Bayesian Structure Learning in Graphical Models using Birth-Death MCMC

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Documentation for package ‘BDgraph’ version 2.72

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

BDgraph-package	Bayesian Structure Learning in Graphical Models
adj2link	Extract links from an adjacency matrix
auc	Compute the area under the ROC curve
BDgraph	Bayesian Structure Learning in Graphical Models
bdgraph	Search algorithm in graphical models
bdgraph.dw	Search algorithm for Gaussian copula graphical models for count data
bdgraph.mpl	Search algorithm in graphical models using marginal pseudo-likehlihood
bdgraph.npn	Nonparametric transfer
bdgraph.sim	Graph data simulation
bdw.reg	Bayesian estimation of (zero-inflated) Discrete Weibull regression
bf	Bayes factor for two graphs
calc_joint_dist	Bayesian Structure Learning in Graphical Models
compare	Graph structure comparison
compute_measures	Bayesian Structure Learning in Graphical Models
compute_tp_fp	Bayesian Structure Learning in Graphical Models
conf.mat	Confusion Matrix
conf.mat.plot	Plot Confusion Matrix
covariance	Estimated covariance matrix
ddweibull	The Discrete Weibull Distribution (Type 1)
ddweibull_reg	Bayesian Structure Learning in Graphical Models
detect_cores	Bayesian Structure Learning in Graphical Models
geneExpression	Human gene expression dataset
generate_clique_factors	Bayesian Structure Learning in Graphical Models
get_bounds_dw	Bayesian Structure Learning in Graphical Models
get_cores	Bayesian Structure Learning in Graphical Models
get_Ds_tgm_R	Bayesian Structure Learning in Graphical Models
get_graph	Bayesian Structure Learning in Graphical Models
get_g_prior	Bayesian Structure Learning in Graphical Models
get_g_start	Bayesian Structure Learning in Graphical Models
get_K_start	Bayesian Structure Learning in Graphical Models
get_S_n_p	Bayesian Structure Learning in Graphical Models
get_Ts_R	Bayesian Structure Learning in Graphical Models
global_hc	Bayesian Structure Learning in Graphical Models
global_hc_binary	Bayesian Structure Learning in Graphical Models
gnorm	Normalizing constant for G-Wishart
graph.sim	Graph simulation
hill_climb_mpl	Bayesian Structure Learning in Graphical Models
hill_climb_mpl_binary	Bayesian Structure Learning in Graphical Models
link2adj	Extract links from an adjacency matrix
local_mb_hc	Bayesian Structure Learning in Graphical Models
local_mb_hc_binary	Bayesian Structure Learning in Graphical Models
log_mpl_binary	Bayesian Structure Learning in Graphical Models
log_mpl_disrete	Bayesian Structure Learning in Graphical Models
log_post_cond_dw	Bayesian Structure Learning in Graphical Models
near_positive_definite	Bayesian Structure Learning in Graphical Models
pdweibull	The Discrete Weibull Distribution (Type 1)
pgraph	Posterior probabilities of the graphs
plinks	Estimated posterior link probabilities
plot.bdgraph	Plot function for 'S3' class "'bdgraph'"
plot.graph	Plot function for 'S3' class '"graph"'
plot.sim	Plot function for 'S3' class "'sim'"
plotcoda	Convergence plot
plotroc	ROC plot
posterior.predict	Posterior Predictive Samples
precision	Estimated precision matrix
predict.bdgraph	Predict function for 'S3' class "'bdgraph'"
print.bdgraph	Print function for 'S3' class "'bdgraph'"
print.sim	Print function for 'S3' class "'sim'"
qdweibull	The Discrete Weibull Distribution (Type 1)
rdweibull	The Discrete Weibull Distribution (Type 1)
reinis	Risk factors of coronary heart disease
rgwish	Sampling from G-Wishart distribution
rmvnorm	Generate data from the multivariate Normal distribution
roc	Build a ROC curve
rwish	Sampling from Wishart distribution
sample_ug	Bayesian Structure Learning in Graphical Models
select	Graph selection
sparsity	Compute the sparsity of a graph
summary.bdgraph	Summary function for 'S3' class "'bdgraph'"
surveyData	Labor force survey data
traceplot	Trace plot of graph size
transfer	transfer for count data
update_mu_R	Bayesian Structure Learning in Graphical Models
update_tu_R	Bayesian Structure Learning in Graphical Models