├── .Rbuildignore ├── .covrignore ├── .gitattributes ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── recheck.yml ├── .gitignore ├── .lintr ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── add_draws.R ├── combine_chains.R ├── compare_levels.R ├── compose_data.R ├── density_bins.R ├── deprecated.R ├── emmeans_comparison.R ├── epred_draws.R ├── epred_rvars.R ├── flip_aes.R ├── gather_draws.R ├── gather_emmeans_draws.R ├── gather_pairs.R ├── gather_rvars.R ├── gather_variables.R ├── get_variables.R ├── ggdist-curve_interval.R ├── ggdist-cut_cdf_qi.R ├── ggdist-geom_dotsinterval.R ├── ggdist-geom_interval.R ├── ggdist-geom_lineribbon.R ├── ggdist-geom_pointinterval.R ├── ggdist-geom_slabinterval.R ├── ggdist-lkjcorr_marginal.R ├── ggdist-parse_dist.R ├── ggdist-scales.R ├── ggdist-stat_dist_slabinterval.R ├── ggdist-stat_dotsinterval.R ├── ggdist-stat_interval.R ├── ggdist-stat_lineribbon.R ├── ggdist-stat_pointinterval.R ├── ggdist-stat_sample_slabinterval.R ├── ggdist-stat_slabinterval.R ├── ggdist-student_t.R ├── ggdist-theme_ggdist.R ├── ggdist-tidy_format_translators.R ├── global_variables.R ├── linpred_draws.R ├── linpred_rvars.R ├── nest_rvars.R ├── onAttach.R ├── point_interval.R ├── predict_curve.R ├── predicted_draws.R ├── predicted_rvars.R ├── recover_types.R ├── residual_draws.R ├── sample_draws.R ├── spread_draws.R ├── spread_rvars.R ├── summarise_draws.R ├── testthat.R ├── tidy_draws.R ├── tidybayes-models.R ├── tidybayes-package.R ├── ungather_draws.R ├── unspread_draws.R ├── util.R └── x_at_y.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── benchmarks.Rmd ├── build_test_models.R ├── clean_vignette_cache.sh ├── codecov.yml ├── cran-comments.md ├── docs ├── 404.html ├── LICENSE-text.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── index.html │ ├── slabinterval_family.png │ ├── tidy-brms.html │ ├── tidy-brms_files │ │ └── figure-html │ │ │ ├── hops_lines-1.gif │ │ │ ├── hops_ordinal_ribbon_lines-1.gif │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-27-1.png │ │ │ ├── unnamed-chunk-28-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-30-1.png │ │ │ ├── unnamed-chunk-31-1.png │ │ │ ├── unnamed-chunk-32-1.png │ │ │ ├── unnamed-chunk-33-1.png │ │ │ ├── unnamed-chunk-35-1.png │ │ │ ├── unnamed-chunk-36-1.png │ │ │ ├── unnamed-chunk-37-1.png │ │ │ ├── unnamed-chunk-38-1.png │ │ │ ├── unnamed-chunk-39-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-40-1.png │ │ │ ├── unnamed-chunk-43-1.png │ │ │ ├── unnamed-chunk-45-1.png │ │ │ ├── unnamed-chunk-46-1.png │ │ │ ├── unnamed-chunk-47-1.png │ │ │ ├── unnamed-chunk-48-1.png │ │ │ ├── unnamed-chunk-49-1.png │ │ │ ├── unnamed-chunk-50-1.png │ │ │ ├── unnamed-chunk-51-1.png │ │ │ └── unnamed-chunk-52-1.png │ ├── tidy-brms_hops_lines.gif │ ├── tidy-brms_hops_ordinal_ribbon_lines.gif │ ├── tidy-posterior.html │ ├── tidy-posterior_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-27-1.png │ │ │ ├── unnamed-chunk-28-1.png │ │ │ ├── unnamed-chunk-30-1.png │ │ │ ├── unnamed-chunk-31-1.png │ │ │ ├── unnamed-chunk-32-1.png │ │ │ ├── unnamed-chunk-33-1.png │ │ │ ├── unnamed-chunk-34-1.png │ │ │ ├── unnamed-chunk-35-1.png │ │ │ ├── unnamed-chunk-36-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-40-1.png │ │ │ ├── unnamed-chunk-42-1.png │ │ │ └── unnamed-chunk-46-1.png │ ├── tidy-rstanarm.html │ ├── tidy-rstanarm_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-28-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-30-1.png │ │ │ ├── unnamed-chunk-31-1.png │ │ │ ├── unnamed-chunk-32-1.png │ │ │ ├── unnamed-chunk-33-1.png │ │ │ ├── unnamed-chunk-34-1.png │ │ │ ├── unnamed-chunk-35-1.png │ │ │ ├── unnamed-chunk-39-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-40-1.png │ │ │ └── unnamed-chunk-41-1.png │ ├── tidybayes-residuals.html │ ├── tidybayes-residuals_files │ │ └── figure-html │ │ │ ├── resid_hops_1-1.gif │ │ │ ├── resid_hops_2-1.gif │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── tidybayes-residuals_resid_hops_1.gif │ ├── tidybayes-residuals_resid_hops_2.gif │ ├── tidybayes.html │ └── tidybayes_files │ │ └── figure-html │ │ ├── unnamed-chunk-18-1.png │ │ ├── unnamed-chunk-19-1.png │ │ ├── unnamed-chunk-20-1.png │ │ ├── unnamed-chunk-22-1.png │ │ ├── unnamed-chunk-23-1.png │ │ ├── unnamed-chunk-26-1.png │ │ ├── unnamed-chunk-29-1.png │ │ ├── unnamed-chunk-30-1.png │ │ ├── unnamed-chunk-31-1.png │ │ ├── unnamed-chunk-37-1.png │ │ ├── unnamed-chunk-38-1.png │ │ ├── unnamed-chunk-4-1.png │ │ ├── unnamed-chunk-42-1.png │ │ ├── unnamed-chunk-45-1.png │ │ └── unnamed-chunk-49-1.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── extra.css ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── link.svg ├── logo.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── GeomDots.html │ ├── GeomDotsinterval.html │ ├── GeomInterval.html │ ├── GeomIntervalh.html │ ├── GeomLineribbon.html │ ├── GeomPointinterval.html │ ├── GeomPointintervalh.html │ ├── GeomSlab.html │ ├── GeomSlabinterval.html │ ├── Mode.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── Rplot004.png │ ├── Rplot005.png │ ├── StatDistSlabinterval.html │ ├── StatInterval.html │ ├── StatPointinterval.html │ ├── StatSampleSlabinterval.html │ ├── StatSlabinterval.html │ ├── add_draws-1.png │ ├── add_draws.html │ ├── add_fitted_draws.html │ ├── add_fitted_samples.html │ ├── add_linpred_draws.html │ ├── add_linpred_rvars.html │ ├── add_predicted_draws-1.png │ ├── add_predicted_draws-2.png │ ├── add_predicted_draws.html │ ├── add_predicted_rvars-1.png │ ├── add_predicted_rvars-2.png │ ├── add_predicted_rvars.html │ ├── add_predicted_samples.html │ ├── add_residual_draws.html │ ├── apply_prototypes.html │ ├── as_data_list.character.html │ ├── as_data_list.data.frame.html │ ├── as_data_list.data_list.html │ ├── as_data_list.default.html │ ├── as_data_list.factor.html │ ├── as_data_list.html │ ├── as_data_list.list.html │ ├── as_data_list.logical.html │ ├── as_data_list.numeric.html │ ├── as_sample_data_frame.html │ ├── as_sample_tibble.html │ ├── axis_titles_bottom_left.html │ ├── combine_chains.html │ ├── compare_levels-1.png │ ├── compare_levels-2.png │ ├── compare_levels.html │ ├── compose_data.html │ ├── curve_interval.html │ ├── cut_cdf_qi.html │ ├── data_list.html │ ├── density_bins-1.png │ ├── density_bins.html │ ├── dlkjcorr_marginal.html │ ├── dstudent_t.html │ ├── emmeans_comparison.html │ ├── epred_draws.brmsfit.html │ ├── epred_draws.default.html │ ├── epred_draws.html │ ├── epred_draws.stanreg.html │ ├── epred_rvars.brmsfit.html │ ├── epred_rvars.default.html │ ├── epred_rvars.html │ ├── epred_rvars.stanreg.html │ ├── extract_samples.html │ ├── facet_title_left_horizontal.html │ ├── facet_title_right_horizontal.html │ ├── figures │ │ ├── README │ │ │ ├── broom_bind-1.png │ │ │ ├── dwplot-1.png │ │ │ ├── hops-1.gif │ │ │ ├── make_data-1.png │ │ │ ├── pp_bands-1.png │ │ │ ├── pp_bands_facet-1.png │ │ │ ├── pp_intervals-1.png │ │ │ ├── quantile_dotplots-1.png │ │ │ ├── spaghetti-1.png │ │ │ ├── stat_eye-1.png │ │ │ ├── stat_eyeh-1.png │ │ │ ├── stat_halfeye-1.png │ │ │ └── stat_halfeyeh-1.png │ │ ├── logo.svg │ │ ├── preview.gif │ │ └── slabinterval_family.png │ ├── fitted_draws.default.html │ ├── fitted_draws.html │ ├── fitted_samples.html │ ├── from_broom_names.html │ ├── from_ggmcmc_names.html │ ├── gather_emmeans_draws.default.html │ ├── gather_emmeans_draws.emm_list.html │ ├── gather_emmeans_draws.html │ ├── gather_emmeans_samples.html │ ├── gather_lsmeans_samples.html │ ├── gather_pairs-1.png │ ├── gather_pairs-2.png │ ├── gather_pairs-3.png │ ├── gather_pairs-4.png │ ├── gather_pairs-5.png │ ├── gather_pairs.html │ ├── gather_samples.html │ ├── gather_terms.html │ ├── gather_variables.html │ ├── geom_dots.html │ ├── geom_dotsh.html │ ├── geom_dotsinterval.html │ ├── geom_dotsintervalh.html │ ├── geom_eye.html │ ├── geom_eyeh.html │ ├── geom_halfeyeh.html │ ├── geom_interval.html │ ├── geom_intervalh.html │ ├── geom_lineribbon.html │ ├── geom_pointinterval.html │ ├── geom_pointintervalh.html │ ├── geom_slab.html │ ├── geom_slabh.html │ ├── geom_slabinterval.html │ ├── get_variables.default.html │ ├── get_variables.html │ ├── get_variables.mcmc.html │ ├── get_variables.mcmc.list.html │ ├── ggeye.html │ ├── guide_colorbar2.html │ ├── guide_colourbar2.html │ ├── hdci.html │ ├── hdi.html │ ├── histogram_bins.html │ ├── index.html │ ├── linpred_draws.brmsfit.html │ ├── linpred_draws.default.html │ ├── linpred_draws.html │ ├── linpred_draws.stanreg.html │ ├── linpred_rvars.brmsfit.html │ ├── linpred_rvars.default.html │ ├── linpred_rvars.html │ ├── linpred_rvars.stanreg.html │ ├── marginalize_lkjcorr.html │ ├── mean_hdci.html │ ├── mean_hdcih.html │ ├── mean_hdi.html │ ├── mean_hdih.html │ ├── mean_qi.html │ ├── mean_qih.html │ ├── median_hdci.html │ ├── median_hdcih.html │ ├── median_hdi.html │ ├── median_hdih.html │ ├── median_qi.html │ ├── median_qih.html │ ├── mode_hdci.html │ ├── mode_hdcih.html │ ├── mode_hdi.html │ ├── mode_hdih.html │ ├── mode_qi.html │ ├── mode_qih.html │ ├── n_prefix.html │ ├── nest_rvars.html │ ├── parameters.html │ ├── parse_dist.html │ ├── plkjcorr_marginal.html │ ├── point_interval.html │ ├── point_intervalh.html │ ├── predict_curve.html │ ├── predict_curve_density.html │ ├── predicted_draws.brmsfit.html │ ├── predicted_draws.default.html │ ├── predicted_draws.html │ ├── predicted_draws.stanreg.html │ ├── predicted_rvars.brmsfit.html │ ├── predicted_rvars.default.html │ ├── predicted_rvars.html │ ├── predicted_rvars.stanreg.html │ ├── predicted_samples.html │ ├── pstudent_t.html │ ├── qi.html │ ├── qlkjcorr_marginal.html │ ├── qstudent_t.html │ ├── r_dist_name.html │ ├── recover_types.html │ ├── reexports.html │ ├── residual_draws.brmsfit.html │ ├── residual_draws.default.html │ ├── residual_draws.html │ ├── rlkjcorr_marginal.html │ ├── rstudent_t.html │ ├── sample_draws-1.png │ ├── sample_draws.html │ ├── scale_interval_alpha_continuous.html │ ├── scale_interval_alpha_discrete.html │ ├── scale_interval_color_continuous.html │ ├── scale_interval_color_discrete.html │ ├── scale_interval_colour_continuous.html │ ├── scale_interval_colour_discrete.html │ ├── scale_interval_linetype_continuous.html │ ├── scale_interval_linetype_discrete.html │ ├── scale_interval_size_continuous.html │ ├── scale_interval_size_discrete.html │ ├── scale_point_alpha_continuous.html │ ├── scale_point_alpha_discrete.html │ ├── scale_point_color_continuous.html │ ├── scale_point_color_discrete.html │ ├── scale_point_colour_continuous.html │ ├── scale_point_colour_discrete.html │ ├── scale_point_fill_continuous.html │ ├── scale_point_fill_discrete.html │ ├── scale_point_size_continuous.html │ ├── scale_point_size_discrete.html │ ├── scale_slab_alpha_continuous.html │ ├── scale_slab_alpha_discrete.html │ ├── scale_slab_color_continuous.html │ ├── scale_slab_color_discrete.html │ ├── scale_slab_colour_continuous.html │ ├── scale_slab_colour_discrete.html │ ├── scale_slab_fill_continuous.html │ ├── scale_slab_fill_discrete.html │ ├── scale_slab_linetype_continuous.html │ ├── scale_slab_linetype_discrete.html │ ├── scale_slab_shape_continuous.html │ ├── scale_slab_shape_discrete.html │ ├── scale_slab_size_continuous.html │ ├── scale_slab_size_discrete.html │ ├── spread_draws.html │ ├── spread_rvars.html │ ├── spread_samples.html │ ├── stat_ccdfinterval.html │ ├── stat_ccdfintervalh.html │ ├── stat_cdfinterval.html │ ├── stat_cdfintervalh.html │ ├── stat_dist_ccdfinterval.html │ ├── stat_dist_ccdfintervalh.html │ ├── stat_dist_cdfinterval.html │ ├── stat_dist_cdfintervalh.html │ ├── stat_dist_dots.html │ ├── stat_dist_dotsh.html │ ├── stat_dist_dotsinterval.html │ ├── stat_dist_dotsintervalh.html │ ├── stat_dist_eye.html │ ├── stat_dist_eyeh.html │ ├── stat_dist_gradientinterval.html │ ├── stat_dist_gradientintervalh.html │ ├── stat_dist_halfeye.html │ ├── stat_dist_halfeyeh.html │ ├── stat_dist_interval.html │ ├── stat_dist_intervalh.html │ ├── stat_dist_lineribbon.html │ ├── stat_dist_pointinterval.html │ ├── stat_dist_pointintervalh.html │ ├── stat_dist_slab.html │ ├── stat_dist_slabh.html │ ├── stat_dist_slabinterval.html │ ├── stat_dots.html │ ├── stat_dotsh.html │ ├── stat_dotsinterval.html │ ├── stat_dotsintervalh.html │ ├── stat_eye.html │ ├── stat_eyeh.html │ ├── stat_gradientinterval.html │ ├── stat_gradientintervalh.html │ ├── stat_halfeye.html │ ├── stat_halfeyeh.html │ ├── stat_histinterval.html │ ├── stat_histintervalh.html │ ├── stat_interval.html │ ├── stat_intervalh.html │ ├── stat_lineribbon.html │ ├── stat_pointinterval.html │ ├── stat_pointintervalh.html │ ├── stat_sample_slabinterval.html │ ├── stat_slab.html │ ├── stat_slabh.html │ ├── stat_slabinterval.html │ ├── summarise_draws.grouped_df.html │ ├── summarise_draws.html │ ├── theme_ggdist.html │ ├── theme_tidybayes.html │ ├── tidy_draws.CmdStanFit.html │ ├── tidy_draws.CmdStanMCMC.html │ ├── tidy_draws.MCMCglmm.html │ ├── tidy_draws.brmsfit.html │ ├── tidy_draws.data.frame.html │ ├── tidy_draws.default.html │ ├── tidy_draws.draws.html │ ├── tidy_draws.html │ ├── tidy_draws.jagsUI.html │ ├── tidy_draws.matrix.html │ ├── tidy_draws.mcmc.list.html │ ├── tidy_draws.runjags.html │ ├── tidy_draws.stanfit.html │ ├── tidy_draws.stanreg.html │ ├── tidy_samples.html │ ├── tidybayes-deprecated.html │ ├── tidybayes-models.html │ ├── tidybayes-package.html │ ├── tidybayes.html │ ├── to_broom_names.html │ ├── to_ggmcmc_names.html │ ├── ungather_samples.html │ ├── unnest_rvars.html │ ├── unspread_draws-1.png │ ├── unspread_draws-2.png │ ├── unspread_draws.html │ ├── unspread_samples.html │ └── x_at_y.html └── sitemap.xml ├── figures-source ├── explodey-tables-hops.gif ├── explodey-tables-hops.psd ├── explodey-tables-hops │ ├── 1.png │ ├── 10.png │ ├── 2.png │ ├── 3.png │ ├── 4.png │ ├── 5.png │ ├── 6.png │ ├── 7.png │ ├── 8.png │ └── 9.png ├── explodey-tables-ribbon.png ├── explodey-tables-ribbon_munged.png ├── explodey-tables-ribbon_predicted.png ├── explodey-tables-spaghetti.png ├── explodey-tables.pdf ├── github-preview.pdf ├── github-preview.png ├── logo-diginate-hex-sticker.ai ├── logo-old.pdf ├── logo.pdf ├── logo.png ├── preview-frames.psd ├── preview-hops.gif ├── preview-spaghetti.png ├── preview.pdf ├── preview.prproj ├── preview.psd └── tidybayes-ggdist-evolution.pdf ├── inst ├── CITATION └── WORDLIST ├── man-roxygen ├── details-pred.R ├── param-deprecated-n.R ├── param-draw_indices.R ├── param-model.R ├── param-ndraws.R ├── param-pred-dots.R ├── param-pred-dpar.R ├── param-pred-newdata.R ├── param-pred-object.R ├── param-pred-re_formula.R ├── param-pred-value.R └── param-seed.R ├── man ├── add_draws.Rd ├── add_predicted_draws.Rd ├── add_predicted_rvars.Rd ├── combine_chains.Rd ├── compare_levels.Rd ├── compose_data.Rd ├── data_list.Rd ├── density_bins.Rd ├── emmeans_comparison.Rd ├── figures │ ├── README │ │ ├── broom_bind-1.png │ │ ├── dwplot-1.png │ │ ├── hops-1.gif │ │ ├── make_data-1.png │ │ ├── pp_bands-1.png │ │ ├── pp_bands_facet-1.png │ │ ├── pp_intervals-1.png │ │ ├── quantile_dotplots-1.png │ │ ├── spaghetti-1.png │ │ ├── stat_eye-1.png │ │ ├── stat_eyeh-1.png │ │ ├── stat_halfeye-1.png │ │ └── stat_halfeyeh-1.png │ ├── logo.svg │ ├── preview.gif │ └── slabinterval_family.png ├── gather_emmeans_draws.Rd ├── gather_pairs.Rd ├── gather_variables.Rd ├── get_variables.Rd ├── n_prefix.Rd ├── nest_rvars.Rd ├── predict_curve.Rd ├── recover_types.Rd ├── reexports.Rd ├── sample_draws.Rd ├── spread_draws.Rd ├── spread_rvars.Rd ├── summarise_draws.grouped_df.Rd ├── tidy_draws.Rd ├── tidybayes-deprecated.Rd ├── tidybayes-models.Rd ├── tidybayes-package.Rd ├── unspread_draws.Rd └── x_at_y.Rd ├── pkgdown ├── extra.css └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests ├── models │ ├── models.brms.m_cyl_mpg.rds │ ├── models.brms.m_dirich.rds │ ├── models.brms.m_dpars.rds │ ├── models.brms.m_hp.rds │ ├── models.brms.m_hp_sigma.rds │ ├── models.brms.m_multinom.rds │ ├── models.brms.m_nlpar.rds │ ├── models.brms.m_ranef.rds │ ├── models.rstan.m_ABC.rds │ ├── models.rstan.m_gqs.rds │ ├── models.rstanarm.m_cyl.rds │ ├── models.rstanarm.m_hp_wt.rds │ └── models.rstanarm.m_ranef.rds ├── testthat.R └── testthat │ ├── _snaps │ ├── test.geom_dotsinterval │ │ ├── stat-dotsh-with-a-group-with-1-dot.svg │ │ └── vanilla-geom-dotsh.svg │ ├── test.geom_interval │ │ ├── grouped-intervals-h-stat.svg │ │ └── grouped-intervals-h.svg │ ├── test.geom_pointinterval │ │ ├── grouped-pointintervals-h-stat.svg │ │ └── grouped-pointintervals-h.svg │ ├── test.stat_dist_slabinterval │ │ ├── ccdfintervalh-using-args.svg │ │ └── horizontal-half-eye-using-args.svg │ └── test.stat_eye │ │ ├── one-parameter-horizontal-eye-mode-hdi.svg │ │ ├── one-parameter-horizontal-eye.svg │ │ ├── one-parameter-horizontal-half-eye.svg │ │ ├── one-parameter-vertical-eye.svg │ │ ├── one-parameter-vertical-halfeye.svg │ │ ├── two-parameter-factor-horizontal-eye-fill.svg │ │ └── two-parameter-factor-horizontal-half-eye.svg │ ├── test.add_draws.R │ ├── test.as_constructor.R │ ├── test.combine_chains.R │ ├── test.compare_levels.R │ ├── test.compose_data.R │ ├── test.emmeans_comparison.R │ ├── test.epred_draws.R │ ├── test.epred_rvars.R │ ├── test.gather_draws.R │ ├── test.gather_emmeans_draws.R │ ├── test.gather_pairs.R │ ├── test.gather_rvars.R │ ├── test.gather_variables.R │ ├── test.geom_dotsinterval.R │ ├── test.geom_interval.R │ ├── test.geom_pointinterval.R │ ├── test.get_variables.R │ ├── test.linpred_draws.R │ ├── test.linpred_rvars.R │ ├── test.nest_rvars.R │ ├── test.point_interval.R │ ├── test.predicted_draws.R │ ├── test.predicted_rvars.R │ ├── test.residual_draws.R │ ├── test.sample_draws.R │ ├── test.spread_draws.R │ ├── test.spread_rvars.R │ ├── test.stat_dist_slabinterval.R │ ├── test.stat_eye.R │ ├── test.summarise_draws.R │ ├── test.tidy_draws.R │ ├── test.ungather_draws.R │ ├── test.unspread_draws.R │ ├── test.util.R │ └── test.x_at_y.R └── vignettes ├── .install_extras ├── children └── chunk_options.txt ├── slabinterval_family.png ├── tidy-brms.Rmd ├── tidy-posterior.Rmd ├── tidy-rstanarm.Rmd ├── tidybayes-residuals.Rmd └── tidybayes.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^CRAN-RELEASE$ 2 | ^.*\.Rproj$ 3 | ^\.Rproj\.user$ 4 | ^\.Rhistory$ 5 | ^\.RData$ 6 | ^LICENSE$ 7 | ^.*~$ 8 | ^\.gitignore$ 9 | ^\.gitattributes$ 10 | ^\.git$ 11 | ^\.travis\.yml$ 12 | ^README.Rmd$ 13 | ^README.md$ 14 | ^README_files$ 15 | ^README_cache$ 16 | ^clean_vignette_cache\.sh$ 17 | ^\.lintr$ 18 | ^docs$ 19 | ^_pkgdown\.yml$ 20 | ^pkgdown/.*$ 21 | ^pkgdown$ 22 | ^build_test_models\.R$ 23 | ^codecov\.yml$ 24 | ^\.covrignore$ 25 | ^cran-comments.md$ 26 | ^inst/WORDLIST$ 27 | ^data-raw$ 28 | ^figures-source$ 29 | ^vignettes/.*_cache$ 30 | ^benchmarks.*$ 31 | ^revdep$ 32 | ^man-roxygen$ 33 | ^man/figures/README$ 34 | ^vignettes/models$ 35 | ^README_models$ 36 | ^\.github$ 37 | ^CRAN-SUBMISSION$ 38 | -------------------------------------------------------------------------------- /.covrignore: -------------------------------------------------------------------------------- 1 | R/deprecated.R 2 | R/predict_curve.R 3 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | * text=auto 2 | 3 | -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/workflows/recheck.yml: -------------------------------------------------------------------------------- 1 | on: 2 | workflow_dispatch: 3 | inputs: 4 | which: 5 | type: choice 6 | description: Which dependents to check 7 | options: 8 | - strong 9 | - most 10 | 11 | name: Reverse dependency check 12 | 13 | jobs: 14 | revdep_check: 15 | name: Reverse check ${{ inputs.which }} dependents 16 | uses: r-devel/recheck/.github/workflows/recheck.yml@v1 17 | with: 18 | which: ${{ inputs.which }} 19 | subdirectory: '' #if your package is in a git subdir 20 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *~ 2 | .project 3 | .settings 4 | .Rhistory 5 | .RData 6 | .Rproj* 7 | tidybayes.Rproj 8 | vignettes/ABC.rda 9 | vignettes/ABC.rds 10 | vignettes/*_cache/ 11 | vignettes/models/ 12 | vignettes/*.gif 13 | README_cache/ 14 | README_models/ 15 | benchmarks.md 16 | figures-source/Adobe* 17 | revdep/ 18 | .Rproj.user 19 | -------------------------------------------------------------------------------- /.lintr: -------------------------------------------------------------------------------- 1 | linters: with_defaults( 2 | assignment_linter = NULL, 3 | line_length_linter(120), 4 | open_curly_linter(allow_single_line = TRUE), 5 | closed_curly_linter = NULL, 6 | object_name_linter = NULL, 7 | object_length_linter = NULL, 8 | snake_case_linter = NULL, 9 | camel_case_linter = NULL 10 | ) 11 | -------------------------------------------------------------------------------- /R/gather_draws.R: -------------------------------------------------------------------------------- 1 | # gather_draws 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | 7 | # gather_draws ------------------------------------------------------------ 8 | 9 | #' @rdname spread_draws 10 | #' @importFrom dplyr bind_rows group_by_at 11 | #' @importFrom rlang enquos 12 | #' @export 13 | gather_draws = function( 14 | model, 15 | ..., 16 | regex = FALSE, 17 | sep = "[, ]", 18 | ndraws = NULL, 19 | seed = NULL, 20 | draw_indices = c(".chain", ".iteration", ".draw"), 21 | n 22 | ) { 23 | ndraws = .Deprecated_argument_alias(ndraws, n) 24 | 25 | draws = sample_draws_from_model_(model, ndraws, seed) 26 | 27 | draw_indices = intersect(draw_indices, names(draws)) 28 | tidysamples = lapply(enquos(...), function(variable_spec) { 29 | gather_variables( 30 | spread_draws_(draws, variable_spec, regex = regex, sep = sep, draw_indices = draw_indices), 31 | exclude = c(draw_indices, ".row") 32 | ) 33 | }) 34 | 35 | #get the groups from all the samples --- when we bind them together, 36 | #the grouping information is not always retained, so we'll have to recreate 37 | #the full set of groups from all the data frames after we bind them 38 | groups_ = tidysamples %>% 39 | lapply(group_vars) %>% 40 | reduce_(union) 41 | 42 | bind_rows(tidysamples) %>% 43 | group_by_at(groups_) 44 | } 45 | -------------------------------------------------------------------------------- /R/ggdist-curve_interval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist curve_interval 3 | ggdist::curve_interval 4 | -------------------------------------------------------------------------------- /R/ggdist-cut_cdf_qi.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist cut_cdf_qi 3 | ggdist::cut_cdf_qi 4 | -------------------------------------------------------------------------------- /R/ggdist-geom_dotsinterval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist geom_dotsinterval 3 | ggdist::geom_dotsinterval 4 | 5 | #' @export 6 | #' @importFrom ggdist GeomDotsinterval 7 | ggdist::GeomDotsinterval 8 | 9 | #' @export 10 | #' @importFrom ggdist geom_dots 11 | ggdist::geom_dots 12 | 13 | #' @export 14 | #' @importFrom ggdist GeomDots 15 | ggdist::GeomDots 16 | -------------------------------------------------------------------------------- /R/ggdist-geom_interval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist geom_interval 3 | ggdist::geom_interval 4 | 5 | #' @export 6 | #' @importFrom ggdist GeomInterval 7 | ggdist::GeomInterval 8 | -------------------------------------------------------------------------------- /R/ggdist-geom_lineribbon.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist geom_lineribbon 3 | ggdist::geom_lineribbon 4 | 5 | #' @export 6 | #' @importFrom ggdist GeomLineribbon 7 | ggdist::GeomLineribbon 8 | -------------------------------------------------------------------------------- /R/ggdist-geom_pointinterval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist geom_pointinterval 3 | ggdist::geom_pointinterval 4 | 5 | #' @export 6 | #' @importFrom ggdist GeomPointinterval 7 | ggdist::GeomPointinterval 8 | -------------------------------------------------------------------------------- /R/ggdist-geom_slabinterval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist geom_slabinterval 3 | ggdist::geom_slabinterval 4 | 5 | #' @export 6 | #' @importFrom ggdist GeomSlabinterval 7 | ggdist::GeomSlabinterval 8 | 9 | #' @export 10 | #' @importFrom ggdist geom_slab 11 | ggdist::geom_slab 12 | 13 | #' @export 14 | #' @importFrom ggdist GeomSlab 15 | ggdist::GeomSlab 16 | -------------------------------------------------------------------------------- /R/ggdist-lkjcorr_marginal.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist dlkjcorr_marginal 3 | ggdist::dlkjcorr_marginal 4 | 5 | #' @export 6 | #' @importFrom ggdist plkjcorr_marginal 7 | ggdist::plkjcorr_marginal 8 | 9 | #' @export 10 | #' @importFrom ggdist qlkjcorr_marginal 11 | ggdist::qlkjcorr_marginal 12 | 13 | #' @export 14 | #' @importFrom ggdist rlkjcorr_marginal 15 | ggdist::rlkjcorr_marginal 16 | 17 | #' @export 18 | #' @importFrom ggdist marginalize_lkjcorr 19 | ggdist::marginalize_lkjcorr 20 | -------------------------------------------------------------------------------- /R/ggdist-parse_dist.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist parse_dist 3 | ggdist::parse_dist 4 | 5 | #' @export 6 | #' @importFrom ggdist r_dist_name 7 | ggdist::r_dist_name 8 | -------------------------------------------------------------------------------- /R/ggdist-stat_dist_slabinterval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist stat_dist_slabinterval 3 | ggdist::stat_dist_slabinterval 4 | 5 | #' @export 6 | #' @importFrom ggdist StatDistSlabinterval 7 | ggdist::StatDistSlabinterval 8 | 9 | #' @export 10 | #' @importFrom ggdist stat_dist_halfeye 11 | ggdist::stat_dist_halfeye 12 | 13 | #' @export 14 | #' @importFrom ggdist stat_dist_eye 15 | ggdist::stat_dist_eye 16 | 17 | #' @export 18 | #' @importFrom ggdist stat_dist_ccdfinterval 19 | ggdist::stat_dist_ccdfinterval 20 | 21 | #' @export 22 | #' @importFrom ggdist stat_dist_cdfinterval 23 | ggdist::stat_dist_cdfinterval 24 | 25 | #' @export 26 | #' @importFrom ggdist stat_dist_gradientinterval 27 | ggdist::stat_dist_gradientinterval 28 | 29 | #' @export 30 | #' @importFrom ggdist stat_dist_pointinterval 31 | ggdist::stat_dist_pointinterval 32 | 33 | #' @export 34 | #' @importFrom ggdist stat_dist_interval 35 | ggdist::stat_dist_interval 36 | 37 | #' @export 38 | #' @importFrom ggdist stat_dist_slab 39 | ggdist::stat_dist_slab 40 | -------------------------------------------------------------------------------- /R/ggdist-stat_dotsinterval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist stat_dotsinterval 3 | ggdist::stat_dotsinterval 4 | 5 | #' @export 6 | #' @importFrom ggdist stat_dots 7 | ggdist::stat_dots 8 | 9 | #' @export 10 | #' @importFrom ggdist stat_dist_dotsinterval 11 | ggdist::stat_dist_dotsinterval 12 | 13 | #' @export 14 | #' @importFrom ggdist stat_dist_dots 15 | ggdist::stat_dist_dots 16 | -------------------------------------------------------------------------------- /R/ggdist-stat_interval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist stat_interval 3 | ggdist::stat_interval 4 | 5 | #' @export 6 | #' @importFrom ggdist StatInterval 7 | ggdist::StatInterval 8 | -------------------------------------------------------------------------------- /R/ggdist-stat_lineribbon.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist stat_lineribbon 3 | ggdist::stat_lineribbon 4 | 5 | #' @export 6 | #' @importFrom ggdist stat_dist_lineribbon 7 | ggdist::stat_dist_lineribbon 8 | -------------------------------------------------------------------------------- /R/ggdist-stat_pointinterval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist stat_pointinterval 3 | ggdist::stat_pointinterval 4 | 5 | #' @export 6 | #' @importFrom ggdist StatPointinterval 7 | ggdist::StatPointinterval 8 | -------------------------------------------------------------------------------- /R/ggdist-stat_sample_slabinterval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist stat_sample_slabinterval 3 | ggdist::stat_sample_slabinterval 4 | 5 | #' @export 6 | #' @importFrom ggdist StatSampleSlabinterval 7 | ggdist::StatSampleSlabinterval 8 | 9 | #' @export 10 | #' @importFrom ggdist stat_halfeye 11 | ggdist::stat_halfeye 12 | 13 | #' @export 14 | #' @importFrom ggdist stat_eye 15 | ggdist::stat_eye 16 | 17 | #' @export 18 | #' @importFrom ggdist stat_ccdfinterval 19 | ggdist::stat_ccdfinterval 20 | 21 | #' @export 22 | #' @importFrom ggdist stat_cdfinterval 23 | ggdist::stat_cdfinterval 24 | 25 | #' @export 26 | #' @importFrom ggdist stat_gradientinterval 27 | ggdist::stat_gradientinterval 28 | 29 | #' @export 30 | #' @importFrom ggdist stat_histinterval 31 | ggdist::stat_histinterval 32 | 33 | #' @export 34 | #' @importFrom ggdist stat_slab 35 | ggdist::stat_slab 36 | -------------------------------------------------------------------------------- /R/ggdist-stat_slabinterval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist stat_slabinterval 3 | ggdist::stat_slabinterval 4 | 5 | #' @export 6 | #' @importFrom ggdist StatSlabinterval 7 | ggdist::StatSlabinterval 8 | -------------------------------------------------------------------------------- /R/ggdist-student_t.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist dstudent_t 3 | ggdist::dstudent_t 4 | 5 | #' @export 6 | #' @importFrom ggdist pstudent_t 7 | ggdist::pstudent_t 8 | 9 | #' @export 10 | #' @importFrom ggdist qstudent_t 11 | ggdist::qstudent_t 12 | 13 | #' @export 14 | #' @importFrom ggdist rstudent_t 15 | ggdist::rstudent_t 16 | -------------------------------------------------------------------------------- /R/ggdist-theme_ggdist.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist theme_ggdist 3 | ggdist::theme_ggdist 4 | 5 | #' @export 6 | #' @importFrom ggdist theme_tidybayes 7 | ggdist::theme_tidybayes 8 | 9 | #' @export 10 | #' @importFrom ggdist facet_title_left_horizontal 11 | ggdist::facet_title_left_horizontal 12 | 13 | #' @export 14 | #' @importFrom ggdist facet_title_right_horizontal 15 | ggdist::facet_title_right_horizontal 16 | 17 | #' @export 18 | #' @importFrom ggdist axis_titles_bottom_left 19 | ggdist::axis_titles_bottom_left 20 | -------------------------------------------------------------------------------- /R/ggdist-tidy_format_translators.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist to_broom_names 3 | ggdist::to_broom_names 4 | 5 | #' @export 6 | #' @importFrom ggdist from_broom_names 7 | ggdist::from_broom_names 8 | 9 | #' @export 10 | #' @importFrom ggdist to_ggmcmc_names 11 | ggdist::to_ggmcmc_names 12 | 13 | #' @export 14 | #' @importFrom ggdist from_ggmcmc_names 15 | ggdist::from_ggmcmc_names 16 | -------------------------------------------------------------------------------- /R/global_variables.R: -------------------------------------------------------------------------------- 1 | # Names that should be suppressed from global variable check by codetools 2 | # Names used broadly should be put here; Names used in specific files should 3 | # be put at the top of the corresponding file. 4 | # 5 | # Author: mjskay 6 | ############################################################################### 7 | 8 | # names used in dlpyr functions 9 | globalVariables(c(".", ".data")) 10 | -------------------------------------------------------------------------------- /R/onAttach.R: -------------------------------------------------------------------------------- 1 | # On package load 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | # Nothing here at the moment :) 7 | -------------------------------------------------------------------------------- /R/point_interval.R: -------------------------------------------------------------------------------- 1 | #' @export 2 | #' @importFrom ggdist point_interval 3 | ggdist::point_interval 4 | 5 | #' @export 6 | #' @importFrom ggdist qi 7 | ggdist::qi 8 | 9 | #' @export 10 | #' @importFrom ggdist hdi 11 | ggdist::hdi 12 | 13 | #' @export 14 | #' @importFrom ggdist Mode 15 | ggdist::Mode 16 | 17 | #' @export 18 | #' @importFrom ggdist hdci 19 | ggdist::hdci 20 | 21 | #' @export 22 | #' @importFrom ggdist mean_qi 23 | ggdist::mean_qi 24 | 25 | #' @export 26 | #' @importFrom ggdist median_qi 27 | ggdist::median_qi 28 | 29 | #' @export 30 | #' @importFrom ggdist mode_qi 31 | ggdist::mode_qi 32 | 33 | #' @export 34 | #' @importFrom ggdist mean_hdi 35 | ggdist::mean_hdi 36 | 37 | #' @export 38 | #' @importFrom ggdist median_hdi 39 | ggdist::median_hdi 40 | 41 | #' @export 42 | #' @importFrom ggdist mode_hdi 43 | ggdist::mode_hdi 44 | 45 | #' @export 46 | #' @importFrom ggdist mean_hdci 47 | ggdist::mean_hdci 48 | 49 | #' @export 50 | #' @importFrom ggdist median_hdci 51 | ggdist::median_hdci 52 | 53 | #' @export 54 | #' @importFrom ggdist mode_hdci 55 | ggdist::mode_hdci 56 | -------------------------------------------------------------------------------- /R/testthat.R: -------------------------------------------------------------------------------- 1 | # Helpers for testthat tests 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | 7 | # skips ------------------------------------------------------------------- 8 | 9 | #' skip tests sensitive to minor changes in density() in R 4.4 10 | #' @noRd 11 | skip_if_sensitive_to_density = function() { 12 | testthat::skip_if(getRversion() < "4.4", "density() output changed in R 4.4") 13 | } 14 | 15 | # skip tests if there is no vdiffr setup or if the setup is likely 16 | # to produce false positive test failures (e.g. old version of ggplot2) 17 | skip_if_no_vdiffr = function() { 18 | testthat::skip_if_not_installed("vdiffr") 19 | testthat::skip_if_not_installed("svglite") 20 | testthat::skip_if_not_installed("ggplot2", "3.3.3.9000") 21 | # unlike ggdist tests, these tests are all for deprecated stuff so minor 22 | # changes in images on CI are more trouble than they are worth 23 | testthat::skip_on_ci() 24 | } 25 | -------------------------------------------------------------------------------- /clean_vignette_cache.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | rm -rf vignettes/models 3 | rm -rf vignettes/*_cache/ 4 | -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- 1 | comment: false 2 | 3 | coverage: 4 | status: 5 | project: 6 | default: 7 | target: auto 8 | threshold: 1% 9 | patch: 10 | default: 11 | target: auto 12 | threshold: 1% 13 | -------------------------------------------------------------------------------- /cran-comments.md: -------------------------------------------------------------------------------- 1 | ## Submission comments 2 | This submission fixes a few minor bugs, including a NOTE and an ERROR on CRAN. 3 | 4 | ## Test environments 5 | * MacOS (github), R-release 6 | * Windows (github), R-release 7 | * Windows (winbuilder), R-release 8 | * Windows (winbuilder), R-devel 9 | * Linux (github), R-devel 10 | * Linux (github), R-release 11 | * Linux (github), R-oldrelease-1 12 | * Linux (github), R-oldrelease-2 13 | * Linux (github), R-oldrelease-3 14 | * Linux (github), R-oldrelease-4 15 | 16 | ## R CMD check results 17 | 0 errors | 0 warnings | 0 notes 18 | 19 | ## revdepcheck results 20 | 21 | We checked 14 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. 22 | 23 | * We saw 0 new problems 24 | * We failed to check 0 packages 25 | -------------------------------------------------------------------------------- /docs/apple-touch-icon-120x120.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mjskay/tidybayes/fb494368784350b0269fda406a37c1195d5401d6/docs/apple-touch-icon-120x120.png -------------------------------------------------------------------------------- /docs/apple-touch-icon-152x152.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mjskay/tidybayes/fb494368784350b0269fda406a37c1195d5401d6/docs/apple-touch-icon-152x152.png 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-------------------------------------------------------------------------------- 1 | year <- sub("-.*", "", meta$Date) 2 | note <- sprintf("R package version %s", meta$Version) 3 | 4 | bibentry( 5 | bibtype = "Manual", 6 | title = paste("{tidybayes}: Tidy Data and Geoms for {Bayesian} Models"), 7 | author = c(person("Matthew", "Kay")), 8 | year = year, 9 | note = note, 10 | url = "http://mjskay.github.io/tidybayes/", 11 | doi = "10.5281/zenodo.1308151" 12 | ) 13 | -------------------------------------------------------------------------------- /man-roxygen/param-deprecated-n.R: -------------------------------------------------------------------------------- 1 | #' @param n (Deprecated). Use `ndraws`. 2 | -------------------------------------------------------------------------------- /man-roxygen/param-draw_indices.R: -------------------------------------------------------------------------------- 1 | #' @param draw_indices Character vector of column names that should be treated 2 | #' as indices of draws. Operations are done within combinations of these values. 3 | #' The default is `c(".chain", ".iteration", ".draw")`, which is the same names 4 | #' used for chain, iteration, and draw indices returned by [tidy_draws()]. 5 | #' Names in `draw_indices` that are not found in the data are ignored. 6 | -------------------------------------------------------------------------------- /man-roxygen/param-model.R: -------------------------------------------------------------------------------- 1 | #' @param model A supported Bayesian model fit. Tidybayes supports a variety of model objects; 2 | #' for a full list of supported models, see [tidybayes-models]. 3 | -------------------------------------------------------------------------------- /man-roxygen/param-ndraws.R: -------------------------------------------------------------------------------- 1 | #' @param ndraws The number of draws to return, or `NULL` to return all draws. 2 | -------------------------------------------------------------------------------- /man-roxygen/param-pred-dots.R: -------------------------------------------------------------------------------- 1 | #' @param ... Additional arguments passed to the underlying prediction method for the type of 2 | #' model given. 3 | -------------------------------------------------------------------------------- /man-roxygen/param-pred-dpar.R: -------------------------------------------------------------------------------- 1 | #' @param dpar For `add_epred_<%=pred_type%>()` and `add_linpred_<%=pred_type%>()`: Should distributional regression 2 | #' parameters be included in the output? Valid only for models that support distributional regression parameters, 3 | #' such as submodels for variance parameters (as in `brms::brm()`). If `TRUE`, distributional regression 4 | #' parameters are included in the output as additional columns named after each parameter 5 | #' (alternative names can be provided using a list or named vector, e.g. `c(sigma.hat = "sigma")` 6 | #' would output the `"sigma"` parameter from a model as a column named `"sigma.hat"`). 7 | #' If `NULL` or `FALSE` (the default), distributional regression parameters are not included. 8 | -------------------------------------------------------------------------------- /man-roxygen/param-pred-newdata.R: -------------------------------------------------------------------------------- 1 | #' @param newdata Data frame to generate predictions from. 2 | -------------------------------------------------------------------------------- /man-roxygen/param-pred-object.R: -------------------------------------------------------------------------------- 1 | #' @param object A supported Bayesian model fit that can provide fits and predictions. Supported models 2 | #' are listed in the second section of [tidybayes-models]: *Models Supporting Prediction*. While other 3 | #' functions in this package (like [spread_<%=pred_type%>()]) support a wider range of models, to work with 4 | #' `add_epred_<%=pred_type%>()`, `add_predicted_<%=pred_type%>()`, etc. a model must provide an interface for generating 5 | #' predictions, thus more generic Bayesian modeling interfaces like `runjags` and `rstan` are not directly 6 | #' supported for these functions (only wrappers around those languages that provide predictions, like `rstanarm` 7 | #' and `brm`, are supported here). 8 | -------------------------------------------------------------------------------- /man-roxygen/param-pred-re_formula.R: -------------------------------------------------------------------------------- 1 | #' @param re_formula formula containing group-level effects to be considered in the prediction. 2 | #' If `NULL` (default), include all group-level effects; if `NA`, include no group-level effects. 3 | #' Some model types (such as [brms::brmsfit] and [rstanarm::stanreg-objects]) allow 4 | #' marginalizing over grouping factors by specifying new levels of a factor in `newdata`. In the case of 5 | #' [brms::brm()], you must also pass `allow_new_levels = TRUE` here to include new levels (see 6 | #' [brms::posterior_predict()]). 7 | -------------------------------------------------------------------------------- /man-roxygen/param-pred-value.R: -------------------------------------------------------------------------------- 1 | #' @param value The name of the output column: 2 | #' - for `[add_]epred_<%=pred_type%>()`, defaults to `".epred"`. 3 | #' - for `[add_]predicted_<%=pred_type%>()`, defaults to `".prediction"`. 4 | #' - for `[add_]linpred_<%=pred_type%>()`, defaults to `".linpred"`. 5 | #' <%if(pred_type == "draws") {%> - for `[add_]residual_draws()`, defaults to `".residual"`<%}%> 6 | -------------------------------------------------------------------------------- /man-roxygen/param-seed.R: -------------------------------------------------------------------------------- 1 | #' @param seed A seed to use when subsampling draws (i.e. when `ndraws` is not 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-------------------------------------------------------------------------------- /tests/testthat/test.combine_chains.R: -------------------------------------------------------------------------------- 1 | # Tests for combine_chains 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | library(dplyr) 7 | library(tidyr) 8 | 9 | 10 | 11 | 12 | test_that("combine_chains works on a simple example", { 13 | data(line, package = "coda") 14 | 15 | ref = line %>% 16 | tidy_draws() %>% 17 | mutate( 18 | .draw = as.integer(.iteration + (.chain - 1) * max(.iteration)) 19 | ) 20 | 21 | line %>% 22 | tidy_draws() %>% 23 | combine_chains() %>% 24 | expect_equal(ref) 25 | }) 26 | 27 | test_that("combine_chains works with a named output column", { 28 | data(line, package = "coda") 29 | 30 | ref = line %>% 31 | tidy_draws() %>% 32 | mutate(d = as.integer(.iteration + (.chain - 1) * max(.iteration))) 33 | 34 | line %>% 35 | tidy_draws() %>% 36 | combine_chains(into = "d") %>% 37 | expect_equal(ref) 38 | }) 39 | -------------------------------------------------------------------------------- /tests/testthat/test.emmeans_comparison.R: -------------------------------------------------------------------------------- 1 | # Tests for emmeans_comparison 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | 7 | 8 | 9 | test_that("basic conversion of emmeans contrasts works", { 10 | skip_if_not_installed("emmeans") 11 | 12 | pairwise_ref = list( 13 | `a - b` = quote(1 * a + -1 * b + 0 * c), 14 | `a - c` = quote(1 * a + 0 * b + -1 * c), 15 | `b - c` = quote(0 * a + 1 * b + -1 * c) 16 | ) 17 | expect_equal(emmeans_comparison(emmeans:::pairwise.emmc)(c("a","b","c")), pairwise_ref) 18 | expect_equal(emmeans_comparison("pairwise")(c("a","b","c")), pairwise_ref) 19 | 20 | mean_chg_ref = list( 21 | `a|b` = quote( -1 * a + 0.5 * b + 0.5 * c), 22 | `b|c` = quote(-0.5 * a + -0.5 * b + 1 * c) 23 | ) 24 | expect_equal(emmeans_comparison(emmeans:::mean_chg.emmc)(c("a","b","c")), mean_chg_ref) 25 | expect_equal(emmeans_comparison("mean_chg")(c("a","b","c")), mean_chg_ref) 26 | }) 27 | -------------------------------------------------------------------------------- /tests/testthat/test.gather_variables.R: -------------------------------------------------------------------------------- 1 | # Tests for gather_variables 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | library(dplyr) 7 | library(tidyr) 8 | 9 | 10 | 11 | 12 | test_that("gather_variables works on the results of tidy_draws", { 13 | data(RankCorr, package = "ggdist") 14 | 15 | ref = RankCorr %>% 16 | tidy_draws() %>% 17 | gather(.variable, .value, -.chain, -.iteration, -.draw) %>% 18 | group_by_at(".variable", .add = TRUE) 19 | 20 | result = RankCorr %>% 21 | tidy_draws() %>% 22 | gather_variables() 23 | 24 | expect_equal(result, ref) 25 | expect_equal(group_vars(result), group_vars(ref)) 26 | }) 27 | 28 | 29 | test_that("gather_variables works on the results of spread_draws with multiple variables and dimensions", { 30 | data(RankCorr, package = "ggdist") 31 | 32 | ref = RankCorr %>% 33 | spread_draws(b[i, v], tau[i]) %>% 34 | gather(.variable, .value, -.chain, -.iteration, -.draw, -i, -v) %>% 35 | group_by(i, v, .variable) 36 | 37 | result = RankCorr %>% 38 | spread_draws(b[i, v], tau[i]) %>% 39 | gather_variables() 40 | 41 | expect_equal(result, ref) 42 | expect_equal(group_vars(result), group_vars(ref)) 43 | }) 44 | -------------------------------------------------------------------------------- /tests/testthat/test.geom_dotsinterval.R: -------------------------------------------------------------------------------- 1 | # Tests for dots geoms and stats 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | library(dplyr) 7 | 8 | 9 | 10 | test_that("vanilla dots geoms and stats work", { 11 | skip_if_no_vdiffr() 12 | 13 | 14 | set.seed(1234) 15 | p = tribble( 16 | ~dist, ~x, 17 | "norm", rnorm(20), 18 | "t", rt(20, 3) 19 | ) %>% 20 | unnest(x) %>% 21 | ggplot() 22 | 23 | expect_warning(vdiffr::expect_doppelganger("vanilla geom_dotsh", 24 | p + geom_dotsh(aes(y = dist, x = x)) 25 | ), "Deprecated") 26 | 27 | expect_warning(vdiffr::expect_doppelganger("stat_dotsh with a group with 1 dot", 28 | p + stat_dotsh(aes(y = dist, x = x, color = x > 2)) 29 | ), "Deprecated") 30 | }) 31 | -------------------------------------------------------------------------------- /tests/testthat/test.geom_interval.R: -------------------------------------------------------------------------------- 1 | # Tests for interval geoms 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | library(dplyr) 7 | library(tidyr) 8 | 9 | 10 | 11 | # use a subset of RankCorr so tests are faster 12 | data(RankCorr, package = "ggdist") 13 | RankCorr_s = RankCorr[[1]][1:100,] 14 | RankCorr_u_tau = RankCorr_s %>% 15 | spread_draws(u_tau[i]) %>% 16 | filter(i %in% 1:3) 17 | 18 | test_that("horizontal grouped intervals work", { 19 | skip_if_no_vdiffr() 20 | 21 | 22 | expect_warning(vdiffr::expect_doppelganger("grouped intervals (h)", 23 | RankCorr_u_tau %>% 24 | mean_qi(.width = c(.5, .75, .90)) %>% 25 | ggplot(aes(y = i, x = u_tau)) + 26 | geom_intervalh() + 27 | scale_color_brewer() 28 | ), "Deprecated") 29 | 30 | expect_warning(vdiffr::expect_doppelganger("grouped intervals (h, stat)", 31 | RankCorr_u_tau %>% 32 | ggplot(aes(y = i, x = u_tau)) + 33 | stat_intervalh(.width = c(.5, .75, .90)) + 34 | scale_color_brewer() 35 | ), "Deprecated") 36 | }) 37 | -------------------------------------------------------------------------------- /tests/testthat/test.geom_pointinterval.R: -------------------------------------------------------------------------------- 1 | # Tests for interval geoms 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | library(dplyr) 7 | library(tidyr) 8 | 9 | 10 | 11 | # use a subset of RankCorr so tests are faster 12 | data(RankCorr, package = "ggdist") 13 | RankCorr_u_tau = RankCorr %>% 14 | spread_draws(u_tau[i]) %>% 15 | filter(i %in% 1:3, .iteration %in% 1:50) 16 | 17 | test_that("horizontal grouped pointintervals work", { 18 | skip_if_no_vdiffr() 19 | 20 | 21 | expect_warning(vdiffr::expect_doppelganger("grouped pointintervals (h)", 22 | RankCorr_u_tau %>% 23 | median_hdci(.width = c(.66, .95)) %>% 24 | ggplot(aes(y = i, x = u_tau)) + 25 | geom_pointintervalh(show.legend = TRUE) + 26 | theme_tidybayes() 27 | )) 28 | 29 | expect_warning(vdiffr::expect_doppelganger("grouped pointintervals (h, stat)", 30 | RankCorr_u_tau %>% 31 | ggplot(aes(y = i, x = u_tau)) + 32 | stat_pointintervalh(.width = c(.66, .95)) 33 | ), "Deprecated") 34 | 35 | }) 36 | -------------------------------------------------------------------------------- /tests/testthat/test.get_variables.R: -------------------------------------------------------------------------------- 1 | # Tests for get_variables 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | library(dplyr) 7 | 8 | 9 | 10 | 11 | test_that("mcmc variable extraction works", { 12 | data(RankCorr, package = "ggdist") 13 | 14 | ref = dimnames(RankCorr[[1]])[[2]] 15 | 16 | tidy_draws_ref = RankCorr %>% 17 | tidy_draws() %>% 18 | names() %>% 19 | setdiff(c(".chain", ".iteration", ".draw")) 20 | 21 | expect_equal(get_variables(RankCorr), ref) 22 | expect_equal(get_variables(RankCorr[[1]]), ref) 23 | expect_equal(get_variables(RankCorr), tidy_draws_ref) 24 | }) 25 | 26 | test_that("rstanarm variable extraction works", { 27 | skip_if_not_installed("rstanarm") 28 | 29 | m_hp_wt = readRDS("../models/models.rstanarm.m_hp_wt.rds") 30 | 31 | expect_equal(get_variables(m_hp_wt), 32 | c("(Intercept)", "hp", "wt", "hp:wt", "sigma", "accept_stat__", 33 | "stepsize__", "treedepth__", "n_leapfrog__", "divergent__", "energy__") 34 | ) 35 | }) 36 | -------------------------------------------------------------------------------- /tests/testthat/test.point_interval.R: -------------------------------------------------------------------------------- 1 | # Tests for point_interval 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | library(dplyr) 7 | library(tidyr) 8 | 9 | 10 | 11 | 12 | test_that("point_interval works on vectors", { 13 | set.seed(1234) 14 | x = rnorm(100, mean = 5) 15 | 16 | ref = data.frame( 17 | y = mean(x), 18 | ymin = as.vector(quantile(x, probs = .025)), 19 | ymax = as.vector(quantile(x, probs = .975)), 20 | .width = .95, 21 | .point = "mean", 22 | .interval = "qi", 23 | stringsAsFactors = FALSE 24 | ) 25 | 26 | expect_warning( 27 | expect_equal(mean_qih(x), rename(ref, x = y, xmin = ymin, xmax = ymax)) 28 | , "Deprecated") 29 | }) 30 | -------------------------------------------------------------------------------- /tests/testthat/test.sample_draws.R: -------------------------------------------------------------------------------- 1 | # Tests for sample_draws 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | library(dplyr) 7 | library(tidyr) 8 | 9 | 10 | # use a subset of RankCorr so tests are faster 11 | data(RankCorr, package = "ggdist") 12 | RankCorr_s = RankCorr[[1]][1:100,] 13 | RankCorr_u_tau = RankCorr_s %>% 14 | spread_draws(u_tau[i]) %>% 15 | filter(i %in% 1:3) 16 | 17 | test_that("sample_draws works", { 18 | set.seed(1234) 19 | draws = sample.int(100, 2) 20 | ref = filter(RankCorr_u_tau, .draw %in% draws) 21 | 22 | expect_equal(sample_draws(RankCorr_u_tau, ndraws = 2, seed = 1234), ref) 23 | }) 24 | -------------------------------------------------------------------------------- /tests/testthat/test.stat_dist_slabinterval.R: -------------------------------------------------------------------------------- 1 | # Tests for analytical distribution plots 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | library(dplyr) 7 | 8 | 9 | 10 | test_that("distribution eye plots work with the args aesthetic", { 11 | skip_if_no_vdiffr() 12 | 13 | 14 | p = tribble( 15 | ~dist, ~args, 16 | "norm", list(0, 1), 17 | "beta", list(5, 5), 18 | NA, NA 19 | ) %>% 20 | ggplot(aes(dist = dist, args = args)) 21 | 22 | # test deprecation warning 23 | expect_warning(vdiffr::expect_doppelganger("horizontal half-eye using args", 24 | p + stat_dist_halfeyeh(aes(y = dist), na.rm = TRUE, n = 40) 25 | ), "Deprecated") 26 | 27 | # test deprecation warning 28 | expect_warning(vdiffr::expect_doppelganger("ccdfintervalh using args", 29 | p + stat_dist_ccdfintervalh(aes(y = dist), na.rm = TRUE, n = 40) 30 | ), "Deprecated") 31 | 32 | }) 33 | -------------------------------------------------------------------------------- /tests/testthat/test.summarise_draws.R: -------------------------------------------------------------------------------- 1 | # Tests for summarise_draws.grouped_df 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | library(posterior) 7 | library(dplyr) 8 | 9 | 10 | 11 | 12 | test_that("summarise_draws.grouped_df works", { 13 | d = subset_draws(example_draws(), variable = c("theta[1]", "theta[2]", "theta[3]")) 14 | 15 | ref = summarise_draws(d) %>% 16 | mutate(variable = "theta") %>% 17 | add_column(i = 1:3, .before = 1) %>% 18 | group_by(i) 19 | attr(ref, "num_args") = NULL 20 | 21 | expect_equal(d %>% spread_draws(theta[i]) %>% summarise_draws(), ref) 22 | }) 23 | -------------------------------------------------------------------------------- /tests/testthat/test.util.R: -------------------------------------------------------------------------------- 1 | # Tests for util 2 | # 3 | # Author: mjskay 4 | ############################################################################### 5 | 6 | 7 | 8 | 9 | test_that("combine_chains_for_deprecated_ works properly", { 10 | df = data.frame( 11 | .chain = c(1,1,1,1,1,2,2,2,2,2), 12 | .iteration = c(1:5, 1:5), 13 | .draw = c(1:10) 14 | ) 15 | 16 | ref = data.frame( 17 | .chain = NA_integer_, 18 | .iteration = c(1:10) 19 | ) 20 | 21 | expect_equal(combine_chains_for_deprecated_(df), ref) 22 | }) 23 | 24 | test_that(".Deprecated_argument_alias works properly", { 25 | 26 | expect_warning(point_interval(0:10, .prob = .50), paste0( 27 | "In point_interval\\.numeric\\(\\)\\: The `\\.prob` argument is a deprecated alias for `\\.width`\\.\n", 28 | "Use the `\\.width` argument instead\\.\n", 29 | "See help\\(\"tidybayes-deprecated\"\\).*" 30 | )) 31 | 32 | }) 33 | -------------------------------------------------------------------------------- /vignettes/.install_extras: -------------------------------------------------------------------------------- 1 | ^children 2 | -------------------------------------------------------------------------------- /vignettes/children/chunk_options.txt: -------------------------------------------------------------------------------- 1 | 9 | 10 | ```{r chunk_options, include=FALSE} 11 | if (requireNamespace("pkgdown", quietly = TRUE) && pkgdown::in_pkgdown()) { 12 | tiny_width = small_width = med_width = 6.75 13 | tiny_height = small_height = med_height = 4.5 14 | large_width = 8 15 | large_height = 5.25 16 | } else { 17 | tiny_width = 5.5 18 | tiny_height = 3 + 2/3 19 | small_width = med_width = 6.75 20 | small_height = med_height = 4.5 21 | large_width = 8 22 | large_height = 5.25 23 | } 24 | 25 | eval_chunks = identical(Sys.getenv("NOT_CRAN"), "true") 26 | knitr::opts_chunk$set( 27 | fig.width = small_width, 28 | fig.height = small_height, 29 | eval = eval_chunks, 30 | purl = eval_chunks 31 | ) 32 | if (capabilities("cairo") && Sys.info()[['sysname']] != "Darwin") { 33 | knitr::opts_chunk$set( 34 | dev.args = list(png = list(type = "cairo")) 35 | ) 36 | } 37 | ``` 38 | -------------------------------------------------------------------------------- /vignettes/slabinterval_family.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mjskay/tidybayes/fb494368784350b0269fda406a37c1195d5401d6/vignettes/slabinterval_family.png --------------------------------------------------------------------------------