore factorized as a product of conditional densities, where each node is assumed to be independent of its non-descendents given information on its parent nodes. Since exact, closed-form algorithms are computationally burdensome for inference within hybrid networks that contain a combination of continuous and discrete nodes, particle-based approximation techniques like Markov Chain Monte Carlo are popular. We provide a user-friendly interface to constructing these networks and running inference using the 'rjags' package. Econometric analyses (maximum expected utility under competing policies, value of information) involving decision and utility nodes are also supported.

Install the latest version of this package by entering the following in R:
install.packages("HydeNet")
AuthorJarrod E. Dalton <daltonj@ccf.org> and Benjamin Nutter <benjamin.nutter@gmail.com>
Date of publication2017-01-13 15:26:14
MaintainerBenjamin Nutter <benjamin.nutter@gmail.com>
LicenseMIT + file LICENSE
Version0.10.5
https://github.com/nutterb/HydeNet,

View on CRAN

Man pages

bindPosterior: Bind Posterior Distributions

BJDealer: Blackjack Dealer Outcome Probabilities

BlackJack: Black Jack Hybrid Decision Network

BlackJackTrain: Black Jack Network Training Dataset

chain: Chain together multiple operations.

compileDecisionModel: Compile JAGS Models to Evaluate the Effect of Decisions in a...

compileJagsModel: Compile Jags Model from a Hyde Network

cpt: Compute a conditional probability table for a factor given...

expectedVariables: List Expected Parameter Names and Expected Variables Names

factorFormula: Convert Factor Levels in Formula to Numeric Values

factorRegex: Produce Regular Expressions for Extracting Factor Names and...

HydeNetSummaries: HydeNet Summary Objects

HydeNetwork: Define a Probablistic Graphical Network

Hyde-package: Hydbrid Decision Networks

HydePosterior: Posterior Distributions of a Decision Network

HydeUtilities: Hyde Network Utility Functions

inputCPTExample: Example Conditional Probability Table Resulting from the...

jagsDists: JAGS Probability Distributions.

jagsFunctions: JAGS Functions Compatible with R.

mergeDefaultPlotOpts: rdname plot.HydeNetwork

modelToNode: Convert a Model Object to a Network Node

PE: Pulmonary Embolism Dataset

plot.HydeNetwork: Plotting Utilities Probabilistic Graphical Network

policyMatrix: Construct Policy and Decision Matrices

print.cpt: Print Method for CPT objects

print.HydeNetwork: Print a HydeNetwork

print.HydePosterior: Print a Hyde Posterior Distribution Object

Resolution.cpt: Conditional Probability Table for resolution of side effects...

rewriteHydeFormula: Rewrite HydeNetwork Graph Model Formula

SE.cpt: Conditional Probability Table for side effects as a function...

setDecisionNodes: Classify Multiple Nodes as Decision or Utility Nodes

setNode: Set Node Relationships

setNodeModels: Set Node Properties Using Model Objects

setPolicyValues: Assign Default Policy Values

TranslateFormula: Translate R Formula to JAGS

update.HydeNetwork: Update Probabilistic Graphical Network

vectorProbs: Convert a vector to JAGS Probabilities

writeJagsFormula: Write the JAGS Formula for a Hyde Node

writeJagsModel: Write a Node's JAGS Model

writeNetworkModel: Generate JAGS Code for a Network's Model

Functions

\%>\% Man page
\%$\% Man page
bindPosterior Man page
BJDealer Man page
BlackJack Man page
BlackJackTrain Man page
compileDecisionModel Man page
compileJagsModel Man page
cpt Man page
cpt.formula Man page
cpt.list Man page
customNode Man page
dataframeFactors Man page
decisionOptions Man page
defaultPolicyMatrix Man page
expectedParameters Man page
expectedVariables Man page
factorFormula Man page
factor_reference Man page
factorRegex Man page
fromData Man page
fromFormula Man page
Hyde Man page
HydeNetSummaries Man page
HydeNetwork Man page
HydeNetwork.formula Man page
HydeNetwork.list Man page
Hyde-package Man page
HydePlotOptions Man page
HydePosterior Man page
HydeUtilities Man page
inputCPT Man page
inputCPTExample Man page
inputCPT.formula Man page
inputCPT.list Man page
jagsDists Man page
jagsFunctions Man page
makeFactorRef Man page
makeJagsReady Man page
mapEdges Man page
matchLevelNumber Man page
matchVars Man page
mergeCustomEdges Man page
mergeCustomNodes Man page
mergeDefaultPlotOpts Man page
modelToNode Man page
modelToNode.cpt Man page
modelToNode.default Man page
modelToNode.glm Man page
modelToNode.lm Man page
modelToNode.multinom Man page
modelToNode.survreg Man page
modelToNode.xtabs Man page
nodeFromFunction Man page
PE Man page
plotHydeNetwork Man page
plot.HydeNetwork Man page
policyMatrix Man page
policyMatrixValues Man page
polyToPow Man page
print.cpt Man page
print.HydeNetwork Man page
print.HydePosterior Man page
Resolution.cpt Man page
rewriteHydeFormula Man page
rToJags Man page
SE.cpt Man page
setDecisionNodes Man page
setNode Man page
setNodeModels Man page
setPolicyValues Man page
setUtilityNodes Man page
summary.HydeNetwork Man page
termName Man page
TranslateFormula Man page
update.HydeNetwork Man page
validateParameters Man page
vectorProbs Man page
writeJagsFormula Man page
writeJagsFormula.cpt Man page
writeJagsFormula.glm Man page
writeJagsFormula.lm Man page
writeJagsFormula.multinom Man page
writeJagsFormula.survreg Man page
writeJagsFormula.xtabs Man page
writeJagsModel Man page
writeJagsModel_dbern Man page
writeJagsModel_dcat Man page
writeJagsModel_default Man page
writeJagsModel_determ Man page
writeJagsModel_dnorm Man page
writeJagsModel_dnorm_default Man page
writeJagsModel_dpois Man page
writeNetworkModel Man page

Files

inst
inst/img
inst/img/HydeNet.png
inst/doc
inst/doc/WorkingWithHydeNetObjects.html
inst/doc/DecisionNetworks.html
inst/doc/WorkingWithHydeNetObjects.Rmd
inst/doc/GettingStartedWithHydeNet.Rmd
inst/doc/GettingStartedWithHydeNet.html
inst/doc/DecisionNetworks.R inst/doc/WorkingWithHydeNetObjects.R
inst/doc/HydeNetPlots.Rmd
inst/doc/GettingStartedWithHydeNet.R
inst/doc/HydeNetPlots.html
inst/doc/HydeNetPlots.R
inst/doc/DecisionNetworks.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test-modelToNode.R tests/testthat/test-setNodeModels.R tests/testthat/test-print.HydePosterior.R tests/testthat/test-compileJagsModel.R tests/testthat/test-policyMatrix.R tests/testthat/test-bindPosterior.R tests/testthat/test-plot.HydeNetwork.R tests/testthat/test-writeJagsModel.R tests/testthat/test-print.HydeNetwork.R tests/testthat/test_compileDecisionModel.R tests/testthat/test-HydeUtilities.R tests/testthat/test-HydePosterior.R tests/testthat/test-HydeNetwork.R tests/testthat/test-setUtilityNodes.R tests/testthat/test-expectedVariables.R tests/testthat/test-update.HydeNetwork.R tests/testthat/test-setNode.R tests/testthat/test-writeNetworkModel.R tests/testthat/test-rToJags.R tests/testthat/test-cpt.R tests/testthat/test-factorFormula.R tests/testthat/test-writeJagsFormula.R
NAMESPACE
NEWS
data
data/PE.RData
data/BJDealer.RData
data/BlackJack.RData
data/jagsDists.RData
data/jagsFunctions.RData
data/BlackJackTrain.RData
data/inputCPTExample.RData
data/SE.cpt.RData
data/Resolution.cpt.RData
R
R/print.HydeNetwork.R R/factorFormula.R R/plot.HydeNetwork.R R/HydeUtilities.R R/writeJagsModel.R R/setNodeModels.R R/expectedVariables.R R/setPolicyValues.R R/rewriteHydeFormula.R R/PolicyMatrix.R
R/sysdata.rda
R/setDecisionNodes.R R/summary.HydeNetwork.R R/print.HydePosterior.R R/cpt.R R/data.R R/inputCPT.R R/modelToNode.R R/bindPosterior.R R/rToJags.R R/factorRegex.R R/setNode.R R/writeNetworkModel.R R/Hyde-package.R R/chain.R R/vectorProbs.R R/plot_nondeterm_only.R R/update.HydeNetwork.R R/writeJagsFormula.R R/HydePosterior.R R/HydeNetwork.R R/zzz.R R/compileJagsModel.R R/print.cpt.R R/compileDecisionModel.R
vignettes
vignettes/vignette_images
vignettes/vignette_images/HydeNetPlots7.jpeg
vignettes/vignette_images/HydeNetPlots9.jpeg
vignettes/vignette_images/HydeNetPlots5.jpeg
vignettes/vignette_images/HydeNetPlots8.jpeg
vignettes/vignette_images/WorkingWithHydeNetObjects2.jpeg
vignettes/vignette_images/HydeNetPlots1.jpeg
vignettes/vignette_images/HydeNetPlots3.jpeg
vignettes/vignette_images/DecisionNetworks2.jpeg
vignettes/vignette_images/GettingStarted1.jpeg
vignettes/vignette_images/DecisionNetworks1.jpeg
vignettes/vignette_images/HydeNetPlots6.jpeg
vignettes/vignette_images/HydeNetPlots2.jpeg
vignettes/vignette_images/WorkingWithHydeNetObjects3.jpeg
vignettes/vignette_images/HydeNetPlots4.jpeg
vignettes/vignette_images/WorkingWithHydeNetObjects1.jpeg
vignettes/WorkingWithHydeNetObjects.Rmd
vignettes/GettingStartedWithHydeNet.Rmd
vignettes/HydeNetPlots.Rmd
vignettes/DecisionNetworks.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/setPolicyValues.Rd man/SE.cpt.Rd man/TranslateFormula.Rd man/BlackJack.Rd man/compileJagsModel.Rd man/chain.Rd man/print.HydePosterior.Rd man/writeJagsFormula.Rd man/plot.HydeNetwork.Rd man/BlackJackTrain.Rd man/vectorProbs.Rd man/setDecisionNodes.Rd man/writeNetworkModel.Rd man/modelToNode.Rd man/Resolution.cpt.Rd man/Hyde-package.Rd man/writeJagsModel.Rd man/rewriteHydeFormula.Rd man/HydePosterior.Rd man/cpt.Rd man/factorRegex.Rd man/print.cpt.Rd man/print.HydeNetwork.Rd man/setNodeModels.Rd man/BJDealer.Rd man/PE.Rd man/policyMatrix.Rd man/HydeNetSummaries.Rd man/expectedVariables.Rd man/jagsDists.Rd man/factorFormula.Rd man/HydeUtilities.Rd man/inputCPTExample.Rd man/jagsFunctions.Rd man/update.HydeNetwork.Rd man/HydeNetwork.Rd man/setNode.Rd man/mergeDefaultPlotOpts.Rd man/bindPosterior.Rd man/compileDecisionModel.Rd
LICENSE

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