Package: abn 3.1.1

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]

abn_3.1.1.tar.gz
abn_3.1.1.tar.gz(r-4.5-noble)abn_3.1.1.tar.gz(r-4.4-noble)
abn_3.1.1.tgz(r-4.4-emscripten)abn_3.1.1.tgz(r-4.3-emscripten)
abn.pdf |abn.html
abn/json (API)

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

Peer review:

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

Pkgdown 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

gslopenblascppopenmpjags

5.88 score 1 stars 90 scripts 820 downloads 6 mentions 112 exports 28 dependencies

Last updated 7 months agofrom:a68c8622c9. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 27 2024
R-4.5-linux-x86_64OKDec 27 2024

Exports:abn.versionAIC.abnFitbern_bugsbern_bugsGroupBIC.abnFitbuild.controlbuildcachematrixbuildScoreCachebuildScoreCache.bayesbuildScoreCache.mlecalc.node.inla.glmcalc.node.inla.glmmcategorical_bugscategorical_bugsGroupcheck.valid.buildControlscheck.valid.dagcheck.valid.datacheck.valid.fitControlscheck.valid.groupscheck.valid.parentscheck.which.valid.nodescheckforcyclescoef.abnFitcompareDagcompareEGcreateAbnDagdiscretizationentropyDataessentialGrapheval.across.gridexpitexpit_cppfactorialfactorial_fastfamily.abnFitfind.next.left.xfind.next.right.xfit_single_nodefit.controlfitAbnfitabn_marginalsfitAbn.bayesfitAbn.mleforLoopContentforLoopContentBayesforLoopContentFitBayesformula_abngauss_bugsgauss_bugsGroupget.ind.quantilesget.quantilesget.var.typesgetmarginalsgetMargsINLAgetModeVectorgetMSEfromModesinfoDagirls_binomial_cppirls_binomial_cpp_brirls_binomial_cpp_fastirls_binomial_cpp_fast_brirls_gaussian_cppirls_gaussian_cpp_fastirls_poisson_cppirls_poisson_cpp_fastlinkStrengthlogitlogit_cpplogLik.abnFitmakebugsmakebugsGroupmbmi_cppmiDatamodes2coefsmostProbablemostprobable_Cnobs.abnFitoddsorplot.abnDagplot.abnFitplot.abnHeuristicplot.abnHillClimberplot.abnMostprobableplotAbnpois_bugspois_bugsGroupprint.abnCacheprint.abnDagprint.abnFitprint.abnHeuristicprint.abnHillClimberprint.abnMostprobablerank_cppregressionLoopscoreContributionsearchHeuristicsearchhillsearchHillClimbersimulateAbnsimulateDagskewnessstd.area.under.gridstrsplitssummary.abnDagsummary.abnFitsummary.abnMostprobabletidy.cachetoGraphvizvalidate_abnDagvalidate_dists

Dependencies:BiocGenericsbootcodacodetoolsdata.tabledoParallelforeachgenericsgraphiteratorsjsonlitelatticelme4MASSMatrixmclogitmemiscminqanlmenloptrnnetRcppRcppArmadilloRcppEigenRgraphvizrjagsstringiyaml

Bayesian Network Structure Learning

Rendered fromstructure_learning.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2024-03-23
Started: 2024-03-23

Data Simulation

Rendered fromdata_simulation.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2024-03-23
Started: 2024-03-23

Mixed-effect Bayesian Network Model

Rendered frommixed_effect_BN_model.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2024-03-23
Started: 2024-03-23

Model Specification: Build a Cache of Scores

Rendered frommodel_specification.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2024-03-23
Started: 2024-03-23

Parallelisation

Rendered frommultiprocessing.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2024-05-31
Started: 2024-03-23

Parameter Learning

Rendered fromparameter_learning.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2024-03-23
Started: 2024-03-23

Quick Start Example

Rendered fromquick_start_example.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2024-03-23
Started: 2024-03-23

Readme and manuals

Help Manual

Help pageTopics
Print AIC of objects of class 'abnFit'AIC.abnFit
Print BIC of objects of class 'abnFit'BIC.abnFit
Control the iterations in 'buildScoreCache'build.control
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
Print family of objects of class 'abnFit'family.abnFit
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
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
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
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