Package: BDgraph 2.73

Reza Mohammadi

BDgraph: Bayesian Structure Learning in Graphical Models using Birth-Death MCMC

Advanced statistical tools for Bayesian structure learning in undirected graphical models, accommodating continuous, ordinal, discrete, count, and mixed data. It integrates recent advancements in Bayesian graphical models as presented in the literature, including the works of Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Mohammadi et al. (2021) <doi:10.1080/01621459.2021.1996377>, Dobra and Mohammadi (2018) <doi:10.1214/18-AOAS1164>, and Mohammadi et al. (2023) <doi:10.48550/arXiv.2307.00127>.

Authors:Reza Mohammadi [aut, cre], Ernst Wit [aut], Adrian Dobra [ctb]

BDgraph_2.73.tar.gz
BDgraph_2.73.tar.gz(r-4.5-noble)BDgraph_2.73.tar.gz(r-4.4-noble)
BDgraph_2.73.tgz(r-4.4-emscripten)BDgraph_2.73.tgz(r-4.3-emscripten)
BDgraph.pdf |BDgraph.html
BDgraph/json (API)
NEWS

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

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

7.43 score 8 stars 7 packages 218 scripts 2.5k downloads 3 mentions 57 exports 33 dependencies

Last updated 4 months agofrom:66de8c40e7. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-linux-x86_64OKNov 22 2024

Exports:adj2linkaucbdgraphbdgraph.dwbdgraph.mplbdgraph.npnbdgraph.simbdw.regbfcompareconf.matconf.mat.plotcovarianceddweibullddweibull_regdetect_coresget_bounds_dwget_coresget_Ds_tgm_Rget_g_priorget_g_startget_graphget_K_startget_S_n_pget_Ts_Rgnormgraph.simlink2adjlog_post_cond_dwmsenear_positive_definitepdweibullpgraphplinksplot.bdgraphplot.graphplot.simplotcodaplotrocposterior.predictprecisionpredict.bdgraphprint.bdgraphprint.simqdweibullrdweibullrgwishrmvnormrocrwishselectsparsitysummary.bdgraphtraceplottransferupdate_mu_Rupdate_tu_R

Dependencies:clicolorspacecpp11fansifarverggplot2gluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrpROCR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr

BDgraph with Simple Examples

Rendered fromBDgraph-Examples.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-08-24
Started: 2022-04-14

Introduction to BDgraph

Rendered fromIntroduction-BDgraph.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-08-24
Started: 2022-08-08

Readme and manuals

Help Manual

Help pageTopics
Bayesian Structure Learning in Graphical ModelsBDgraph-package BDgraph calc_joint_dist compute_measures compute_tp_fp ddweibull_reg detect_cores generate_clique_factors get_bounds_dw get_cores get_Ds_tgm_R get_graph get_g_prior get_g_start get_K_start get_S_n_p get_Ts_R global_hc global_hc_binary hill_climb_mpl hill_climb_mpl_binary local_mb_hc local_mb_hc_binary log_mpl_binary log_mpl_disrete log_post_cond_dw near_positive_definite sample_ug update_mu_R update_tu_R
Extract links from an adjacency matrixadj2link
Compute the area under the ROC curveauc
Search algorithm in graphical modelsbdgraph
Search algorithm for Gaussian copula graphical models for count databdgraph.dw
Search algorithm in graphical models using marginal pseudo-likehlihoodbdgraph.mpl
Nonparametric transferbdgraph.npn
Graph data simulationbdgraph.sim
Bayesian estimation of (zero-inflated) Discrete Weibull regressionbdw.reg
Bayes factor for two graphsbf
Graph structure comparisoncompare
Confusion Matrixconf.mat
Plot Confusion Matrixconf.mat.plot
Estimated covariance matrixcovariance
The Discrete Weibull Distribution (Type 1)ddweibull pdweibull qdweibull rdweibull
Human gene expression datasetgeneExpression
Normalizing constant for G-Wishartgnorm
Graph simulationgraph.sim
Extract links from an adjacency matrixlink2adj
Graph structure comparisonmse
Posterior probabilities of the graphspgraph
Estimated posterior link probabilitiesplinks
Plot function for 'S3' class "'bdgraph'"plot.bdgraph
Plot function for 'S3' class '"graph"'plot.graph
Plot function for 'S3' class "'sim'"plot.sim
Convergence plotplotcoda
ROC plotplotroc
Posterior Predictive Samplesposterior.predict
Estimated precision matrixprecision
Predict function for 'S3' class "'bdgraph'"predict.bdgraph
Print function for 'S3' class "'bdgraph'"print.bdgraph
Print function for 'S3' class "'sim'"print.sim
Risk factors of coronary heart diseasereinis
Sampling from G-Wishart distributionrgwish
Generate data from the multivariate Normal distributionrmvnorm
Build a ROC curveroc
Sampling from Wishart distributionrwish
Graph selectionselect
Compute the sparsity of a graphsparsity
Summary function for 'S3' class "'bdgraph'"summary.bdgraph
Labor force survey datasurveyData
Trace plot of graph sizetraceplot
transfer for count datatransfer