Understand and Describe Bayesian Models and Posterior Distributions


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Documentation for package ‘bayestestR’ version 0.10.5

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A B C D E H M O P R S U W

-- A --

area_under_curve Area under the Curve (AUC)
as.data.frame.density Coerce to a Data Frame
as.matrix.bayesfactor_models Bayes Factors (BF) for model comparison
as.numeric.map_estimate Convert to Numeric
as.numeric.p_direction Convert to Numeric
as.numeric.p_map Convert to Numeric
as.numeric.p_significance Convert to Numeric
auc Area under the Curve (AUC)

-- B --

bayesfactor Bayes Factors (BF)
bayesfactor_inclusion Inclusion Bayes Factors for testing predictors across Bayesian models
bayesfactor_models Bayes Factors (BF) for model comparison
bayesfactor_parameters Bayes Factors (BF) for a Single Parameter
bayesfactor_parameters.blavaan Bayes Factors (BF) for a Single Parameter
bayesfactor_parameters.brmsfit Bayes Factors (BF) for a Single Parameter
bayesfactor_parameters.data.frame Bayes Factors (BF) for a Single Parameter
bayesfactor_parameters.numeric Bayes Factors (BF) for a Single Parameter
bayesfactor_parameters.stanreg Bayes Factors (BF) for a Single Parameter
bayesfactor_pointnull Bayes Factors (BF) for a Single Parameter
bayesfactor_restricted Bayes Factors (BF) for Order Restricted Models
bayesfactor_restricted.blavaan Bayes Factors (BF) for Order Restricted Models
bayesfactor_restricted.brmsfit Bayes Factors (BF) for Order Restricted Models
bayesfactor_restricted.emmGrid Bayes Factors (BF) for Order Restricted Models
bayesfactor_restricted.stanreg Bayes Factors (BF) for Order Restricted Models
bayesfactor_rope Bayes Factors (BF) for a Single Parameter
bayesian_as_frequentist Convert (refit) a Bayesian model to frequentist
bcai Bias Corrected and Accelerated Interval (BCa)
bci Bias Corrected and Accelerated Interval (BCa)
bci.BFBayesFactor Bias Corrected and Accelerated Interval (BCa)
bci.brmsfit Bias Corrected and Accelerated Interval (BCa)
bci.data.frame Bias Corrected and Accelerated Interval (BCa)
bci.emmGrid Bias Corrected and Accelerated Interval (BCa)
bci.MCMCglmm Bias Corrected and Accelerated Interval (BCa)
bci.numeric Bias Corrected and Accelerated Interval (BCa)
bci.sim Bias Corrected and Accelerated Interval (BCa)
bci.sim.merMod Bias Corrected and Accelerated Interval (BCa)
bci.stanreg Bias Corrected and Accelerated Interval (BCa)
bf_inclusion Inclusion Bayes Factors for testing predictors across Bayesian models
bf_models Bayes Factors (BF) for model comparison
bf_parameters Bayes Factors (BF) for a Single Parameter
bf_pointnull Bayes Factors (BF) for a Single Parameter
bf_restricted Bayes Factors (BF) for Order Restricted Models
bf_rope Bayes Factors (BF) for a Single Parameter
bic_to_bf Convert BIC indices to Bayes Factors via the BIC-approximation method.

-- C --

check_prior Check if Prior is Informative
ci Confidence/Credible/Compatibility Interval (CI)
ci.BFBayesFactor Confidence/Credible/Compatibility Interval (CI)
ci.brmsfit Confidence/Credible/Compatibility Interval (CI)
ci.data.frame Confidence/Credible/Compatibility Interval (CI)
ci.MCMCglmm Confidence/Credible/Compatibility Interval (CI)
ci.numeric Confidence/Credible/Compatibility Interval (CI)
ci.sim Confidence/Credible/Compatibility Interval (CI)
ci.sim.merMod Confidence/Credible/Compatibility Interval (CI)
ci.stanreg Confidence/Credible/Compatibility Interval (CI)
contr.bayes Orthonormal Contrast Matrices for Bayesian Estimation
contr.orthonorm Orthonormal Contrast Matrices for Bayesian Estimation
convert_bayesian_as_frequentist Convert (refit) a Bayesian model to frequentist
convert_pd_to_p Convert between Probability of Direction (pd) and p-value.
convert_p_to_pd Convert between Probability of Direction (pd) and p-value.

-- D --

density_at Density Probability at a Given Value
describe_posterior Describe Posterior Distributions
describe_posterior.BFBayesFactor Describe Posterior Distributions
describe_posterior.brmsfit Describe Posterior Distributions
describe_posterior.MCMCglmm Describe Posterior Distributions
describe_posterior.numeric Describe Posterior Distributions
describe_posterior.stanmvreg Describe Posterior Distributions
describe_posterior.stanreg Describe Posterior Distributions
describe_prior Describe Priors
diagnostic_draws Diagnostic values for each iteration
diagnostic_posterior Posteriors Sampling Diagnostic
diagnostic_posterior.brmsfit Posteriors Sampling Diagnostic
diagnostic_posterior.stanmvreg Posteriors Sampling Diagnostic
diagnostic_posterior.stanreg Posteriors Sampling Diagnostic
distribution Empirical Distributions
distribution_beta Empirical Distributions
distribution_binom Empirical Distributions
distribution_binomial Empirical Distributions
distribution_cauchy Empirical Distributions
distribution_chisq Empirical Distributions
distribution_chisquared Empirical Distributions
distribution_custom Empirical Distributions
distribution_gamma Empirical Distributions
distribution_gaussian Empirical Distributions
distribution_mixture_normal Empirical Distributions
distribution_nbinom Empirical Distributions
distribution_normal Empirical Distributions
distribution_poisson Empirical Distributions
distribution_student Empirical Distributions
distribution_student_t Empirical Distributions
distribution_t Empirical Distributions
distribution_tweedie Empirical Distributions
distribution_uniform Empirical Distributions

-- E --

effective_sample Effective Sample Size (ESS)
effective_sample.blavaan Effective Sample Size (ESS)
effective_sample.brmsfit Effective Sample Size (ESS)
effective_sample.MCMCglmm Effective Sample Size (ESS)
effective_sample.stanreg Effective Sample Size (ESS)
equivalence_test Test for Practical Equivalence
equivalence_test.BFBayesFactor Test for Practical Equivalence
equivalence_test.brmsfit Test for Practical Equivalence
equivalence_test.data.frame Test for Practical Equivalence
equivalence_test.default Test for Practical Equivalence
equivalence_test.emmGrid Test for Practical Equivalence
equivalence_test.numeric Test for Practical Equivalence
equivalence_test.stanreg Test for Practical Equivalence
estimate_density Density Estimation
estimate_density.data.frame Density Estimation
eti Equal-Tailed Interval (ETI)
eti.BFBayesFactor Equal-Tailed Interval (ETI)
eti.brmsfit Equal-Tailed Interval (ETI)
eti.data.frame Equal-Tailed Interval (ETI)
eti.emmGrid Equal-Tailed Interval (ETI)
eti.MCMCglmm Equal-Tailed Interval (ETI)
eti.numeric Equal-Tailed Interval (ETI)
eti.sim Equal-Tailed Interval (ETI)
eti.sim.merMod Equal-Tailed Interval (ETI)
eti.stanreg Equal-Tailed Interval (ETI)

-- H --

hdi Highest Density Interval (HDI)
hdi.BFBayesFactor Highest Density Interval (HDI)
hdi.brmsfit Highest Density Interval (HDI)
hdi.data.frame Highest Density Interval (HDI)
hdi.emmGrid Highest Density Interval (HDI)
hdi.MCMCglmm Highest Density Interval (HDI)
hdi.numeric Highest Density Interval (HDI)
hdi.sim Highest Density Interval (HDI)
hdi.sim.merMod Highest Density Interval (HDI)
hdi.stanreg Highest Density Interval (HDI)

-- M --

map_estimate Maximum A Posteriori probability estimate (MAP)
map_estimate.bayesQR Maximum A Posteriori probability estimate (MAP)
map_estimate.brmsfit Maximum A Posteriori probability estimate (MAP)
map_estimate.data.frame Maximum A Posteriori probability estimate (MAP)
map_estimate.emmGrid Maximum A Posteriori probability estimate (MAP)
map_estimate.numeric Maximum A Posteriori probability estimate (MAP)
map_estimate.stanreg Maximum A Posteriori probability estimate (MAP)
mcse Monte-Carlo Standard Error (MCSE)
mcse.stanreg Monte-Carlo Standard Error (MCSE)
mediation Summary of Bayesian multivariate-response mediation-models
mediation.brmsfit Summary of Bayesian multivariate-response mediation-models
mediation.stanmvreg Summary of Bayesian multivariate-response mediation-models

-- O --

overlap Overlap Coefficient

-- P --

pd Probability of Direction (pd)
pd_to_p Convert between Probability of Direction (pd) and p-value.
point_estimate Point-estimates of posterior distributions
point_estimate.BFBayesFactor Point-estimates of posterior distributions
point_estimate.brmsfit Point-estimates of posterior distributions
point_estimate.numeric Point-estimates of posterior distributions
point_estimate.stanreg Point-estimates of posterior distributions
p_direction Probability of Direction (pd)
p_direction.BFBayesFactor Probability of Direction (pd)
p_direction.brmsfit Probability of Direction (pd)
p_direction.data.frame Probability of Direction (pd)
p_direction.emmGrid Probability of Direction (pd)
p_direction.MCMCglmm Probability of Direction (pd)
p_direction.numeric Probability of Direction (pd)
p_direction.stanreg Probability of Direction (pd)
p_map Bayesian p-value based on the density at the Maximum A Posteriori (MAP)
p_map.brmsfit Bayesian p-value based on the density at the Maximum A Posteriori (MAP)
p_map.stanreg Bayesian p-value based on the density at the Maximum A Posteriori (MAP)
p_pointnull Bayesian p-value based on the density at the Maximum A Posteriori (MAP)
p_rope Probability of being in the ROPE
p_rope.BFBayesFactor Probability of being in the ROPE
p_rope.brmsfit Probability of being in the ROPE
p_rope.data.frame Probability of being in the ROPE
p_rope.default Probability of being in the ROPE
p_rope.emmGrid Probability of being in the ROPE
p_rope.MCMCglmm Probability of being in the ROPE
p_rope.numeric Probability of being in the ROPE
p_rope.stanreg Probability of being in the ROPE
p_significance Practical Significance (ps)
p_significance.brmsfit Practical Significance (ps)
p_significance.emmGrid Practical Significance (ps)
p_significance.numeric Practical Significance (ps)
p_significance.stanreg Practical Significance (ps)
p_to_pd Convert between Probability of Direction (pd) and p-value.

-- R --

reshape_draws Reshape estimations with multiple iterations (draws) to long format
reshape_iterations Reshape estimations with multiple iterations (draws) to long format
rnorm_perfect Empirical Distributions
rope Region of Practical Equivalence (ROPE)
rope.BFBayesFactor Region of Practical Equivalence (ROPE)
rope.brmsfit Region of Practical Equivalence (ROPE)
rope.data.frame Region of Practical Equivalence (ROPE)
rope.default Region of Practical Equivalence (ROPE)
rope.emmGrid Region of Practical Equivalence (ROPE)
rope.MCMCglmm Region of Practical Equivalence (ROPE)
rope.numeric Region of Practical Equivalence (ROPE)
rope.stanreg Region of Practical Equivalence (ROPE)
rope_range Find Default Equivalence (ROPE) Region Bounds
rope_range.default Find Default Equivalence (ROPE) Region Bounds

-- S --

sensitivity_to_prior Sensitivity to Prior
sexit Sequential Effect eXistence and sIgnificance Testing (SEXIT)
sexit_thresholds Find Effect Size Thresholds
si Compute Support Intervals
si.blavaan Compute Support Intervals
si.brmsfit Compute Support Intervals
si.data.frame Compute Support Intervals
si.emmGrid Compute Support Intervals
si.numeric Compute Support Intervals
si.stanreg Compute Support Intervals
simulate_correlation Data Simulation
simulate_difference Data Simulation
simulate_prior Returns Priors of a Model as Empirical Distributions
simulate_simpson Simpson's paradox dataset simulation
simulate_ttest Data Simulation

-- U --

update.bayesfactor_models Bayes Factors (BF) for model comparison

-- W --

weighted_posteriors Generate posterior distributions weighted across models
weighted_posteriors.BFBayesFactor Generate posterior distributions weighted across models
weighted_posteriors.blavaan Generate posterior distributions weighted across models
weighted_posteriors.brmsfit Generate posterior distributions weighted across models
weighted_posteriors.data.frame Generate posterior distributions weighted across models
weighted_posteriors.stanreg Generate posterior distributions weighted across models