catnet: Categorical Bayesian Network Inference

Structure learning and parameter estimation of discrete Bayesian networks using likelihood-based criteria. Exhaustive search for fixed node orders and stochastic search of optimal orders via simulated annealing algorithm are implemented.

Install the latest version of this package by entering the following in R:
install.packages("catnet")
AuthorNikolay Balov, Peter Salzman
Date of publication2016-06-12 19:03:05
MaintainerNikolay Balov <nhbalov@gmail.com>
LicenseGPL (>= 2)
Version1.15.0

View on CRAN

Man pages

alarm: The ALARM network

breast: Breast cancer data

catnet-package: catnet: Categorical Bayesian network inference

catNetwork-class: Class "catNetwork"

catNetworkDistance-class: Class "catNetworkDistance"

catNetworkEvaluate-class: Class "catNetworkEvaluate"

classification: Classification demonstration

cnCatnetFromEdges: catNetwork from Edges

cnCatnetFromSif: Categorical Network from Simple Interaction File (SIF) and...

cnCluster: Network Clustering

cnCompare: Network Comparison

cnComplexity: Network Complexity

cnDiscretize: Data Categorization

cnDot: Network Description File

cnEdges: Network Edges

cnEntropy: Pairwise Node Entropy

cnFind: Find Network by Complexity

cnFindAIC: Find Network by AIC

cnFindBIC: Find Network by BIC

cnLoglik: Sample Log-likelihood

cnMatEdges: Network Edge Matrix

cnMatParents: Network Parent Matrix

cnNew: New catNetwork

cnNodeLoglik: Node Log-likelihood

cnNodeMarginalProb: Probability Calculations

cnNodes: Netwok Nodes

cnNodeSampleLoglik: Node Log-likelihood

cnNumNodes: Network Size

cnOrder: Network Node Order

cnParents: Network Parent Structure

cnParHist: Parenthood Histogram

cnPearsonTest: Goodness of Fit Test

cnPlot: Plot Network

cnPredict: Prediction

cnProb: Conditional Probability Structure

cnRandomCatnet: Random Network

cnReorderNodes: Reorder Network Nodes

cnSamples: Samples from Network

cnSearchHist: Parent Histogram Matrix

cnSearchOrder: Network Search for Given Node Order

cnSearchSA: Stochastic Network Search

cnSetProb: Set Probability from Data

cnSetSeed: Random Generator Seed

cnSubNetwork: Sub-Network

CPDAG-class: Class CPDAG

dag2cpdag: Complete Network Representation

isDAG: Check Direct Acyclic Graph (DAG) Condition

novartis: Novartis multi-tissue data

Functions

alarmnet Man page
boston Man page
breast Man page
catnet Man page
catnet-package Man page
catNetwork Man page
catNetwork-class Man page
catNetworkDistance Man page
catNetworkDistance-class Man page
catNetworkEvaluate Man page
catNetworkEvaluate-class Man page
cnCatnetFromBif Man page
cnCatnetFromBif,character-method Man page
cnCatnetFromEdges Man page
cnCatnetFromEdges,character-method Man page
cnCatnetFromSif Man page
cnCatnetFromSif,character-method Man page
cnCluster Man page
cnCluster,catNetwork-method Man page
cnClusterMI Man page
cnClusterSep Man page
cnClusterSep,catNetwork-method Man page
cnCompare Man page
cnCompare,catNetwork,catNetworkEvaluate-method Man page
cnCompare,catNetwork,catNetwork-method Man page
cnCompare,catNetwork,list-method Man page
cnCompare,catNetwork,matrix-method Man page
cnComplexity Man page
cnComplexity,catNetwork,integer-method Man page
cnComplexity,catNetwork-method Man page
cnCondProb Man page
cnCondProb,catNetwork-method Man page
cnDiscretize Man page
cnDot Man page
cnDot,catNetwork,character-method Man page
cnDot,catNetwork,character-method,character-method Man page
cnDot,catNetwork-method Man page
cnDot,list,character-method Man page
cnDot,list,character-method,character-method Man page
cnDot,list-method Man page
cnDot,matrix,character-method Man page
cnDot,matrix,character-method,character-method Man page
cnDot,matrix-method Man page
cnEdgeDistanceKL Man page
cnEdgeDistancePearson Man page
cnEdges Man page
cnEdges,catNetwork,character-method Man page
cnEdges,catNetwork,missing-method Man page
cnEdges,catNetwork,vector-method Man page
cnEntropy Man page
cnEntropyOrder Man page
cnFind Man page
cnFindAIC Man page
cnFindAIC,catNetworkEvaluate-method Man page
cnFindAIC,list-method Man page
cnFindBIC Man page
cnFindBIC,catNetworkEvaluate-method Man page
cnFindBIC,list-method Man page
cnFind,catNetworkEvaluate-method Man page
cnFindKL Man page
cnFindKL,catNetworkEvaluate-method Man page
cnFindKL,list-method Man page
cnFind,list-method Man page
cnJointProb Man page
cnJointProb,catNetwork-method Man page
cnKLComplexity Man page
cnKLComplexity,catNetwork-method Man page
cnKLComplexity,catNetwork-method,integer-method Man page
cnLoglik Man page
cnLoglik,catNetwork-method Man page
cnMatEdges Man page
cnMatEdges,catNetwork-method Man page
cnMatParents Man page
cnMatParents,catNetwork,missing-method Man page
cnMatParents,catNetwork,vector-method Man page
cnNew Man page
cnNodeLoglik Man page
cnNodeLoglik,catNetwork-method Man page
cnNodeMarginalProb Man page
cnNodeMarginalProb,catNetwork-method Man page
cnNodes Man page
cnNodeSampleLoglik Man page
cnNodeSampleProb Man page
cnNodes,catNetwork,missing-method Man page
cnNodes,catNetwork,vector-method Man page
cnNumNodes Man page
cnNumNodes,catNetwork-method Man page
cnOrder Man page
cnOrder,catNetwork-method Man page
cnOrder,list-method Man page
cnParents Man page
cnParents,catNetwork,character-method Man page
cnParents,catNetwork,missing-method Man page
cnParents,catNetwork,vector-method Man page
cnParHist Man page
cnParHist,catNetworkEvaluate-method Man page
cnParHist,list-method Man page
cnPearsonTest Man page
cnPearsonTest,catNetwork-method Man page
cnPlot Man page
cnPlot,catNetworkEvaluate-method Man page
cnPlot,catNetwork-method Man page
cnPlotProb Man page
cnPlotProb,catNetwork-method Man page
cnPredict Man page
cnPredict,catNetwork-method Man page
cnProb Man page
cnProb,catNetwork-method Man page
cnRandomCatnet Man page
cnReorderNodes Man page
cnReorderNodes,catNetwork,vector-method Man page
cnSamples Man page
cnSamples,catNetwork-method Man page
cnSearchHist Man page
cnSearchOrder Man page
cnSearchSA Man page
cnSetProb Man page
cnSetProb,catNetwork-method Man page
cnSetProb,catSampleNetwork-method Man page
cnSetSeed Man page
cnSubNetwork Man page
cnSubNetwork,catNetwork-method Man page
cnSubNetwork,catNetwork,vector,logical-method Man page
CPDAG Man page
CPDAG-class Man page
cvKfold Man page
dag2cpdag Man page
dag2cpdag,catNetwork-method Man page
diabetes Man page
diabetesLoad Man page
isDAG Man page
lungLoad Man page
novartis Man page

Files

inst
inst/doc
inst/doc/catnet.pdf
inst/doc/catnet.Rnw
inst/doc/catnet.R
src
src/rcatnet_sa.h
src/cache.h
src/pthread.cpp
src/ccnInit.c
src/rcatnet.h
src/rcatnet_search.h
src/catnet_rexport.cpp
src/catnet_search2.h
src/problist.h
src/thread.h
src/rcatnet_search.cpp
src/rcatnet_sa.cpp
src/utils.h
src/utils.cpp
src/catnet_search.h
src/catnet_rexport.h
src/search_params.h
src/catnet_class.h
src/rcatnet.cpp
src/catnet_entropy.cpp
src/rcatnet_hist.cpp
src/cache.cpp
src/rcatnet_hist.h
NAMESPACE
demo
demo/lung.r demo/breast.r demo/diabetesLoad.r demo/diabetes.r demo/lungLoad.r demo/novartis.r
demo/00Index
demo/test.r demo/cvKfold.r demo/dirprob.r demo/alarm.r
data
data/novartis.rda
data/breast.rda
data/alarmnet.rda
R
R/catnet.cluster.R R/catnet.categor.R R/catnet.probs.R R/catnet.chisq.R R/catnet.bif.R R/catnet.predict.R R/catnet.def.R R/catnet.dags.R R/catnet.find.R R/catnet.plot.R R/catnet.histo.R R/catnet.quant.R R/catnet.dist.R R/catnet.entropy.R R/catnet.class.R R/catnet.joint.prob.R R/graph2catnet.R R/catnet.marginal.prob.R R/catnet.samples.R R/zzz.R R/catnet.pathway.R R/catnet.search.R R/catnet.loglik.R
vignettes
vignettes/catnet.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/cnCompare.Rd man/cnNodes.Rd man/cnFindAIC.Rd man/cnNumNodes.Rd man/cnDiscretize.Rd man/cnComplexity.Rd man/catNetworkDistance-class.Rd man/cnMatEdges.Rd man/cnSubNetwork.Rd man/cnPredict.Rd man/breast.Rd man/cnNodeSampleLoglik.Rd man/cnEntropy.Rd man/cnNodeMarginalProb.Rd man/cnMatParents.Rd man/dag2cpdag.Rd man/catNetwork-class.Rd man/cnEdges.Rd man/cnNew.Rd man/cnSamples.Rd man/cnSearchSA.Rd man/cnCluster.Rd man/cnProb.Rd man/cnLoglik.Rd man/classification.Rd man/cnSetProb.Rd man/CPDAG-class.Rd man/cnNodeLoglik.Rd man/cnSearchHist.Rd man/cnPearsonTest.Rd man/isDAG.Rd man/cnOrder.Rd man/novartis.Rd man/cnFind.Rd man/cnParHist.Rd man/cnDot.Rd man/cnCatnetFromEdges.Rd man/catNetworkEvaluate-class.Rd man/cnFindBIC.Rd man/cnSearchOrder.Rd man/cnRandomCatnet.Rd man/cnParents.Rd man/cnSetSeed.Rd man/cnReorderNodes.Rd man/cnCatnetFromSif.Rd man/cnPlot.Rd man/catnet-package.Rd man/alarm.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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