# Bayesian Applied Regression Modeling via Stan

## Documentation for package ‘rstanarm’ version 2.19.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

A B C D E F H K L M N P Q R S T U V W

rstanarm-package | Applied Regression Modeling via RStan

## -- A --

adapt_delta | 'adapt_delta': Target average acceptance probability
as.array.stanreg | Extract the posterior sample
as.data.frame.stanreg | Extract the posterior sample
as.data.frame.summary.stanreg | Summary method for stanreg objects
as.matrix.stanreg | Extract the posterior sample
available-algorithms | Estimation algorithms available for 'rstanarm' models
available-models | Modeling functions available in 'rstanarm'

## -- B --

bayes_R2 | Compute a Bayesian version of R-squared or LOO-adjusted R-squared for regression models.
bayes_R2.stanreg | Compute a Bayesian version of R-squared or LOO-adjusted R-squared for regression models.
bball1970 | Datasets for rstanarm examples
bball2006 | Datasets for rstanarm examples

## -- C --

cauchy | Prior distributions and options
coef.stanmvreg | Methods for stanmvreg objects
coef.stanreg | Methods for stanreg objects
compare_models | Information criteria and cross-validation
confint.stanreg | Methods for stanreg objects

## -- D --

decov | Prior distributions and options
dirichlet | Prior distributions and options

## -- E --

example_jm | Example joint longitudinal and time-to-event model
example_model | Example model
exponential | Prior distributions and options

## -- F --

fitted.stanmvreg | Methods for stanmvreg objects
fitted.stanreg | Methods for stanreg objects
fixef | Methods for stanreg objects
fixef.stanmvreg | Methods for stanmvreg objects
fixef.stanreg | Methods for stanreg objects
formula.stanmvreg | Methods for stanmvreg objects

## -- H --

hs | Prior distributions and options
hs_plus | Prior distributions and options

## -- K --

kfold | K-fold cross-validation
kfold.stanreg | K-fold cross-validation
kidiq | Datasets for rstanarm examples

## -- L --

laplace | Prior distributions and options
lasso | Prior distributions and options
launch_shinystan | Using the ShinyStan GUI with rstanarm models
launch_shinystan.stanreg | Using the ShinyStan GUI with rstanarm models
lkj | Prior distributions and options
log_lik | Pointwise log-likelihood matrix
log_lik.stanjm | Pointwise log-likelihood matrix
log_lik.stanmvreg | Pointwise log-likelihood matrix
log_lik.stanreg | Pointwise log-likelihood matrix
loo | Information criteria and cross-validation
loo.stanreg | Information criteria and cross-validation
loo_compare | Information criteria and cross-validation
loo_compare.stanreg | Information criteria and cross-validation
loo_compare.stanreg_list | Information criteria and cross-validation
loo_linpred | Compute weighted expectations using LOO
loo_linpred.stanreg | Compute weighted expectations using LOO
loo_model_weights | Information criteria and cross-validation
loo_model_weights.stanreg_list | Information criteria and cross-validation
loo_predict | Compute weighted expectations using LOO
loo_predict.stanreg | Compute weighted expectations using LOO
loo_predictive_interval | Compute weighted expectations using LOO
loo_predictive_interval.stanreg | Compute weighted expectations using LOO
loo_R2 | Compute a Bayesian version of R-squared or LOO-adjusted R-squared for regression models.
loo_R2.stanreg | Compute a Bayesian version of R-squared or LOO-adjusted R-squared for regression models.

## -- M --

mortality | Datasets for rstanarm examples

## -- N --

neg_binomial_2 | Family function for negative binomial GLMs
ngrps | Methods for stanreg objects
ngrps.stanmvreg | Methods for stanmvreg objects
ngrps.stanreg | Methods for stanreg objects
nobs.stanmvreg | Methods for stanreg objects
nobs.stanreg | Methods for stanreg objects
normal | Prior distributions and options
nsamples | Methods for stanreg objects
nsamples.stanreg | Methods for stanreg objects

## -- P --

pairs.stanreg | Pairs method for stanreg objects
pairs_condition | Pairs method for stanreg objects
pairs_style_np | Pairs method for stanreg objects
pbcLong | Datasets for rstanarm examples
pbcSurv | Datasets for rstanarm examples
plot.predict.stanjm | Plot the estimated subject-specific or marginal longitudinal trajectory
plot.stanreg | Plot method for stanreg objects
plot.survfit.stanjm | Plot the estimated subject-specific or marginal survival function
plot_nonlinear | Bayesian generalized linear additive models with optional group-specific terms via Stan
plot_stack_jm | Plot the estimated subject-specific or marginal survival function
posterior_interval | Posterior uncertainty intervals
posterior_interval.stanreg | Posterior uncertainty intervals
posterior_linpred | Posterior distribution of the linear predictor
posterior_linpred.stanreg | Posterior distribution of the linear predictor
posterior_predict | Draw from posterior predictive distribution
posterior_predict.stanmvreg | Draw from posterior predictive distribution
posterior_predict.stanreg | Draw from posterior predictive distribution
posterior_survfit | Estimate subject-specific or standardised survival probabilities
posterior_traj | Estimate the subject-specific or marginal longitudinal trajectory
posterior_vs_prior | Juxtapose prior and posterior
posterior_vs_prior.stanreg | Juxtapose prior and posterior
pp_check | Graphical posterior predictive checks
pp_check.stanreg | Graphical posterior predictive checks
pp_validate | Model validation via simulation
predict.stanreg | Predict method for stanreg objects
predictive_error | In-sample or out-of-sample predictive errors
predictive_error.ppd | In-sample or out-of-sample predictive errors
predictive_error.stanreg | In-sample or out-of-sample predictive errors
predictive_interval | Predictive intervals
predictive_interval.ppd | Predictive intervals
predictive_interval.stanreg | Predictive intervals
print.stanmvreg | Print method for stanreg objects
print.stanreg | Print method for stanreg objects
print.stanreg_list | Create lists of fitted model objects, combine them, or append new models to existing lists of models.
print.summary.stanmvreg | Summary method for stanreg objects
print.summary.stanreg | Summary method for stanreg objects
priors | Prior distributions and options
prior_options | Deprecated functions
prior_summary | Summarize the priors used for an rstanarm model
prior_summary.stanreg | Summarize the priors used for an rstanarm model
product_normal | Prior distributions and options
ps_check | Graphical checks of the estimated survival function

## -- Q --

QR-argument | The 'QR' argument

## -- R --

R2 | Prior distributions and options
radon | Datasets for rstanarm examples
ranef | Methods for stanreg objects
ranef.stanmvreg | Methods for stanmvreg objects
ranef.stanreg | Methods for stanreg objects
residuals.stanmvreg | Methods for stanmvreg objects
residuals.stanreg | Methods for stanreg objects
roaches | Datasets for rstanarm examples
rstanarm | Applied Regression Modeling via RStan
rstanarm-datasets | Datasets for rstanarm examples
rstanarm-deprecated | Deprecated functions

## -- S --

se.stanmvreg | Methods for stanmvreg objects
se.stanreg | Methods for stanreg objects
sigma | Methods for stanreg objects
sigma.stanmvreg | Methods for stanmvreg objects
sigma.stanreg | Methods for stanreg objects
stanjm_list | Create lists of fitted model objects, combine them, or append new models to existing lists of models.
stanmvreg-methods | Methods for stanmvreg objects
stanmvreg_list | Create lists of fitted model objects, combine them, or append new models to existing lists of models.
stanreg-methods | Methods for stanreg objects
stanreg-objects | Fitted model objects
stanreg_list | Create lists of fitted model objects, combine them, or append new models to existing lists of models.
stan_aov | Bayesian regularized linear models via Stan
stan_betareg | Bayesian beta regression models via Stan
stan_betareg.fit | Bayesian beta regression models via Stan
stan_biglm | Bayesian regularized linear but big models via Stan
stan_biglm.fit | Bayesian regularized linear but big models via Stan
stan_clogit | Conditional logistic (clogit) regression models via Stan
stan_gamm4 | Bayesian generalized linear additive models with optional group-specific terms via Stan
stan_glm | Bayesian generalized linear models via Stan
stan_glm.fit | Bayesian generalized linear models via Stan
stan_glm.nb | Bayesian generalized linear models via Stan
stan_glmer | Bayesian generalized linear models with group-specific terms via Stan
stan_glmer.nb | Bayesian generalized linear models with group-specific terms via Stan
stan_jm | Bayesian joint longitudinal and time-to-event models via Stan
stan_lm | Bayesian regularized linear models via Stan
stan_lm.fit | Bayesian regularized linear models via Stan
stan_lm.wfit | Bayesian regularized linear models via Stan
stan_lmer | Bayesian generalized linear models with group-specific terms via Stan
stan_mvmer | Bayesian multivariate generalized linear models with correlated group-specific terms via Stan
stan_nlmer | Bayesian nonlinear models with group-specific terms via Stan
stan_polr | Bayesian ordinal regression models via Stan
stan_polr.fit | Bayesian ordinal regression models via Stan
student_t | Prior distributions and options
summary.stanmvreg | Summary method for stanreg objects
summary.stanreg | Summary method for stanreg objects

## -- T --

tumors | Datasets for rstanarm examples

## -- U --

update.stanjm | Methods for stanmvreg objects
update.stanmvreg | Methods for stanmvreg objects
update.stanreg | Methods for stanreg objects

## -- V --

VarCorr | Methods for stanreg objects
VarCorr.stanreg | Methods for stanreg objects
vcov.stanreg | Methods for stanreg objects

## -- W --

waic | Information criteria and cross-validation
waic.stanreg | Information criteria and cross-validation
wells | Datasets for rstanarm examples