Package: tidybayes 3.0.7.9000
tidybayes: Tidy Data and 'Geoms' for Bayesian Models
Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided to help extract tidy data frames of draws from Bayesian models and that generate point summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus densities), and fit curves with multiple, arbitrary uncertainty bands.
Authors:
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tidybayes.pdf |tidybayes.html✨
tidybayes/json (API)
NEWS
| # Install 'tidybayes' in R: |
| install.packages('tidybayes', repos = c('https://mjskay.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mjskay/tidybayes/issues
bayesian-data-analysisbrmsggplot2jagsstantidy-datavisualization
Last updated 2 months agofrom:fb49436878. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 16 2024 |
| R-4.5-win | OK | Nov 16 2024 |
| R-4.5-linux | OK | Nov 16 2024 |
| R-4.4-win | OK | Nov 16 2024 |
| R-4.4-mac | OK | Nov 16 2024 |
| R-4.3-win | OK | Nov 16 2024 |
| R-4.3-mac | OK | Nov 16 2024 |
Exports:add_drawsadd_epred_drawsadd_epred_rvarsadd_fitted_drawsadd_fitted_samplesadd_linpred_drawsadd_linpred_rvarsadd_predicted_drawsadd_predicted_rvarsadd_predicted_samplesadd_residual_drawsapply_prototypesas_data_listas_sample_data_frameas_sample_tibbleaxis_titles_bottom_leftcombine_chainscompare_levelscompose_datacurve_intervalcut_cdf_qidata_listdensity_binsdlkjcorr_marginaldstudent_temmeans_comparisonepred_drawsepred_rvarsextract_samplesfacet_title_left_horizontalfacet_title_right_horizontalfitted_drawsfitted_samplesfrom_broom_namesfrom_ggmcmc_namesgather_drawsgather_emmeans_drawsgather_emmeans_samplesgather_lsmeans_samplesgather_pairsgather_rvarsgather_samplesgather_termsgather_variablesgeom_dotsgeom_dotshgeom_dotsintervalgeom_dotsintervalhgeom_eyegeom_eyehgeom_halfeyehgeom_intervalgeom_intervalhgeom_lineribbongeom_pointintervalgeom_pointintervalhgeom_slabgeom_slabhgeom_slabintervalGeomDotsGeomDotsintervalGeomIntervalGeomIntervalhGeomLineribbonGeomPointintervalGeomPointintervalhGeomSlabGeomSlabintervalget_variablesggeyeguide_colorbar2guide_colourbar2hdcihdihistogram_binslinpred_drawslinpred_rvarsmarginalize_lkjcorrmean_hdcimean_hdcihmean_hdimean_hdihmean_qimean_qihmedian_hdcimedian_hdcihmedian_hdimedian_hdihmedian_qimedian_qihModemode_hdcimode_hdcihmode_hdimode_hdihmode_qimode_qihn_prefixnest_rvarsparametersparse_distplkjcorr_marginalpoint_intervalpoint_intervalhpredict_curvepredict_curve_densitypredicted_drawspredicted_rvarspredicted_samplespstudent_tqiqlkjcorr_marginalqstudent_tr_dist_namerecover_typesresidual_drawsrlkjcorr_marginalrstudent_tsample_drawsscale_interval_alpha_continuousscale_interval_alpha_discretescale_interval_color_continuousscale_interval_color_discretescale_interval_colour_continuousscale_interval_colour_discretescale_interval_linetype_continuousscale_interval_linetype_discretescale_interval_size_continuousscale_interval_size_discretescale_point_alpha_continuousscale_point_alpha_discretescale_point_color_continuousscale_point_color_discretescale_point_colour_continuousscale_point_colour_discretescale_point_fill_continuousscale_point_fill_discretescale_point_size_continuousscale_point_size_discretescale_slab_alpha_continuousscale_slab_alpha_discretescale_slab_color_continuousscale_slab_color_discretescale_slab_colour_continuousscale_slab_colour_discretescale_slab_fill_continuousscale_slab_fill_discretescale_slab_linetype_continuousscale_slab_linetype_discretescale_slab_shape_continuousscale_slab_shape_discretescale_slab_size_continuousscale_slab_size_discretespread_drawsspread_rvarsspread_samplesstat_ccdfintervalstat_ccdfintervalhstat_cdfintervalstat_cdfintervalhstat_dist_ccdfintervalstat_dist_ccdfintervalhstat_dist_cdfintervalstat_dist_cdfintervalhstat_dist_dotsstat_dist_dotshstat_dist_dotsintervalstat_dist_dotsintervalhstat_dist_eyestat_dist_eyehstat_dist_gradientintervalstat_dist_gradientintervalhstat_dist_halfeyestat_dist_halfeyehstat_dist_intervalstat_dist_intervalhstat_dist_lineribbonstat_dist_pointintervalstat_dist_pointintervalhstat_dist_slabstat_dist_slabhstat_dist_slabintervalstat_dotsstat_dotshstat_dotsintervalstat_dotsintervalhstat_eyestat_eyehstat_gradientintervalstat_gradientintervalhstat_halfeyestat_halfeyehstat_histintervalstat_histintervalhstat_intervalstat_intervalhstat_lineribbonstat_pointintervalstat_pointintervalhstat_sample_slabintervalstat_slabstat_slabhstat_slabintervalStatDistSlabintervalStatIntervalStatPointintervalStatSampleSlabintervalStatSlabintervalsummarise_drawstheme_ggdisttheme_tidybayestidy_drawstidy_samplesto_broom_namesto_ggmcmc_namesungather_drawsungather_samplesunnest_rvarsunspread_drawsunspread_samplesx_at_y
Dependencies:abindarrayhelpersbackportscheckmateclicodacolorspacecpp11distributionaldplyrfansifarvergenericsggdistggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgconfigposteriorpurrrquadprogR6RColorBrewerRcpprlangscalesstringistringrsvUnittensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr
Extracting and visualizing tidy draws from brms models
Rendered fromtidy-brms.Rmdusingknitr::rmarkdownon Nov 16 2024.Last update: 2024-09-17
Started: 2017-11-16
Extracting and visualizing tidy draws from rstanarm models
Rendered fromtidy-rstanarm.Rmdusingknitr::rmarkdownon Nov 16 2024.Last update: 2024-09-17
Started: 2017-03-12
Extracting and visualizing tidy residuals from Bayesian models
Rendered fromtidybayes-residuals.Rmdusingknitr::rmarkdownon Nov 16 2024.Last update: 2024-09-17
Started: 2019-01-05
Using tidy data with Bayesian models
Rendered fromtidybayes.Rmdusingknitr::rmarkdownon Nov 16 2024.Last update: 2024-09-17
Started: 2016-11-12
Using tidybayes with the posterior package
Rendered fromtidy-posterior.Rmdusingknitr::rmarkdownon Nov 16 2024.Last update: 2024-09-17
Started: 2021-07-05
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Tidy Data and 'Geoms' for Bayesian Models | tidybayes-package tidybayes |
| Add draws to a data frame in tidy format | add_draws |
| Add draws from the posterior fit, predictions, or residuals of a model to a data frame | add_epred_draws add_linpred_draws add_predicted_draws add_residual_draws epred_draws epred_draws.brmsfit epred_draws.default epred_draws.stanreg linpred_draws linpred_draws.brmsfit linpred_draws.default linpred_draws.stanreg predicted_draws predicted_draws.brmsfit predicted_draws.default predicted_draws.stanreg residual_draws residual_draws.brmsfit residual_draws.default |
| Add 'rvar's for the linear predictor, posterior expectation, posterior predictive, or residuals of a model to a data frame | add_epred_rvars add_linpred_rvars add_predicted_rvars epred_rvars epred_rvars.brmsfit epred_rvars.default epred_rvars.stanreg linpred_rvars linpred_rvars.brmsfit linpred_rvars.default linpred_rvars.stanreg predicted_rvars predicted_rvars.brmsfit predicted_rvars.default predicted_rvars.stanreg |
| Combine the chain and iteration columns of tidy data frames of draws | combine_chains |
| Compare the value of draws of some variable from a Bayesian model for different levels of a factor | compare_levels |
| Compose data for input into a Bayesian model | compose_data |
| Data lists for input into Bayesian models | as_data_list as_data_list.character as_data_list.data.frame as_data_list.data_list as_data_list.default as_data_list.factor as_data_list.list as_data_list.logical as_data_list.numeric data_list |
| Density bins and histogram bins as data frames | density_bins histogram_bins |
| Use emmeans contrast methods with compare_levels | emmeans_comparison |
| Extract draws of variables in a Bayesian model fit into a tidy data format | gather_draws spread_draws |
| Extract a tidy data frame of draws of posterior distributions of "estimated marginal means" (emmeans/lsmeans) from a Bayesian model fit. | gather_emmeans_draws gather_emmeans_draws.default gather_emmeans_draws.emm_list |
| Gather pairwise combinations of values from key/value columns in a long-format data frame | gather_pairs |
| Extract draws from a Bayesian model into tidy data frames of random variables | gather_rvars spread_rvars |
| Gather variables from a tidy data frame of draws from variables into a single column | gather_variables |
| Get the names of the variables in a fitted Bayesian model | get_variables get_variables.default get_variables.mcmc get_variables.mcmc.list |
| Prefix function generator for composing dimension index columns | n_prefix |
| Nest and unnest 'rvar' columns in data frames | nest_rvars unnest_rvars |
| Deprecated: Prediction curves for arbitrary functions of posteriors | predict_curve predict_curve_density |
| Decorate a model fit or sample with data types recovered from the input data | apply_prototypes recover_types |
| Sample draws from a tidy-format data frame of draws | sample_draws |
| Summaries of draws in 'grouped_df' objects | summarise_draws.grouped_df |
| Get a sample of posterior draws from a model as a tibble | tidy_draws tidy_draws.brmsfit tidy_draws.CmdStanFit tidy_draws.CmdStanMCMC tidy_draws.data.frame tidy_draws.default tidy_draws.draws tidy_draws.jagsUI tidy_draws.matrix tidy_draws.mcmc.list tidy_draws.MCMCglmm tidy_draws.runjags tidy_draws.stanfit tidy_draws.stanreg |
| Deprecated functions, arguments, and column names in tidybayes | add_fitted_draws add_fitted_samples add_predicted_samples as_sample_data_frame as_sample_tibble extract_samples fitted_draws fitted_draws.default fitted_samples gather_emmeans_samples gather_lsmeans_samples gather_samples gather_terms GeomIntervalh GeomPointintervalh geom_dotsh geom_dotsintervalh geom_eye geom_eyeh geom_halfeyeh geom_intervalh geom_pointintervalh geom_slabh ggeye mean_hdcih mean_hdih mean_qih median_hdcih median_hdih median_qih mode_hdcih mode_hdih mode_qih parameters point_intervalh predicted_samples spread_samples stat_ccdfintervalh stat_cdfintervalh stat_dist_ccdfintervalh stat_dist_cdfintervalh stat_dist_dotsh stat_dist_dotsintervalh stat_dist_eyeh stat_dist_gradientintervalh stat_dist_halfeyeh stat_dist_intervalh stat_dist_pointintervalh stat_dist_slabh stat_dotsh stat_dotsintervalh stat_eyeh stat_gradientintervalh stat_halfeyeh stat_histintervalh stat_intervalh stat_pointintervalh stat_slabh tidybayes-deprecated tidy_samples ungather_samples unspread_samples |
| Models supported by tidybayes | tidybayes-models |
| Turn tidy data frames of variables from a Bayesian model back into untidy data | ungather_draws unspread_draws |
| Generate lookup vectors for composing nested indices | x_at_y |
