Package: BDgraph 2.73

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
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BDgraph.pdf |BDgraph.html✨
BDgraph/json (API)
NEWS

# Install 'BDgraph' in R:

install.packages('BDgraph', repos = c('https://rezamoammadi.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

geneExpression - Human gene expression dataset
reinis - Risk factors of coronary heart disease
surveyData - Labor force survey data

On CRAN:

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 3 months agofrom:66de8c40e7. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 22 2024
R-4.5-win-x86_64	OK	Nov 22 2024
R-4.5-linux-x86_64	OK	Nov 22 2024
R-4.4-win-x86_64	OK	Nov 22 2024
R-4.4-mac-x86_64	OK	Nov 22 2024
R-4.4-mac-aarch64	OK	Nov 22 2024
R-4.3-win-x86_64	OK	Nov 22 2024
R-4.3-mac-x86_64	OK	Nov 22 2024
R-4.3-mac-aarch64	OK	Nov 22 2024

Exports:adj2link auc bdgraph bdgraph.dw bdgraph.mpl bdgraph.npn bdgraph.sim bdw.reg bf compare conf.mat conf.mat.plot covariance ddweibull ddweibull_reg detect_cores get_bounds_dw get_cores get_Ds_tgm_R get_g_prior get_g_start get_graph get_K_start get_S_n_p get_Ts_R gnorm graph.sim link2adj log_post_cond_dw mse near_positive_definite pdweibull pgraph plinks plot.bdgraph plot.graph plot.sim plotcoda plotroc posterior.predict precision predict.bdgraph print.bdgraph print.sim qdweibull rdweibull rgwish rmvnorm roc rwish select sparsity summary.bdgraph traceplot transfer update_mu_R update_tu_R

Dependencies:cli colorspace cpp11 fansi farver ggplot2 glue gtable igraph isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig plyr pROC R6 RColorBrewer Rcpp rlang scales tibble utf8 vctrs viridisLite withr

BDgraph with Simple Examples

Reza Mohammadi (https://orcid.org/0000-0001-9538-0648)

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

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

Introduction to BDgraph

Reza Mohammadi (https://orcid.org/0000-0001-9538-0648)

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

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

Citation

Readme and manuals

Help Manual

Help page	Topics
Bayesian Structure Learning in Graphical Models	BDgraph-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 matrix	adj2link
Compute the area under the ROC curve	auc
Search algorithm in graphical models	bdgraph
Search algorithm for Gaussian copula graphical models for count data	bdgraph.dw
Search algorithm in graphical models using marginal pseudo-likehlihood	bdgraph.mpl
Nonparametric transfer	bdgraph.npn
Graph data simulation	bdgraph.sim
Bayesian estimation of (zero-inflated) Discrete Weibull regression	bdw.reg
Bayes factor for two graphs	bf
Graph structure comparison	compare
Confusion Matrix	conf.mat
Plot Confusion Matrix	conf.mat.plot
Estimated covariance matrix	covariance
The Discrete Weibull Distribution (Type 1)	ddweibull pdweibull qdweibull rdweibull
Human gene expression dataset	geneExpression
Normalizing constant for G-Wishart	gnorm
Graph simulation	graph.sim
Extract links from an adjacency matrix	link2adj
Graph structure comparison	mse
Posterior probabilities of the graphs	pgraph
Estimated posterior link probabilities	plinks
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 plot	plotcoda
ROC plot	plotroc
Posterior Predictive Samples	posterior.predict
Estimated precision matrix	precision
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 disease	reinis
Sampling from G-Wishart distribution	rgwish
Generate data from the multivariate Normal distribution	rmvnorm
Build a ROC curve	roc
Sampling from Wishart distribution	rwish
Graph selection	select
Compute the sparsity of a graph	sparsity
Summary function for 'S3' class "'bdgraph'"	summary.bdgraph
Labor force survey data	surveyData
Trace plot of graph size	traceplot
transfer for count data	transfer