Bayesian Regression Models using 'Stan'


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Documentation for package ‘brms’ version 2.16.3

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brms-package Bayesian Regression Models using 'Stan'

-- A --

acat Special Family Functions for 'brms' Models
acformula Linear and Non-linear formulas in 'brms'
addition-terms Additional Response Information
add_criterion Add model fit criteria to model objects
add_criterion.brmsfit Add model fit criteria to model objects
add_ic Add model fit criteria to model objects
add_ic.brmsfit Add model fit criteria to model objects
add_ic<- Add model fit criteria to model objects
add_loo Add model fit criteria to model objects
add_rstan_model Add compiled 'rstan' models to 'brmsfit' objects
add_waic Add model fit criteria to model objects
and Index 'brmsfit' objects
ar Set up AR(p) correlation structures
arma Set up ARMA(p,q) correlation structures
as.array.brmsfit Extract Posterior Draws
as.data.frame.brmsfit Extract Posterior Draws
as.matrix.brmsfit Extract Posterior Draws
as.mcmc Extract posterior samples for use with the 'coda' package
as.mcmc.brmsfit Extract posterior samples for use with the 'coda' package
AsymLaplace The Asymmetric Laplace Distribution
asym_laplace Special Family Functions for 'brms' Models
as_draws Transform 'brmsfit' to 'draws' objects
as_draws.brmsfit Transform 'brmsfit' to 'draws' objects
as_draws_array Transform 'brmsfit' to 'draws' objects
as_draws_array.brmsfit Transform 'brmsfit' to 'draws' objects
as_draws_df Transform 'brmsfit' to 'draws' objects
as_draws_df.brmsfit Transform 'brmsfit' to 'draws' objects
as_draws_list Transform 'brmsfit' to 'draws' objects
as_draws_list.brmsfit Transform 'brmsfit' to 'draws' objects
as_draws_matrix Transform 'brmsfit' to 'draws' objects
as_draws_matrix.brmsfit Transform 'brmsfit' to 'draws' objects
as_draws_rvars Transform 'brmsfit' to 'draws' objects
as_draws_rvars.brmsfit Transform 'brmsfit' to 'draws' objects
autocor (Deprecated) Extract Autocorrelation Objects
autocor-terms Autocorrelation structures
autocor.brmsfit (Deprecated) Extract Autocorrelation Objects

-- B --

bayes_factor Bayes Factors from Marginal Likelihoods
bayes_factor.brmsfit Bayes Factors from Marginal Likelihoods
bayes_R2 Compute a Bayesian version of R-squared for regression models
bayes_R2.brmsfit Compute a Bayesian version of R-squared for regression models
bernoulli Special Family Functions for 'brms' Models
Beta Special Family Functions for 'brms' Models
bf Set up a model formula for use in 'brms'
bf-helpers Linear and Non-linear formulas in 'brms'
bridge_sampler Log Marginal Likelihood via Bridge Sampling
bridge_sampler.brmsfit Log Marginal Likelihood via Bridge Sampling
brm Fit Bayesian Generalized (Non-)Linear Multivariate Multilevel Models
brms Bayesian Regression Models using 'Stan'
brmsfamily Special Family Functions for 'brms' Models
brmsfit Class 'brmsfit' of models fitted with the 'brms' package
brmsfit-class Class 'brmsfit' of models fitted with the 'brms' package
brmsformula Set up a model formula for use in 'brms'
brmsformula-helpers Linear and Non-linear formulas in 'brms'
brmshypothesis Descriptions of 'brmshypothesis' Objects
brmsprior Prior Definitions for 'brms' Models
brmsprior-class Prior Definitions for 'brms' Models
brmsterms Parse Formulas of 'brms' Models
brmsterms.brmsformula Parse Formulas of 'brms' Models
brmsterms.default Parse Formulas of 'brms' Models
brmsterms.mvbrmsformula Parse Formulas of 'brms' Models
brm_multiple Run the same 'brms' model on multiple datasets

-- C --

car Spatial conditional autoregressive (CAR) structures
categorical Special Family Functions for 'brms' Models
chains, Index 'brmsfit' objects
coef.brmsfit Extract Model Coefficients
combine_models Combine Models fitted with 'brms'
compare_ic Compare Information Criteria of Different Models
conditional_effects Display Conditional Effects of Predictors
conditional_effects.brmsfit Display Conditional Effects of Predictors
conditional_smooths Display Smooth Terms
conditional_smooths.brmsfit Display Smooth Terms
control_params Extract Control Parameters of the NUTS Sampler
control_params.brmsfit Extract Control Parameters of the NUTS Sampler
cor_ar (Deprecated) AR(p) correlation structure
cor_arma (Deprecated) ARMA(p,q) correlation structure
cor_arma-class (Deprecated) ARMA(p,q) correlation structure
cor_brms (Deprecated) Correlation structure classes for the 'brms' package
cor_brms-class (Deprecated) Correlation structure classes for the 'brms' package
cor_car (Deprecated) Spatial conditional autoregressive (CAR) structures
cor_cosy (Deprecated) Compound Symmetry (COSY) Correlation Structure
cor_cosy-class (Deprecated) Compound Symmetry (COSY) Correlation Structure
cor_errorsar (Deprecated) Spatial simultaneous autoregressive (SAR) structures
cor_fixed (Deprecated) Fixed user-defined covariance matrices
cor_icar (Deprecated) Spatial conditional autoregressive (CAR) structures
cor_lagsar (Deprecated) Spatial simultaneous autoregressive (SAR) structures
cor_ma (Deprecated) MA(q) correlation structure
cor_sar (Deprecated) Spatial simultaneous autoregressive (SAR) structures
cosy Set up COSY correlation structures
cov_fixed (Deprecated) Fixed user-defined covariance matrices
cox Special Family Functions for 'brms' Models
cratio Special Family Functions for 'brms' Models
cs Category Specific Predictors in 'brms' Models
cse Category Specific Predictors in 'brms' Models
cumulative Special Family Functions for 'brms' Models
customfamily Custom Families in 'brms' Models
custom_family Custom Families in 'brms' Models

-- D --

dasym_laplace The Asymmetric Laplace Distribution
ddirichlet The Dirichlet Distribution
density_ratio Compute Density Ratios
dexgaussian The Exponentially Modified Gaussian Distribution
dfrechet The Frechet Distribution
dgen_extreme_value The Generalized Extreme Value Distribution
dhurdle_gamma Hurdle Distributions
dhurdle_lognormal Hurdle Distributions
dhurdle_negbinomial Hurdle Distributions
dhurdle_poisson Hurdle Distributions
diagnostic-quantities Extract Diagnostic Quantities of 'brms' Models
dinv_gaussian The Inverse Gaussian Distribution
Dirichlet The Dirichlet Distribution
dirichlet Special Family Functions for 'brms' Models
dmulti_normal The Multivariate Normal Distribution
dmulti_student_t The Multivariate Student-t Distribution
draws-brms Transform 'brmsfit' to 'draws' objects
draws-index-brms Index 'brmsfit' objects
draws. Index 'brmsfit' objects
dshifted_lnorm The Shifted Log Normal Distribution
dskew_normal The Skew-Normal Distribution
dstudent_t The Student-t Distribution
dvon_mises The von Mises Distribution
dwiener The Wiener Diffusion Model Distribution
dzero_inflated_beta Zero-Inflated Distributions
dzero_inflated_binomial Zero-Inflated Distributions
dzero_inflated_negbinomial Zero-Inflated Distributions
dzero_inflated_poisson Zero-Inflated Distributions

-- E --

emmeans-brms-helpers Support Functions for 'emmeans'
emm_basis.brmsfit Support Functions for 'emmeans'
empty_prior Prior Definitions for 'brms' Models
epilepsy Epileptic seizure counts
ExGaussian The Exponentially Modified Gaussian Distribution
exgaussian Special Family Functions for 'brms' Models
exponential Special Family Functions for 'brms' Models
expose_functions Expose user-defined 'Stan' functions
expose_functions.brmsfit Expose user-defined 'Stan' functions
expp1 Exponential function plus one.
extract_draws Prepare Predictions

-- F --

family.brmsfit Extract Model Family Objects
fcor Fixed residual correlation (FCOR) structures
fitted.brmsfit Expected Values of the Posterior Predictive Distribution
fixef Extract Population-Level Estimates
fixef.brmsfit Extract Population-Level Estimates
Frechet The Frechet Distribution
frechet Special Family Functions for 'brms' Models

-- G --

GenExtremeValue The Generalized Extreme Value Distribution
gen_extreme_value Special Family Functions for 'brms' Models
geometric Special Family Functions for 'brms' Models
get_dpar Draws of a Distributional Parameter
get_prior Overview on Priors for 'brms' Models
get_refmodel.brmsfit Projection Predictive Variable Selection: Get Reference Model
gp Set up Gaussian process terms in 'brms'
gr Set up basic grouping terms in 'brms'

-- H --

horseshoe Regularized horseshoe priors in 'brms'
Hurdle Hurdle Distributions
hurdle_gamma Special Family Functions for 'brms' Models
hurdle_lognormal Special Family Functions for 'brms' Models
hurdle_negbinomial Special Family Functions for 'brms' Models
hurdle_poisson Special Family Functions for 'brms' Models
hypothesis Non-Linear Hypothesis Testing
hypothesis.brmsfit Non-Linear Hypothesis Testing
hypothesis.default Non-Linear Hypothesis Testing

-- I --

Index Index 'brmsfit' objects
inhaler Clarity of inhaler instructions
InvGaussian The Inverse Gaussian Distribution
inv_logit_scaled Scaled inverse logit-link
is.brmsfit Checks if argument is a 'brmsfit' object
is.brmsfit_multiple Checks if argument is a 'brmsfit_multiple' object
is.brmsformula Checks if argument is a 'brmsformula' object
is.brmsprior Checks if argument is a 'brmsprior' object
is.brmsterms Checks if argument is a 'brmsterms' object
is.cor_arma Check if argument is a correlation structure
is.cor_brms Check if argument is a correlation structure
is.cor_car Check if argument is a correlation structure
is.cor_cosy Check if argument is a correlation structure
is.cor_fixed Check if argument is a correlation structure
is.cor_sar Check if argument is a correlation structure
is.mvbrmsformula Checks if argument is a 'mvbrmsformula' object
is.mvbrmsterms Checks if argument is a 'mvbrmsterms' object
iterations, Index 'brmsfit' objects

-- K --

kfold K-Fold Cross-Validation
kfold.brmsfit K-Fold Cross-Validation
kfold_predict Predictions from K-Fold Cross-Validation
kidney Infections in kidney patients

-- L --

lasso Set up a lasso prior in 'brms'
launch_shinystan Interface to 'shinystan'
launch_shinystan.brmsfit Interface to 'shinystan'
lf Linear and Non-linear formulas in 'brms'
logit_scaled Scaled logit-link
logLik.brmsfit Compute the Pointwise Log-Likelihood
logm1 Logarithm with a minus one offset.
lognormal Special Family Functions for 'brms' Models
log_lik Compute the Pointwise Log-Likelihood
log_lik.brmsfit Compute the Pointwise Log-Likelihood
log_posterior Extract Diagnostic Quantities of 'brms' Models
log_posterior.brmsfit Extract Diagnostic Quantities of 'brms' Models
LOO Efficient approximate leave-one-out cross-validation (LOO)
loo Efficient approximate leave-one-out cross-validation (LOO)
LOO.brmsfit Efficient approximate leave-one-out cross-validation (LOO)
loo.brmsfit Efficient approximate leave-one-out cross-validation (LOO)
loo_compare Model comparison with the 'loo' package
loo_compare.brmsfit Model comparison with the 'loo' package
loo_linpred Compute Weighted Expectations Using LOO
loo_linpred.brmsfit Compute Weighted Expectations Using LOO
loo_model_weights Model averaging via stacking or pseudo-BMA weighting.
loo_model_weights.brmsfit Model averaging via stacking or pseudo-BMA weighting.
loo_moment_match Moment matching for efficient approximate leave-one-out cross-validation
loo_moment_match.brmsfit Moment matching for efficient approximate leave-one-out cross-validation
loo_predict Compute Weighted Expectations Using LOO
loo_predict.brmsfit Compute Weighted Expectations Using LOO
loo_predictive_interval Compute Weighted Expectations Using LOO
loo_predictive_interval.brmsfit Compute Weighted Expectations Using LOO
loo_R2 Compute a LOO-adjusted R-squared for regression models
loo_R2.brmsfit Compute a LOO-adjusted R-squared for regression models
loo_subsample Efficient approximate leave-one-out cross-validation (LOO) using subsampling
loo_subsample.brmsfit Efficient approximate leave-one-out cross-validation (LOO) using subsampling
loss Cumulative Insurance Loss Payments

-- M --

ma Set up MA(q) correlation structures
make_conditions Prepare Fully Crossed Conditions
make_stancode Stan Code for 'brms' Models
make_standata Data for 'brms' Models
marginal_effects Display Conditional Effects of Predictors
marginal_effects.brmsfit Display Conditional Effects of Predictors
marginal_smooths Display Smooth Terms
marginal_smooths.brmsfit Display Smooth Terms
mcmc_plot MCMC Plots Implemented in 'bayesplot'
mcmc_plot.brmsfit MCMC Plots Implemented in 'bayesplot'
me Predictors with Measurement Error in 'brms' Models
mi Predictors with Missing Values in 'brms' Models
mixture Finite Mixture Families in 'brms'
mm Set up multi-membership grouping terms in 'brms'
mmc Multi-Membership Covariates
mo Monotonic Predictors in 'brms' Models
model_weights Model Weighting Methods
model_weights.brmsfit Model Weighting Methods
multinomial Special Family Functions for 'brms' Models
MultiNormal The Multivariate Normal Distribution
MultiStudentT The Multivariate Student-t Distribution
mvbf Set up a multivariate model formula for use in 'brms'
mvbind Bind response variables in multivariate models
mvbrmsformula Set up a multivariate model formula for use in 'brms'

-- N --

nchains Index 'brmsfit' objects
nchains.brmsfit Index 'brmsfit' objects
ndraws Index 'brmsfit' objects
ndraws.brmsfit Index 'brmsfit' objects
neff_ratio Extract Diagnostic Quantities of 'brms' Models
neff_ratio.brmsfit Extract Diagnostic Quantities of 'brms' Models
negbinomial Special Family Functions for 'brms' Models
ngrps Number of Grouping Factor Levels
ngrps.brmsfit Number of Grouping Factor Levels
niterations Index 'brmsfit' objects
niterations.brmsfit Index 'brmsfit' objects
nlf Linear and Non-linear formulas in 'brms'
nsamples (Deprecated) Number of Posterior Samples
nsamples.brmsfit (Deprecated) Number of Posterior Samples
nuts_params Extract Diagnostic Quantities of 'brms' Models
nuts_params.brmsfit Extract Diagnostic Quantities of 'brms' Models
nvariables Index 'brmsfit' objects
nvariables.brmsfit Index 'brmsfit' objects

-- O --

opencl GPU support in Stan via OpenCL

-- P --

pairs.brmsfit Create a matrix of output plots from a 'brmsfit' object
parnames Extract Parameter Names
parnames.brmsfit Extract Parameter Names
parse_bf Parse Formulas of 'brms' Models
pasym_laplace The Asymmetric Laplace Distribution
pexgaussian The Exponentially Modified Gaussian Distribution
pfrechet The Frechet Distribution
pgen_extreme_value The Generalized Extreme Value Distribution
phurdle_gamma Hurdle Distributions
phurdle_lognormal Hurdle Distributions
phurdle_negbinomial Hurdle Distributions
phurdle_poisson Hurdle Distributions
pinv_gaussian The Inverse Gaussian Distribution
plot.brmsfit Trace and Density Plots for MCMC Draws
plot.brmshypothesis Descriptions of 'brmshypothesis' Objects
plot.brms_conditional_effects Display Conditional Effects of Predictors
posterior_average Posterior draws of parameters averaged across models
posterior_average.brmsfit Posterior draws of parameters averaged across models
posterior_epred Expected Values of the Posterior Predictive Distribution
posterior_epred.brmsfit Expected Values of the Posterior Predictive Distribution
posterior_interval Compute posterior uncertainty intervals
posterior_interval.brmsfit Compute posterior uncertainty intervals
posterior_linpred Posterior Draws of the Linear Predictor
posterior_linpred.brmsfit Posterior Draws of the Linear Predictor
posterior_predict Draws from the Posterior Predictive Distribution
posterior_predict.brmsfit Draws from the Posterior Predictive Distribution
posterior_samples (Deprecated) Extract Posterior Samples
posterior_samples.brmsfit (Deprecated) Extract Posterior Samples
posterior_smooths Posterior Predictions of Smooth Terms
posterior_smooths.brmsfit Posterior Predictions of Smooth Terms
posterior_summary Summarize Posterior draws
posterior_summary.brmsfit Summarize Posterior draws
posterior_summary.default Summarize Posterior draws
posterior_table Table Creation for Posterior Draws
post_prob Posterior Model Probabilities from Marginal Likelihoods
post_prob.brmsfit Posterior Model Probabilities from Marginal Likelihoods
pp_average Posterior predictive draws averaged across models
pp_average.brmsfit Posterior predictive draws averaged across models
pp_check Posterior Predictive Checks for 'brmsfit' Objects
pp_check.brmsfit Posterior Predictive Checks for 'brmsfit' Objects
pp_expect Expected Values of the Posterior Predictive Distribution
pp_mixture Posterior Probabilities of Mixture Component Memberships
pp_mixture.brmsfit Posterior Probabilities of Mixture Component Memberships
predict.brmsfit Draws from the Posterior Predictive Distribution
predictive_error Posterior Draws of Predictive Errors
predictive_error.brmsfit Posterior Draws of Predictive Errors
predictive_interval Predictive Intervals
predictive_interval.brmsfit Predictive Intervals
prepare_predictions Prepare Predictions
prepare_predictions.brmsfit Prepare Predictions
print.brmsfit Print a summary for a fitted model represented by a 'brmsfit' object
print.brmshypothesis Descriptions of 'brmshypothesis' Objects
print.brmsprior Print method for 'brmsprior' objects
print.brmssummary Print a summary for a fitted model represented by a 'brmsfit' object
prior Prior Definitions for 'brms' Models
prior_ Prior Definitions for 'brms' Models
prior_draws Extract Prior Draws
prior_draws.brmsfit Extract Prior Draws
prior_samples Extract Prior Draws
prior_string Prior Definitions for 'brms' Models
prior_summary Extract Priors of a Bayesian Model Fitted with 'brms'
prior_summary.brmsfit Extract Priors of a Bayesian Model Fitted with 'brms'
pshifted_lnorm The Shifted Log Normal Distribution
pskew_normal The Skew-Normal Distribution
pstudent_t The Student-t Distribution
pvon_mises The von Mises Distribution
pzero_inflated_beta Zero-Inflated Distributions
pzero_inflated_binomial Zero-Inflated Distributions
pzero_inflated_negbinomial Zero-Inflated Distributions
pzero_inflated_poisson Zero-Inflated Distributions

-- Q --

qasym_laplace The Asymmetric Laplace Distribution
qfrechet The Frechet Distribution
qshifted_lnorm The Shifted Log Normal Distribution
qskew_normal The Skew-Normal Distribution
qstudent_t The Student-t Distribution

-- R --

R2D2 R2-D2 Priors in 'brms'
ranef Extract Group-Level Estimates
ranef.brmsfit Extract Group-Level Estimates
rasym_laplace The Asymmetric Laplace Distribution
rdirichlet The Dirichlet Distribution
recompile_model Recompile Stan models in 'brmsfit' objects
recover_data.brmsfit Support Functions for 'emmeans'
reloo Compute exact cross-validation for problematic observations
reloo.brmsfit Compute exact cross-validation for problematic observations
reloo.loo Compute exact cross-validation for problematic observations
rename_pars Rename Parameters
residuals.brmsfit Posterior Draws of Residuals/Predictive Errors
resp_cat Additional Response Information
resp_cens Additional Response Information
resp_dec Additional Response Information
resp_index Additional Response Information
resp_mi Additional Response Information
resp_rate Additional Response Information
resp_se Additional Response Information
resp_subset Additional Response Information
resp_thres Additional Response Information
resp_trials Additional Response Information
resp_trunc Additional Response Information
resp_vint Additional Response Information
resp_vreal Additional Response Information
resp_weights Additional Response Information
restructure Restructure Old 'brmsfit' Objects
rexgaussian The Exponentially Modified Gaussian Distribution
rfrechet The Frechet Distribution
rgen_extreme_value The Generalized Extreme Value Distribution
rhat Extract Diagnostic Quantities of 'brms' Models
rhat.brmsfit Extract Diagnostic Quantities of 'brms' Models
rinv_gaussian The Inverse Gaussian Distribution
rmulti_normal The Multivariate Normal Distribution
rmulti_student_t The Multivariate Student-t Distribution
rows2labels Convert Rows to Labels
rshifted_lnorm The Shifted Log Normal Distribution
rskew_normal The Skew-Normal Distribution
rstudent_t The Student-t Distribution
rvon_mises The von Mises Distribution
rwiener The Wiener Diffusion Model Distribution

-- S --

s Defining smooths in 'brms' formulas
sar Spatial simultaneous autoregressive (SAR) structures
save_pars Control Saving of Parameter Draws
set_mecor Linear and Non-linear formulas in 'brms'
set_nl Linear and Non-linear formulas in 'brms'
set_prior Prior Definitions for 'brms' Models
set_rescor Linear and Non-linear formulas in 'brms'
Shifted_Lognormal The Shifted Log Normal Distribution
shifted_lognormal Special Family Functions for 'brms' Models
SkewNormal The Skew-Normal Distribution
skew_normal Special Family Functions for 'brms' Models
sratio Special Family Functions for 'brms' Models
stancode Extract Stan model code
stancode.brmsfit Extract Stan model code
standata Extract data passed to Stan
standata.brmsfit Extract data passed to Stan
stanplot MCMC Plots Implemented in 'bayesplot'
stanplot.brmsfit MCMC Plots Implemented in 'bayesplot'
stanvar User-defined variables passed to Stan
stanvars User-defined variables passed to Stan
student Special Family Functions for 'brms' Models
StudentT The Student-t Distribution
summary.brmsfit Create a summary of a fitted model represented by a 'brmsfit' object

-- T --

t2 Defining smooths in 'brms' formulas
theme_black (Deprecated) Black Theme for 'ggplot2' Graphics
theme_default Default 'bayesplot' Theme for 'ggplot2' Graphics
threading Threading in Stan

-- U --

update.brmsfit Update 'brms' models
update.brmsfit_multiple Update 'brms' models based on multiple data sets
update_adterms Update Formula Addition Terms

-- V --

validate_newdata Validate New Data
validate_prior Validate Prior for 'brms' Models
VarCorr Extract Variance and Correlation Components
VarCorr.brmsfit Extract Variance and Correlation Components
variables Index 'brmsfit' objects
variables, Index 'brmsfit' objects
variables.brmsfit Index 'brmsfit' objects
vcov.brmsfit Covariance and Correlation Matrix of Population-Level Effects
VonMises The von Mises Distribution
von_mises Special Family Functions for 'brms' Models

-- W --

WAIC Widely Applicable Information Criterion (WAIC)
waic Widely Applicable Information Criterion (WAIC)
WAIC.brmsfit Widely Applicable Information Criterion (WAIC)
waic.brmsfit Widely Applicable Information Criterion (WAIC)
weibull Special Family Functions for 'brms' Models
Wiener The Wiener Diffusion Model Distribution
wiener Special Family Functions for 'brms' Models

-- Z --

ZeroInflated Zero-Inflated Distributions
zero_inflated_beta Special Family Functions for 'brms' Models
zero_inflated_binomial Special Family Functions for 'brms' Models
zero_inflated_negbinomial Special Family Functions for 'brms' Models
zero_inflated_poisson Special Family Functions for 'brms' Models
zero_one_inflated_beta Special Family Functions for 'brms' Models