Package: BGGM 2.1.3.9000

Philippe Rast

BGGM: Bayesian Gaussian Graphical Models

Fit Bayesian Gaussian graphical models. The methods are separated into two Bayesian approaches for inference: hypothesis testing and estimation. There are extensions for confirmatory hypothesis testing, comparing Gaussian graphical models, and node wise predictability. These methods were recently introduced in the Gaussian graphical model literature, including Williams (2019) <doi:10.31234/osf.io/x8dpr>, Williams and Mulder (2019) <doi:10.31234/osf.io/ypxd8>, Williams, Rast, Pericchi, and Mulder (2019) <doi:10.31234/osf.io/yt386>.

Authors:Donald Williams [aut], Joris Mulder [aut], Philippe Rast [aut, cre]

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

# Install 'BGGM' in R:

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

Bug tracker:https://github.com/donaldrwilliams/bggm/issues

Uses libs:

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

Datasets:

Sachs - Data: Sachs Network
asd_ocd - Data: Autism and Obssesive Compulsive Disorder
bfi - Data: 25 Personality items representing 5 factors
csws - Data: Contingencies of Self-Worth Scale
depression_anxiety_t1 - Data: Depression and Anxiety
depression_anxiety_t2 - Data: Depression and Anxiety
gss - Data: 1994 General Social Survey
ifit - Data: ifit Intensive Longitudinal Data
iri - Data: Interpersonal Reactivity Index
ptsd - Data: Post-Traumatic Stress Disorder
ptsd_cor1 - Data: Post-Traumatic Stress Disorder
ptsd_cor2 - Data: Post-Traumatic Stress Disorder
ptsd_cor3 - Data: Post-Traumatic Stress Disorder
ptsd_cor4 - Data: Post-Traumatic Stress Disorder
rsa - Data: Resilience Scale of Adults
tas - Data: Toronto Alexithymia Scale
women_math - Data: Women and Mathematics

On CRAN:

bayes-factors bayesian-hypothesis-testing gaussian-graphical-models

9.61 score 54 stars 1 packages 103 scripts 783 downloads 2 mentions 33 exports 104 dependencies

Last updated 23 days agofrom:d70df48ad1. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	OK	Oct 31 2024
R-4.5-linux-x86_64	OK	Oct 31 2024
R-4.4-win-x86_64	OK	Oct 31 2024
R-4.4-mac-x86_64	OK	Oct 31 2024
R-4.4-mac-aarch64	OK	Oct 31 2024
R-4.3-win-x86_64	OK	Oct 31 2024
R-4.3-mac-x86_64	OK	Oct 31 2024
R-4.3-mac-aarch64	OK	Oct 31 2024

Exports:bggm_missing confirm constrained_posterior convergence estimate explore fisher_r_to_z fisher_z_to_r gen_net gen_ordinal ggm_compare_confirm ggm_compare_estimate ggm_compare_explore ggm_compare_ppc impute_data map pcor_mat pcor_sum pcor_to_cor plot_prior posterior_predict posterior_samples precision predictability predicted_probability prior_belief_ggm prior_belief_var regression_summary roll_your_own select var_estimate weighted_adj_mat zero_order_cors

Dependencies:bain Bergm BFpack BH boot cachem cli coda colorspace cpp11 crayon DEoptimR dplyr ergm evaluate extraDistr fansi farver fastmap forcats generics GGally ggplot2 ggridges ggstats glue gsl gtable highr hms isoband knitr labeling lattice lavaan lifecycle lme4 lpSolveAPI magrittr MASS Matrix matrixcalc MatrixModels mcmc MCMCpack memoise mgcv minqa mnormt munsell mvnfast mvtnorm network nlme nloptr numDeriv patchwork pbivnorm pillar pkgconfig plyr pracma prettyunits progress purrr QRM quadprog quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppDist RcppEigen RcppProgress Rdpack reshape Rglpk rlang rle robustbase sandwich scales slam sna SparseM statnet.common stringi stringr survival tibble tidyr tidyselect timeDate timeSeries trust utf8 vctrs viridisLite withr xfun yaml zoo

Controlling for Variables

Donny Williams

Rendered fromcontrol.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-05-27

Custom Network Comparisons

Donny Williams

Rendered fromppc_custom.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-05-19

Custom Network Statistics

Donny Williams

Rendered fromnetstat_custom.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-05-20

Graphical VAR

Donny Williams

Rendered fromvar_model.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-06-04

In Tandem: Confirmatory and Exploratory Testing

Donny Williams

Rendered fromin_tandem.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-05-24

MCMC Diagnostics

Donny Williams

Rendered frommcmc_diagnostics.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-05-21

Network Plots

Donny Williams

Rendered fromnetplot.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-05-21

Predictability: Binary, Ordinal, and Continuous

Donny Williams

Rendered frompredictability.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-05-20

Testing Sums

Donny Williams

Rendered fromtest_sum.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-05-25

Three Ways to Test the Same Hypothesis

Donny Williams

Rendered fromhyp_3_ways.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-05-23

Troubleshoot

Donny Williams

Rendered frominstallation.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-21
Started: 2020-05-24

Help page	Topics
Data: Autism and Obssesive Compulsive Disorder	asd_ocd
Data: 25 Personality items representing 5 factors	bfi
GGM: Missing Data	bggm_missing
Compute Regression Parameters for 'estimate' Objects	coef.estimate
Compute Regression Parameters for 'explore' Objects	coef.explore
GGM: Confirmatory Hypothesis Testing	confirm
Constrained Posterior Distribution	constrained_posterior
MCMC Convergence	convergence
Data: Contingencies of Self-Worth Scale (CSWS)	csws
Data: Depression and Anxiety (Time 1)	depression_anxiety_t1
Data: Depression and Anxiety (Time 2)	depression_anxiety_t2
GGM: Estimation	estimate
GGM: Exploratory Hypothesis Testing	explore
Fisher Z Transformation	fisher_r_to_z
Fisher Z Back Transformation	fisher_z_to_r
Simulate a Partial Correlation Matrix	gen_net
Generate Ordinal and Binary data	gen_ordinal
GGM Compare: Confirmatory Hypothesis Testing	ggm_compare_confirm
GGM Compare: Estimate	ggm_compare_estimate
GGM Compare: Exploratory Hypothesis Testing	ggm_compare_explore
GGM Compare: Posterior Predictive Check	ggm_compare_ppc
Data: 1994 General Social Survey	gss
Data: ifit Intensive Longitudinal Data	ifit
Obtain Imputed Datasets	impute_data
Data: Interpersonal Reactivity Index (IRI)	iri
Maximum A Posteriori Precision Matrix	map
Extract the Partial Correlation Matrix	pcor_mat
Partial Correlation Sum	pcor_sum
Compute Correlations from the Partial Correlations	pcor_to_cor
Plot: Prior Distribution	plot_prior
Plot 'confirm' objects	plot.confirm
Plot 'ggm_compare_ppc' Objects	plot.ggm_compare_ppc
Plot 'pcor_sum' Object	plot.pcor_sum
Plot 'predictability' Objects	plot.predictability
Plot 'roll_your_own' Objects	plot.roll_your_own
Network Plot for 'select' Objects	plot.select
Plot 'summary.estimate' Objects	plot.summary.estimate
Plot 'summary.explore' Objects	plot.summary.explore
Plot 'summary.ggm_compare_estimate' Objects	plot.summary.ggm_compare_estimate
Plot 'summary.ggm_compare_explore' Objects	plot.summary.ggm_compare_explore
Plot 'summary.select.explore' Objects	plot.summary.select.explore
Plot 'summary.var_estimate' Objects	plot.summary.var_estimate
Posterior Predictive Distribution	posterior_predict
Extract Posterior Samples	posterior_samples
Precision Matrix Posterior Distribution	precision
Model Predictions for 'estimate' Objects	predict.estimate
Model Predictions for 'explore' Objects	predict.explore
Model Predictions for 'var_estimate' Objects	predict.var_estimate
Predictability: Bayesian Variance Explained (R2)	predictability
Predicted Probabilities	predicted_probability
Print method for 'BGGM' objects	print.BGGM
Prior Belief Gaussian Graphical Model	prior_belief_ggm
Prior Belief Graphical VAR	prior_belief_var
Data: Post-Traumatic Stress Disorder	ptsd
Data: Post-Traumatic Stress Disorder (Sample # 1)	ptsd_cor1
Data: Post-Traumatic Stress Disorder (Sample # 2)	ptsd_cor2
Data: Post-Traumatic Stress Disorder (Sample # 3)	ptsd_cor3
Data: Post-Traumatic Stress Disorder (Sample # 4)	ptsd_cor4
Summarary Method for Multivariate or Univarate Regression	regression_summary
Compute Custom Network Statistics	roll_your_own
Data: Resilience Scale of Adults (RSA)	rsa
Data: Sachs Network	Sachs
S3 'select' method	select
Graph Selection for 'estimate' Objects	select.estimate
Graph selection for 'explore' Objects	select.explore
Graph Selection for 'ggm_compare_estimate' Objects	select.ggm_compare_estimate
Graph selection for 'ggm_compare_explore' Objects	select.ggm_compare_explore
Graph Selection for 'var.estimate' Object	select.var_estimate
Summarize 'coef' Objects	summary.coef
Summary method for 'estimate.default' objects	summary.estimate
Summary Method for 'explore.default' Objects	summary.explore
Summary method for 'ggm_compare_estimate' objects	summary.ggm_compare_estimate
Summary Method for 'ggm_compare_explore' Objects	summary.ggm_compare_explore
Summary Method for 'predictability' Objects	summary.predictability
Summary Method for 'select.explore' Objects	summary.select.explore
Summary Method for 'var_estimate' Objects	summary.var_estimate
Data: Toronto Alexithymia Scale (TAS)	tas
VAR: Estimation	var_estimate
Extract the Weighted Adjacency Matrix	weighted_adj_mat
Data: Women and Mathematics	women_math
Zero-Order Correlations	zero_order_cors

Package: BGGM 2.1.3.9000

BGGM: Bayesian Gaussian Graphical Models

Controlling for Variables

Custom Network Comparisons

Custom Network Statistics

Graphical VAR

In Tandem: Confirmatory and Exploratory Testing

MCMC Diagnostics

Network Plots

Predictability: Binary, Ordinal, and Continuous

Testing Sums

Three Ways to Test the Same Hypothesis

Troubleshoot

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)