brms: Bayesian Regression Models using Stan

Fit Bayesian generalized (non-)linear multilevel models using Stan for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit linear, robust linear, binomial, Poisson, survival, response times, ordinal, zero-inflated, hurdle, and even non-linear models all in a multilevel context. Further modeling options include auto-correlation and smoothing terms, user defined dependence structures, censored data, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. In addition, model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation.

AuthorPaul-Christian Bürkner [aut, cre]
Date of publication2016-12-22 00:38:18
MaintainerPaul-Christian Bürkner <paul.buerkner@gmail.com>
LicenseGPL (>= 3)
Version1.3.1
https://github.com/paul-buerkner/brms

View on CRAN

Man pages

as.mcmc.brmsfit: Extract posterior samples for use with the 'coda' package

brm: Fit Bayesian Generalized (Non-)Linear Multilevel Models

brmsfamily: Special Family Functions for 'brms' Models

brmsfit-class: Class 'brmsfit' of models fitted with the 'brms' package

brmsformula: Set up a model formula for use in the 'brms' package

brms-package: Bayesian Regression Models using Stan

coef.brmsfit: Extract model coefficients

cor_ar: AR(p) correlation structure

cor_arma: ARMA(p,q) correlation structure

cor_arr: ARR(r) correlation structure

cor_brms: Correlation structure classes for the 'brms' package

cor_bsts: Basic Bayesian Structural Time Series

cor_ma: MA(q) correlation structure

cov_fixed: Fixed user-defined covariance matrices

cs: Category Specific Predictors in 'brms' Models

diagnostic-quantities: Extract Diagnostic Quantities of 'brms' Models

epilepsy: Epileptic seizure counts

expose_functions: Expose user-defined 'Stan' functions

fitted.brmsfit: Extract Model Fitted Values of 'brmsfit' Objects

fixef.brmsfit: Extract Population-Level Estimates

get_prior: Overview on Priors for 'brms' Models

gr: Set up basic grouping terms in 'brms'

hypothesis: Non-linear hypothesis testing

inhaler: Clarity of inhaler instructions

kidney: Infections in kidney patients

launch_shiny: Interface to 'shinystan'

log_lik.brmsfit: Compute the Pointwise Log-Likelihood

LOO: Compute the LOO information criterion

make_stancode: Stan Code for 'brms' Models

make_standata: Data for 'brms' Models

marginal_effects: Display marginal effects of predictors

marginal_smooths: Display Smooth Terms

me: Predictors with Measurement Error in 'brms' Models

mm: Set up multi-membership grouping terms in 'brms'

mo: Monotonic Predictors in 'brms' Models

ngrps.brmsfit: Number of levels

pairs.brmsfit: Create a matrix of output plots from a 'brmsfit' object

parnames: Extract Parameter Names

plot.brmsfit: Trace and Density Plots for MCMC Samples

posterior_samples: Extract posterior samples

pp_check.brmsfit: Posterior Predictive Checks for 'brmsfit' Objects

predict.brmsfit: Model Predictions of 'brmsfit' Objects

print.brmsfit: Print a summary for a fitted model represented by a 'brmsfit'...

print.brmsprior: Print method for 'brmsprior' objects

prior_samples: Extract prior samples

prior_summary.brmsfit: Extract Priors of a Bayesian Model Fitted with 'brms'

ranef.brmsfit: Extract Group-Level Estimates

residuals.brmsfit: Extract Model Residuals from brmsfit Objects

set_prior: Prior Definitions for 'brms' Models

stancode: Extract Stan Model Code

standata: Extract Data passed to Stan

stanplot: MCMC Plots Implemented in 'bayesplot'

summary.brmsfit: Create a summary of a fitted model represented by a 'brmsfit'...

update.brmsfit: Update 'brms' models

VarCorr.brmsfit: Extract variance and correlation components

vcov.brmsfit: Covariance and Correlation Matrix of Population-Level Effects

WAIC: Compute the WAIC

Files in this package

brms
brms/inst
brms/inst/CITATION
brms/inst/NEWS.Rd
brms/inst/doc
brms/inst/doc/brms_phylogenetics.html
brms/inst/doc/brms_distreg.Rmd
brms/inst/doc/brms_nonlinear.R
brms/inst/doc/brms_monotonic.Rmd
brms/inst/doc/brms_phylogenetics.Rmd
brms/inst/doc/brms_overview.ltx
brms/inst/doc/brms_monotonic.html
brms/inst/doc/brms_families.Rmd
brms/inst/doc/brms_phylogenetics.R
brms/inst/doc/brms_monotonic.R
brms/inst/doc/brms_families.html
brms/inst/doc/brms_nonlinear.html
brms/inst/doc/brms_overview.pdf
brms/inst/doc/brms_distreg.R
brms/inst/doc/brms_distreg.html
brms/inst/doc/brms_nonlinear.Rmd
brms/inst/chunks
brms/inst/chunks/fun_cauchit.stan
brms/inst/chunks/fun_hurdle_lognormal.stan
brms/inst/chunks/fun_cloglog.stan
brms/inst/chunks/data_arma.stan
brms/inst/chunks/fun_cov_matrix_ar1.stan
brms/inst/chunks/tdataD_inv_gaussian.stan
brms/inst/chunks/fun_zero_inflated_beta.stan
brms/inst/chunks/fun_zero_inflated_binomial.stan
brms/inst/chunks/fun_zero_inflated_poisson.stan
brms/inst/chunks/data_mv.stan
brms/inst/chunks/fun_monotonic.stan
brms/inst/chunks/fun_exgaussian.stan
brms/inst/chunks/fun_kronecker.stan
brms/inst/chunks/fun_normal_cov.stan
brms/inst/chunks/tdataD_sparse_X.stan
brms/inst/chunks/fun_von_mises.stan
brms/inst/chunks/fun_student_t_cov.stan
brms/inst/chunks/fun_inv_gaussian.stan
brms/inst/chunks/fun_cov_matrix_ma1.stan
brms/inst/chunks/fun_hurdle_negbinomial.stan
brms/inst/chunks/data_arma_cov.stan
brms/inst/chunks/fun_hurdle_poisson.stan
brms/inst/chunks/fun_tan_half.stan
brms/inst/chunks/fun_hurdle_gamma.stan
brms/inst/chunks/fun_wiener_diffusion.stan
brms/inst/chunks/tdataC_sparse_X.stan
brms/inst/chunks/fun_cov_matrix_arma1.stan
brms/inst/chunks/fun_zero_inflated_negbinomial.stan
brms/inst/chunks/fun_as_matrix.stan
brms/inst/chunks/tdataC_inv_gaussian.stan
brms/tests
brms/tests/testthat.R
brms/tests/testthat
brms/tests/testthat/tests.stan_functions.R
brms/tests/testthat/tests.rename.R
brms/tests/testthat/tests.make_standata.R
brms/tests/testthat/tests.misc.R
brms/tests/testthat/tests.predict.R
brms/tests/testthat/tests.brm.R
brms/tests/testthat/tests.brmsfit-methods.R
brms/tests/testthat/tests.validate.R
brms/tests/testthat/tests.brmsformula.R
brms/tests/testthat/tests.families.R
brms/tests/testthat/tests.fitted.R
brms/tests/testthat/tests.data-helpers.R
brms/tests/testthat/tests.loglik.R
brms/tests/testthat/tests.priors.R
brms/tests/testthat/tests.brmsfit-helpers.R
brms/tests/testthat/tests.make_stancode.R
brms/tests/testthat/tests.stan-helpers.R
brms/tests/testthat/tests.distributions.R
brms/tests/testthat/tests.plots.R
brms/NAMESPACE
brms/data
brms/data/epilepsy.rda
brms/data/inhaler.rda
brms/data/kidney.rda
brms/R
brms/R/misc-methods.R brms/R/extract_draws.R brms/R/brmsfit-methods.R brms/R/correlations.R brms/R/stan-predictor.R brms/R/linear_predictor.R brms/R/make_stancode.R brms/R/priors.R brms/R/brmsformula.R brms/R/stan-helpers.R brms/R/predict.R
brms/R/sysdata.rda
brms/R/families.R brms/R/generics.R brms/R/fitted.R brms/R/brmsfit-helpers.R brms/R/loglik.R brms/R/plots.R brms/R/distributions.R brms/R/brm.R brms/R/make_standata.R brms/R/data-helpers.R brms/R/rename.R brms/R/formula-helpers.R brms/R/lsp.R brms/R/misc.R brms/R/validate.R brms/R/datasets.R brms/R/zzz.R
brms/vignettes
brms/vignettes/brms_distreg.Rmd
brms/vignettes/inhaler_plot.pdf
brms/vignettes/brms_monotonic.Rmd
brms/vignettes/kidney_marginal_effects.pdf
brms/vignettes/brms_phylogenetics.Rmd
brms/vignettes/brms_overview.ltx
brms/vignettes/brms_families.Rmd
brms/vignettes/flowchart.pdf
brms/vignettes/kidney_plot.pdf
brms/vignettes/brms_nonlinear.Rmd
brms/vignettes/citations.bib
brms/README.md
brms/MD5
brms/build
brms/build/vignette.rds
brms/DESCRIPTION
brms/man
brms/man/plot.brmsfit.Rd brms/man/me.Rd brms/man/cs.Rd brms/man/diagnostic-quantities.Rd brms/man/LOO.Rd brms/man/set_prior.Rd brms/man/marginal_effects.Rd brms/man/make_standata.Rd brms/man/expose_functions.Rd brms/man/summary.brmsfit.Rd brms/man/brmsfamily.Rd brms/man/update.brmsfit.Rd brms/man/fixef.brmsfit.Rd brms/man/brmsformula.Rd brms/man/parnames.Rd brms/man/cov_fixed.Rd brms/man/stancode.Rd brms/man/epilepsy.Rd brms/man/brm.Rd brms/man/prior_samples.Rd brms/man/pp_check.brmsfit.Rd brms/man/cor_bsts.Rd brms/man/hypothesis.Rd brms/man/as.mcmc.brmsfit.Rd brms/man/vcov.brmsfit.Rd brms/man/coef.brmsfit.Rd brms/man/cor_brms.Rd brms/man/predict.brmsfit.Rd brms/man/WAIC.Rd brms/man/launch_shiny.Rd brms/man/VarCorr.brmsfit.Rd brms/man/ranef.brmsfit.Rd brms/man/stanplot.Rd brms/man/ngrps.brmsfit.Rd brms/man/mo.Rd brms/man/cor_ar.Rd brms/man/print.brmsfit.Rd brms/man/marginal_smooths.Rd brms/man/prior_summary.brmsfit.Rd brms/man/cor_ma.Rd brms/man/print.brmsprior.Rd brms/man/brms-package.Rd brms/man/log_lik.brmsfit.Rd brms/man/gr.Rd brms/man/kidney.Rd brms/man/make_stancode.Rd brms/man/cor_arma.Rd brms/man/mm.Rd brms/man/brmsfit-class.Rd brms/man/pairs.brmsfit.Rd brms/man/standata.Rd brms/man/inhaler.Rd brms/man/cor_arr.Rd brms/man/fitted.brmsfit.Rd brms/man/residuals.brmsfit.Rd brms/man/get_prior.Rd brms/man/posterior_samples.Rd

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