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BGGM (version 2.0.3)

Bayesian Gaussian Graphical Models

Description

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) , Williams and Mulder (2019) , Williams, Rast, Pericchi, and Mulder (2019) .

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Version

Install

install.packages('BGGM')

Monthly Downloads

12,621

Version

2.0.3

License

GPL-2

Maintainer

Donald Williams

Last Published

December 3rd, 2020

Functions in BGGM (2.0.3)

Data: Autism and Obssesive Compulsive Disorder

BGGM: Bayesian Gaussian Graphical Models

Compute Regression Parameters for estimate Objects

GGM: Missing Data

GGM: Confirmatory Hypothesis Testing

Bayesian Model Averaged Posterior Distribution

Compute Regression Parameters for explore Objects

constrained_posterior

Constrained Posterior Distribution

Data: 25 Personality items representing 5 factors

Data: Sachs Network

Fisher Z Transformation

GGM: Estimation

GGM: Exploratory Hypothesis Testing

Fisher Z Back Transformation

depression_anxiety_t2

Data: Depression and Anxiety (Time 2)

ggm_compare_explore

GGM Compare: Exploratory Hypothesis Testing

Multivariate Normal Imputation

Extract the Partial Correlation Matrix

ggm_compare_estimate

GGM Compare: Estimate

plot.roll_your_own

Plot roll_your_own Objects

MCMC Convergence

depression_anxiety_t1

Data: Depression and Anxiety (Time 1)

Network Plot for select Objects

Data: Contingencies of Self-Worth Scale (CSWS)

regression_summary

Summarary Method for Multivariate or Univarate Regression

predict.explore

Model Predictions for explore Objects

predict.var_estimate

Model Predictions for var_estimate Objects

Data: Post-Traumatic Stress Disorder (Sample # 4)

Partial Correlation Sum

Compute Correlations from the Partial Correlations

Generate Ordinal and Binary data

ggm_compare_confirm

GGM Compare: Confirmatory Hypothesis Testing

ggm_compare_ppc

GGM Compare: Posterior Predictive Check

Data: 1994 General Social Survey

Data: Interpersonal Reactivity Index (IRI)

plot.summary.var_estimate

Plot summary.var_estimate Objects

plot.summary.select.explore

Plot summary.select.explore Objects

Plot pcor_sum Object

Maximum A Posteriori Precision Matrix

plot.predictability

Plot predictability Objects

Data: Post-Traumatic Stress Disorder

S3 select method

plot.summary.estimate

Plot summary.estimate Objects

Data: ifit Intensive Longitudinal Data

Search Algorithm

plot.summary.explore

Plot summary.explore Objects

Data: Post-Traumatic Stress Disorder (Sample # 2)

select.estimate

Graph Selection for estimate Objects

Summarize coef Objects

Data: Post-Traumatic Stress Disorder (Sample # 3)

summary.estimate

Summary method for estimate.default objects

summary.var_estimate

Summary Method for var_estimate Objects

summary.select.explore

Summary Method for select.explore Objects

Precision Matrix Posterior Distribution

select.ggm_compare_explore

Graph selection for ggm_compare_explore Objects

predict.estimate

Model Predictions for estimate Objects

select.var_estimate

Graph Selection for var.estimate Object

Data: Post-Traumatic Stress Disorder (Sample # 1)

summary.explore

Summary Method for explore.default Objects

summary.ggm_compare_estimate

Summary method for ggm_compare_estimate objects

weighted_adj_mat

Extract the Weighted Adjacency Matrix

zero_order_cors

Zero-Order Correlations

Plot confirm objects

plot.summary.ggm_compare_explore

Plot summary.ggm_compare_explore Objects

Predictability: Bayesian Variance Explained (R2)

plot.summary.ggm_compare_estimate

Plot summary.ggm_compare_estimate Objects

plot.ggm_compare_ppc

Plot ggm_compare_ppc Objects

Data: Women and Mathematics

Print method for BGGM objects

VAR: Estimation

Plot: Prior Distribution

Data: Toronto Alexithymia Scale (TAS)

posterior_samples

Extract Posterior Samples

select.ggm_compare_estimate

Graph Selection for ggm_compare_estimate Objects

Data: Resilience Scale of Adults (RSA)

Compute Custom Network Statistics

Graph selection for explore Objects

summary.ggm_compare_explore

Summary Method for ggm_compare_explore Objects

summary.predictability

Summary Method for predictability Objects