Files in rjbgoudie/structmcmc
Structural inference for Bayesian Networks and Variable Selection.
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/constraints.R
R/cross-validation.R
R/diagnostics.R
R/graph-ops.R
R/mcmc-bigflips.R
R/mcmc-gibbs.R
R/mcmc-grzeg.R
R/mcmc-mh.R
R/mcmc-mj.R
R/mcmc-order.R
R/mcmc-pt.R
R/mcmc.R
R/param-bayes.R
R/param-ml.R
R/parents-table.R
R/post-exact.R
R/post-mcmc.R
R/post.R
R/priors.R
R/query.R
R/routes.R
R/score-bic.R
R/score-multdir.R
R/score-normal.R
R/score.R
R/structmcmc.R
R/utils.R
R/utils.rjbg.R
README.md
data/structmcmc.internal.nets2.RData
data/structmcmc.internal.nets3.RData
data/structmcmc.internal.nets4.RData
data/structmcmc.internal.nets5.RData
doc/structmcmc.Rnw
inst/CITATION
inst/tests/data/diagnostics-plot-control/.!76775!control-1-copy.pdf
inst/tests/data/diagnostics-plot-control/.!76776!control-1.pdf
inst/tests/data/diagnostics-plot-control/.!76777!control-1.png
inst/tests/data/diagnostics-plot-control/.!80840!control-1-copy.pdf
inst/tests/data/diagnostics-plot-control/.!80841!control-1.pdf
inst/tests/data/diagnostics-plot-control/.!80842!control-1.png
inst/tests/data/diagnostics-plot-control/.!84394!control-1-copy.pdf
inst/tests/data/diagnostics-plot-control/.!84395!control-1.pdf
inst/tests/data/diagnostics-plot-control/.!84396!control-1.png
inst/tests/data/diagnostics-plot-control/control-1-copy.pdf
inst/tests/data/diagnostics-plot-control/control-1.pdf
inst/tests/data/diagnostics-plot-control/control-1.png
inst/tests/data/diagnostics-plot-control/control-log.xml
inst/tests/data/diagnostics-plot-test/.!76796!test-1-pdf+control-1-pdf.png
inst/tests/data/diagnostics-plot-test/.!76797!test-1.pdf
inst/tests/data/diagnostics-plot-test/.!76798!test-1.png
inst/tests/data/diagnostics-plot-test/.!80846!test-1-pdf+control-1-pdf.png
inst/tests/data/diagnostics-plot-test/.!80847!test-1.pdf
inst/tests/data/diagnostics-plot-test/.!80848!test-1.png
inst/tests/data/diagnostics-plot-test/.!84406!test-1-pdf+control-1-pdf.png
inst/tests/data/diagnostics-plot-test/.!84407!test-1.pdf
inst/tests/data/diagnostics-plot-test/.!84408!test-1.png
inst/tests/data/diagnostics-plot-test/test+control-compareExprLog.xml
inst/tests/data/diagnostics-plot-test/test-1-pdf+control-1-pdf.diff
inst/tests/data/diagnostics-plot-test/test-1-pdf+control-1-pdf.png
inst/tests/data/diagnostics-plot-test/test-1.pdf
inst/tests/data/diagnostics-plot-test/test-1.png
inst/tests/data/diagnostics-plot-test/test-log.xml
inst/tests/data/structmcmc-plot-control/.!76820!control-1-copy.pdf
inst/tests/data/structmcmc-plot-control/.!76821!control-1.pdf
inst/tests/data/structmcmc-plot-control/.!76822!control-1.png
inst/tests/data/structmcmc-plot-control/.!76823!control-2-copy.pdf
inst/tests/data/structmcmc-plot-control/.!76824!control-2.pdf
inst/tests/data/structmcmc-plot-control/.!76825!control-2.png
inst/tests/data/structmcmc-plot-control/.!80850!control-1-copy.pdf
inst/tests/data/structmcmc-plot-control/.!80851!control-1.pdf
inst/tests/data/structmcmc-plot-control/.!80852!control-1.png
inst/tests/data/structmcmc-plot-control/.!80853!control-2-copy.pdf
inst/tests/data/structmcmc-plot-control/.!80854!control-2.pdf
inst/tests/data/structmcmc-plot-control/.!80855!control-2.png
inst/tests/data/structmcmc-plot-control/.!84417!control-1-copy.pdf
inst/tests/data/structmcmc-plot-control/.!84418!control-1.pdf
inst/tests/data/structmcmc-plot-control/.!84419!control-1.png
inst/tests/data/structmcmc-plot-control/.!84420!control-2-copy.pdf
inst/tests/data/structmcmc-plot-control/.!84421!control-2.pdf
inst/tests/data/structmcmc-plot-control/.!84422!control-2.png
inst/tests/data/structmcmc-plot-control/control-1-copy.pdf
inst/tests/data/structmcmc-plot-control/control-1.pdf
inst/tests/data/structmcmc-plot-control/control-1.png
inst/tests/data/structmcmc-plot-control/control-2-copy.pdf
inst/tests/data/structmcmc-plot-control/control-2.pdf
inst/tests/data/structmcmc-plot-control/control-2.png
inst/tests/data/structmcmc-plot-control/control-log.xml
inst/tests/data/structmcmc-plot-test/.!76859!test-1-pdf+control-1-pdf.png
inst/tests/data/structmcmc-plot-test/.!76860!test-1-png+control-1-png.png
inst/tests/data/structmcmc-plot-test/.!76861!test-1.pdf
inst/tests/data/structmcmc-plot-test/.!76862!test-1.png
inst/tests/data/structmcmc-plot-test/.!76866!test-2-pdf+control-2-pdf.png
inst/tests/data/structmcmc-plot-test/.!76867!test-2-png+control-2-png.png
inst/tests/data/structmcmc-plot-test/.!76868!test-2.pdf
inst/tests/data/structmcmc-plot-test/.!76869!test-2.png
inst/tests/data/structmcmc-plot-test/.!80859!test-1-pdf+control-1-pdf.png
inst/tests/data/structmcmc-plot-test/.!80860!test-1-png+control-1-png.png
inst/tests/data/structmcmc-plot-test/.!80861!test-1.pdf
inst/tests/data/structmcmc-plot-test/.!80862!test-1.png
inst/tests/data/structmcmc-plot-test/.!80864!test-2-pdf+control-2-pdf.png
inst/tests/data/structmcmc-plot-test/.!80865!test-2-png+control-2-png.png
inst/tests/data/structmcmc-plot-test/.!80866!test-2.pdf
inst/tests/data/structmcmc-plot-test/.!80867!test-2.png
inst/tests/data/structmcmc-plot-test/.!84437!test-1-pdf+control-1-pdf.png
inst/tests/data/structmcmc-plot-test/.!84438!test-1-png+control-1-png.png
inst/tests/data/structmcmc-plot-test/.!84439!test-1.pdf
inst/tests/data/structmcmc-plot-test/.!84440!test-1.png
inst/tests/data/structmcmc-plot-test/.!84443!test-2-pdf+control-2-pdf.png
inst/tests/data/structmcmc-plot-test/.!84444!test-2-png+control-2-png.png
inst/tests/data/structmcmc-plot-test/.!84445!test-2.pdf
inst/tests/data/structmcmc-plot-test/.!84446!test-2.png
inst/tests/data/structmcmc-plot-test/test+control-compareExprLog.xml
inst/tests/data/structmcmc-plot-test/test-1-pdf+control-1-pdf.diff
inst/tests/data/structmcmc-plot-test/test-1-pdf+control-1-pdf.png
inst/tests/data/structmcmc-plot-test/test-1-png+control-1-png.png
inst/tests/data/structmcmc-plot-test/test-1.pdf
inst/tests/data/structmcmc-plot-test/test-1.png
inst/tests/data/structmcmc-plot-test/test-2-pdf+control-2-pdf.diff
inst/tests/data/structmcmc-plot-test/test-2-pdf+control-2-pdf.png
inst/tests/data/structmcmc-plot-test/test-2-png+control-2-png.png
inst/tests/data/structmcmc-plot-test/test-2.pdf
inst/tests/data/structmcmc-plot-test/test-2.png
inst/tests/data/structmcmc-plot-test/test-log.xml
inst/tests/expectations.R
inst/tests/helper-expectations.R
inst/tests/main.R
inst/tests/test-bayes.R
inst/tests/test-bic.R
inst/tests/test-bvsnet.R
inst/tests/test-cross-validation.R
inst/tests/test-diagnostics.R
inst/tests/test-fast-grzeg.R
inst/tests/test-fast-mcmc-bf.R
inst/tests/test-fast-mcmc-gibbs.R
inst/tests/test-fast-mcmc-indep.R
inst/tests/test-fast-mcmc-order.R
inst/tests/test-fast-mcmc.R
inst/tests/test-fast-ptmcmc.R
inst/tests/test-grain.R
inst/tests/test-graphops.R
inst/tests/test-incrementalNetworkScore.R
inst/tests/test-mcmc-normal.R
inst/tests/test-mj-misc.R
inst/tests/test-ml.R
inst/tests/test-post-exact.R
inst/tests/test-post-mcmc.R
inst/tests/test-post.R
inst/tests/test-priors.R
inst/tests/test-score-normal.R
inst/tests/test-score.mult.dir.offline.R
inst/tests/test-shd-plot.R
inst/tests/test-statistics.R
inst/tests/test-x-slow-mcmc-bf.R
inst/tests/test-x-slow-mcmc-gibbs.R
inst/tests/test-x-slow-mcmc-mj.R
inst/tests/test-x-slow-mcmc.R
man/BNGibbsSampler.Rd
man/BNOrderSampler.Rd
man/BNSampler.Rd
man/BNSamplerBigFlips.Rd
man/BNSamplerGrzeg.Rd
man/BNSamplerMJ.Rd
man/BNSamplerPT.Rd
man/adjustPredictions.Rd
man/allBannedExceptPPNotBannedIfNotRequired.Rd
man/allDescendants.Rd
man/allNonDescendants.Rd
man/as.data.frame.epmx.Rd
man/as.grain.Rd
man/as.roc.Rd
man/as.roc.ep.Rd
man/as.roc.ep.list.Rd
man/as.roc.parental.Rd
man/as.roc.parental.list.Rd
man/auroc.Rd
man/auroc.ep.Rd
man/auroc.ep.list.Rd
man/bayes.Rd
man/bayes.bn.Rd
man/bf.Rd
man/bf.bnpostmcmc.Rd
man/bnpost.Rd
man/bnpostmcmc.Rd
man/bnpostmcmc.list.Rd
man/burnin.Rd
man/burnin.sampler.Rd
man/checkForNonDuplicated.Rd
man/conductance.Rd
man/convertEPMatrixToColumns.Rd
man/cumep.Rd
man/cumep.bnpostmcmc.list.Rd
man/cumep.samplers.Rd
man/cummean.Rd
man/cummean.matrix.Rd
man/cumtvd.Rd
man/cumtvd.list.Rd
man/dagGivenOrder.Rd
man/decim.Rd
man/defaultBanned.Rd
man/dotplot.ep.Rd
man/dotplot.ep.list.Rd
man/dotplot.gp.Rd
man/dotplot.gp.list.Rd
man/draw.Rd
man/drawPT.Rd
man/drawSamplesByStepCount.Rd
man/drawSamplesByTime.Rd
man/eachChangesChoicesForRequired.Rd
man/edgeIsFlippable.Rd
man/eht.Rd
man/eht.bnpost.Rd
man/enforceForbiddenConstraint.Rd
man/entropy.Rd
man/entropy.bnpost.Rd
man/enumerateParentsTable.Rd
man/enumerateParentsTableNode.Rd
man/ep.Rd
man/ep.bnpost.Rd
man/ep.bnpostmcmc.Rd
man/ep.bnpostmcmc.list.Rd
man/ep.list.Rd
man/ep.parental.contingency.Rd
man/ep.parental.list.Rd
man/ep.sampler.Rd
man/ep.table.Rd
man/epmx.Rd
man/epmx.bnpostmcmc.Rd
man/epmx.bnpostmcmc.list.Rd
man/epmx.sampler.Rd
man/epmx.samplers.Rd
man/epmxPlotInternal.Rd
man/eval.prior.Rd
man/exactposterior.Rd
man/fastid.Rd
man/fdfAsInt.Rd
man/gelman.Rd
man/gelman.samplers.Rd
man/getAllConsistentWithDAG.Rd
man/getBannedFromConstraint.Rd
man/getNewGraph.Rd
man/getNijkCounts.Rd
man/getPossibleParents.Rd
man/getRequiredFromConstraint.Rd
man/getRowsThatContain.Rd
man/gp.Rd
man/gp.bnpost.Rd
man/gp.bnpostmcmc.Rd
man/gp.bnpostmcmc.list.Rd
man/gp.list.Rd
man/gp.sampler.Rd
man/graphProbGivenOrder.Rd
man/hp.Rd
man/intAsFDF.Rd
man/internal-onload.Rd
man/intersect2.Rd
man/intersection.Rd
man/is.valid.hyp.Rd
man/is.valid.localPriors.Rd
man/is.valid.prior.Rd
man/isConsistentWithOrder.Rd
man/kronecker_delta.Rd
man/length.bnpostmcmc.Rd
man/length.sampler.Rd
man/levelplot.bnpostmcmc.Rd
man/levelplot.ep.Rd
man/levelplot.ep.list.Rd
man/localLogScoreMultDir.Rd
man/localLogScoreNormal.Rd
man/localPartitionFunction.Rd
man/logNumMHNeighbours.Rd
man/logOrderLikelihood.Rd
man/logScoreMultDir.Rd
man/logScoreMultDir.bn.Rd
man/logScoreMultDir.bn.list.Rd
man/logScoreMultDir.bnpostmcmc.Rd
man/logScoreMultDirFUN.Rd
man/logScoreMultDirIncremental.Rd
man/logScoreMultDirOffline.Rd
man/logScoreMultDirPrepare.Rd
man/logScoreNormal.Rd
man/logScoreNormal.bn.Rd
man/logScoreNormal.bn.list.Rd
man/logScoreNormalFUN.Rd
man/logScoreNormalIncremental.Rd
man/logScoreNormalOffline.Rd
man/logScoreNormalPrepare.Rd
man/logsumexp.Rd
man/makeRowPredictions.Rd
man/map.Rd
man/map.bnpost.Rd
man/map.bnpostmcmc.Rd
man/map.sampler.Rd
man/marginalGivenIntervention.Rd
man/marginalGivenOthers.Rd
man/matrix2.Rd
man/mcmcposterior.Rd
man/ml.Rd
man/ml.bn.Rd
man/mukherjeeBioinformaticsPrior.Rd
man/mwep.Rd
man/mwep.bnpostmcmc.list.Rd
man/mwep.samplers.Rd
man/mwmean.Rd
man/mwmean.matrix.Rd
man/new_queue.Rd
man/new_stack.Rd
man/nonDescendants.Rd
man/numberDAGsGivenOrder.Rd
man/nunique.Rd
man/options.grid.Rd
man/orderFlipOperator.Rd
man/parentalFromEPThreshold.Rd
man/parentalToCPDAG.Rd
man/plot.bnpostmcmc.Rd
man/plotTape.Rd
man/posterior.Rd
man/predict.bn.Rd
man/predictGivenNoParents.Rd
man/predictGivenParents.Rd
man/predictModelAverageNode.Rd
man/predictNode.Rd
man/prepareGPPlot.Rd
man/prepareLevelPlot.Rd
man/print.sampler.Rd
man/priorGraph.Rd
man/priorUniform.Rd
man/queryFinding.Rd
man/removeDuplicates.Rd
man/requireSomethingFromEachParent.Rd
man/residsNormal.Rd
man/residsNormalNode.Rd
man/residualsMultDir.Rd
man/residualsMultDirNode.Rd
man/rocplot.Rd
man/routesAddEdges.Rd
man/routesRemoveEdges.Rd
man/rowProbabiltiesToResponse.Rd
man/rowSums2.Rd
man/sampleNode.Rd
man/samplePair.Rd
man/samplePair2.Rd
man/sampleQuadruple.Rd
man/sampleQuintuple.Rd
man/sampleTriple.Rd
man/samplers.Rd
man/satisfiesConstraint.Rd
man/scoreBIC.Rd
man/scoreParents.Rd
man/scoreParentsTable.Rd
man/scoreParentsTableNode.Rd
man/setdiff3.Rd
man/setupConstraint.Rd
man/shrinkep.Rd
man/splom.bnpostmcmc.list.Rd
man/splom.epmx.Rd
man/square_error.Rd
man/statistics.Rd
man/statistics.sampler.Rd
man/steps.Rd
man/steps.sampler.Rd
man/structmcmc.Rd
man/summary.gp.Rd
man/summary.sampler.Rd
man/top.Rd
man/top.bnpost.Rd
man/top.bnpostmcmc.Rd
man/top.sampler.Rd
man/topScoringGraph.Rd
man/tp.Rd
man/tp.bnpost.Rd
man/transposeEdgeIsAddable.Rd
man/transposeEdgeIsRemovable.Rd
man/transposeEdgeIsTogglable.Rd
man/validStartEnd.Rd
man/whichGraphsNotNeighbours.Rd
man/whichNum.Rd
man/whichParentSetRows.Rd
man/xyplot.cumtvd.Rd
man/xyplot.cumtvd.list.Rd
man/xyplot.epmx.Rd
man/xyplot.gp.Rd
man/xyplot.gp.list.Rd
src/structmcmc.c
tests/test-all.R
