Package: abn 3.1.13

Matteo Delucchi

abn: Modelling Multivariate Data with Additive Bayesian Networks

The 'abn' R package facilitates Bayesian network analysis, a probabilistic graphical model that derives from empirical data a directed acyclic graph (DAG). This DAG describes the dependency structure between random variables. The R package 'abn' provides routines to help determine optimal Bayesian network models for a given data set. These models are used to identify statistical dependencies in messy, complex data. Their additive formulation is equivalent to multivariate generalised linear modelling, including mixed models with independent and identically distributed (iid) random effects. The core functionality of the 'abn' package revolves around model selection, also known as structure discovery. It supports both exact and heuristic structure learning algorithms and does not restrict the data distribution of parent-child combinations, providing flexibility in model creation and analysis. The 'abn' package uses Laplace approximations for metric estimation and includes wrappers to the 'INLA' package. It also employs 'JAGS' for data simulation purposes. For more resources and information, visit the 'abn' website.

Authors:Matteo Delucchi [aut, cre], Reinhard Furrer [aut], Gilles Kratzer [aut], Fraser Iain Lewis [aut], Jonas I. Liechti [ctb], Marta Pittavino [ctb], Kalina Cherneva [ctb]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
abn/json (API)

# Install 'abn' in R:
install.packages('abn', repos = c('https://furrer-lab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/furrer-lab/abn/issues

Pkgdown/docs site:https://r-bayesian-networks.org

Uses libs:
  • gsl– GNU Scientific Library (GSL)
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
  • jags– Just Another Gibbs Sampler for Bayesian MCMC

On CRAN:

Conda:

bayesian-networkbinomialcategorical-datagaussiangrouped-datasetsmixed-effectsmultinomialmultivariatepoissonstructure-learninggslopenblascppopenmpjags

6.58 score 10 stars 102 scripts 1.7k downloads 143 exports 79 dependencies

Last updated from:1003a631a9. Checks:9 WARNING, 5 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING720
linux-devel-x86_64ERROR836
source / vignettesERROR386
linux-release-arm64ERROR666
linux-release-x86_64WARNING654
macos-release-arm64WARNING679
macos-release-x86_64WARNING1146
macos-oldrel-arm64WARNING649
macos-oldrel-x86_64WARNING1067
windows-devel-arm64ERROR571
windows-devel-x86_64WARNING342
windows-release-arm64ERROR416
windows-release-x86_64WARNING309
windows-oldrel-x86_64WARNING465
wasm-releaseOK186

Exports:abn.versionAIC.abnFitas.data.frame.abnDagbern_bugsbern_bugsGroupBIC.abnFitbuild.controlbuildcachematrixbuildScoreCachebuildScoreCache.bayesbuildScoreCache.mlecalc.node.inla.glmcalc.node.inla.glmmcategorical_bugscategorical_bugsGroupcheck_evidencecheck.valid.buildControlscheck.valid.dagcheck.valid.datacheck.valid.fitControlscheck.valid.groupscheck.valid.parentscheck.which.valid.nodescheckforcyclescoef.abnFitcompareDagcompareEGcreateAbnDagdiscretizationentropyDataessentialGrapheval.across.gridexpitexpit_cppexport_abnFitexport_abnFit_bayesexport_abnFit_mleexport_abnFit_mle_arcsexport_abnFit_mle_grouped_nodesexport_abnFit_mle_nodesexport_to_jsonextract_parameters_by_distributionextract_parameters_mixed_effectsextract_states_from_datafamily.abnFitfind_childrenfind_MBfind_parentsfind.next.left.xfind.next.right.xfit_single_nodefit.controlfitAbnfitabn_marginalsfitAbn.bayesfitAbn.mleforLoopContentforLoopContentBayesforLoopContentFitBayesformula_abngauss_bugsgauss_bugsGroupget_link_functionget.ind.quantilesget.quantilesget.var.typesgetmarginalsgetMargsINLAgetModeVectorgetMSEfromModesinfoDagirls_binomial_cpp_fastirls_binomial_cpp_fast_brirls_gaussian_cpp_fastirls_poisson_cpp_fastlinkStrengthlogitlogit_cppLogL_binomialLogL_gaussianlogL_multinomiallogL_multinomial_vectorizedLogL_poissonlogLik.abnFitmakebugsmakebugsGroupmbmi_cppmiDatamodes2coefsmostProbablemostprobable_Cnobs.abnFitoddsorplot.abnDagplot.abnFitplot.abnHeuristicplot.abnHillClimberplot.abnMostprobableplotAbnpois_bugspois_bugsGrouppredict_node_from_childrenpredict_node_from_children_binomialpredict_node_from_children_gaussianpredict_node_from_children_multinomialpredict_node_from_children_poissonpredict_node_from_parentpredict_node_from_parent_binomialpredict_node_from_parent_gaussianpredict_node_from_parent_multinomialpredict_node_from_parent_poissonpredict_rootpredict.abnFitpredictAbnprint.abnCacheprint.abnDagprint.abnFitprint.abnHeuristicprint.abnHillClimberprint.abnMostprobableprint.abnPredictionprior_binomialprior_gaussianprior_poissonrank_cppregressionLoopscoreContributionsearchHeuristicsearchhillsearchHillClimbersimulateAbnsimulateDagskewnessstd.area.under.gridstrsplitssummary.abnDagsummary.abnFitsummary.abnMostprobabletidy.cachetoGraphvizvalidate_dists

Dependencies:backportsBiocGenericsbootbroomclicodacodetoolscolorspacecowplotcpp11data.tableDerivdoBydoParalleldplyrfarverforeachforecastfracdiffgenericsggplot2glmmTMBgluegraphgtableigraphisobanditeratorsjsonlitelabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixmclogitmemiscmgcvminqamodelrnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpurrrR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasRgraphvizrjagsrlangRTMBS7sandwichscalesstringistringrtibbletidyrtidyselecttimeDateTMBurcautf8vctrsviridisLitewithryamlzoo

Readme and manuals

Help Manual

Help pageTopics
Print AIC of objects of class 'abnFit'AIC.abnFit
Transform the adjacency matrix representation of a DAG to a data.frame with columns "from" and "to" representing directed edges.as.data.frame.abnDag
Print BIC of objects of class 'abnFit'BIC.abnFit
Control the iterations in 'buildScoreCache'build.control
Check the evidencecheck_evidence
Simple check on the control parameterscheck.valid.fitControls
Print coefficients of objects of class 'abnFit'coef.abnFit
Compare two DAGs or EGscompareDag
Compare two DAGs or EGscompareEG
Discretization of a Possibly Continuous Data Frame of Random Variables based on their distributiondiscretization
Computes an Empirical Estimation of the Entropy from a Table of CountsentropyData
Construct the essential graphessentialGraph
expit of proportionsexpit
expit functionexpit_cpp
Export abnFit object to structured JSON formatexport_abnFit
Print family of objects of class 'abnFit'family.abnFit
Find the children of a node in a graphfind_children
Find the Markov Blanket of a nodefind_MB
Find the parents of a node in a graphfind_parents
Control the iterations in 'fitAbn'fit.control
Extract Standard Deviations from all Gaussian NodesgetMSEfromModes
Compute standard information for a DAG.infoDag
Returns the strengths of the edge connections in a Bayesian Network learned from observational datalinkStrength
Logit of proportionslogit
logit functionslogit_cpp
Compute the log-likelihood of a binomial variableLogL_binomial
Compute the log-likelihood of a Gaussian variableLogL_gaussian
Compute the log-likelihood of a multinomial variablelogL_multinomial
Compute the log-likelihood of a multinomial variable (Vectorized)logL_multinomial_vectorized
Compute the log-likelihood of a Poisson variableLogL_poisson
Print logLik of objects of class 'abnFit'logLik.abnFit
Compute the Markov blanketmb
Empirical Estimation of the Entropy from a Table of CountsmiData
Convert modes to fitAbn.mle$coefs structuremodes2coefs
Find most probable DAG structuremostProbable
Print number of observations of objects of class 'abnFit'nobs.abnFit
Probability to oddsodds
Odds Ratio from a matrixor
Plots DAG from an object of class 'abnDag'plot.abnDag
Plot objects of class 'abnFit'plot.abnFit
Plot objects of class 'abnHeuristic'plot.abnHeuristic
Plot objects of class 'abnHillClimber'plot.abnHillClimber
Plot objects of class 'abnMostprobable'plot.abnMostprobable
Perform downstream inference with ABNpredict_node_from_children
Perform downstream inference with ABNpredict_node_from_children_binomial
Perform downstream inference with ABNpredict_node_from_children_gaussian
Perform downstream inference with ABNpredict_node_from_children_multinomial
Perform downstream inference with ABNpredict_node_from_children_poisson
Perform upstream inference with ABNpredict_node_from_parent
Perform upstream inference with ABNpredict_node_from_parent_binomial
Perform upstream inference with ABNpredict_node_from_parent_gaussian
Perform upstream inference with ABNpredict_node_from_parent_multinomial
Perform upstream inference with ABNpredict_node_from_parent_poisson
Predict a root nodepredict_root
Perform inference with ABNpredict.abnFit predictAbn
Print objects of class 'abnCache'print.abnCache
Print objects of class 'abnDag'print.abnDag
Print objects of class 'abnFit'print.abnFit
Print objects of class 'abnHeuristic'print.abnHeuristic
Print objects of class 'abnHillClimber'print.abnHillClimber
Print objects of class 'abnMostprobable'print.abnMostprobable
Print method for abnPrediction objectsprint.abnPrediction
Compute prior probability for a binomial prior distributionprior_binomial
Compute Gaussian prior densityprior_gaussian
Compute Prior Probability for a Poisson Distributionprior_poisson
Compute the score's contribution in a network of each observation.scoreContribution
A family of heuristic algorithms that aims at finding high scoring directed acyclic graphssearchHeuristic
Find high scoring directed acyclic graphs using heuristic search.searchHillClimber
Simulate data from a fitted additive Bayesian network.simulateAbn
Simulate a DAG with with arbitrary arcs densitysimulateDag
Computes skewness of a distributionskewness
Prints summary statistics from an object of class 'abnDag'summary.abnDag
Print summary of objects of class 'abnFit'summary.abnFit
Print summary of objects of class 'abnMostprobable'summary.abnMostprobable
Convert a DAG into graphviz formattoGraphviz