Bambi Versions Save

This is the first version of Bambi that is released with a Governance structure. Added in #709. The highlights are the shiny interpret subpackage and the implementation of support for censored models.

New features

• Bambi now supports censored responses (#697)
• Implement "exponential" and "weibull" families (#697)
• Add "kidney" dataset (#697)
• Add interpret submodule (#684, #695, #699, #701, #732, #736)
  • Implements comparisons, predictions, slopes, plot_comparisons, plot_predictions, and plot_slopes
• Support censored families

Maintenance and fixes

• Replace univariate_ordered with ordered (#724)
• Add missing docstring for center_predictors (#726)
• Fix bugs in plot_comparison (#731)

Documentation

• Add docstrings to utility functions (#696)
• Migrate documentation to Quarto (#712)
• Add case study for MRP (#716)
• Add example about ordinal regression (#719)
• Add example about zero inflated models (#725)
• Add example about predictions for new groups (#734)

Deprecation

• Drop official suport for Python 3.8 (#720)
• Change plots submodule name to interpret (#705)

0.12.0

New features

• Implement new families "ordinal" and "sratio" for modeling of ordinal responses (#678)
• Allow families to implement a custom create_extra_pps_coord() (#688)
• Allow predictions on new groups (#693)

Maintenance and fixes

• Robustify how Bambi handles dims (#682)
• Fix links in FAQ (#686)
• Update additional dependencies install command (#689)
• Update predict pps docstring (#690)
• Add warning for aliases athat aren't used (#691)

Documentation

• Add families to the Getting Started guide (#683)

0.11.0

New features

• Add support for Gaussian Processes via the HSGP approximation (#632)
• Add new families: "zero_inflated_poisson", "zero_inflated_binomial", and "zero_inflated_negativebinomial" (#654)
• Add new families: "beta_binomial" and "dirichlet_multinomial" (#659)
• Allow plot_cap() to show predictions at the observation level (#668)
• Add new families: "hurdle_gamma", "hurdle_lognormal", "hurdle_negativebinomial", and "hurdle_poisson" (#676)

Maintenance and fixes

• Modify how HSGP is built in PyMC when there are groups (#661)
• Modify how Bambi is imported in the tests (#662)
• Prevent underscores from being removed in dim names (#664)
• Bump sphinx dependency to a version greater than 7 (#672)

Documentation

• Document how to use custom priors (#656)
• Fix name of arviz traceplot function in the docs (#666)
• Add example that shows how plot_cap() works (#670)

New features

• Refactored the codebase to support distributional models (#607)
• Added a default method to handle posterior predictive sampling for custom families (#625)
• plot_cap() gains a new argument target that allows to plot different parameters of the response distribution (#627)

Maintenance and fixes

• Moved the tests directory to the root of the repository (#607)
• Don't pass dims to the response of the likelihood distribution anymore (#629)
• Remove requirements.txt and replace with pyproject.toml config file to distribute the package (#631)

Documentation

• Update examples to work with the new internals (#607)
• Fixed figure in the Sleepstudy example (#607)
• Add example using distributional models (#641)

Deprecation

• Removed versioned documentation webpage (#616)
• Removed correlated priors for group-specific terms (#607)
• Dictionary with tuple keys are not allowed for priors anymore (#607)

Maintenance and fixes

• Update to PyMC >= 5, which means we use PyTensor instead of Aesara now (#613, #614)

New features

• Implement censored() (#581)
• Add Formula class (#585)
• Add common numpy transforms to extra_namespace (#589)
• Add AsymmetricLaplace family for Quantile Regression (#591)
• Add 'transforms' argument to plot_cap() (#594)
• Add panel covariates to plot_cap() and make it more flexible (#596)

Maintenance and fixes

• Reimplemented predictions to make better usage of xarray data structures (#573)
• Keep 0 dimensional parameters as 0 dimensional instead of 1 dimensional (#575)
• Refactor terms for modularity and extensibility (#582)
• Remove seed argument from model.initial_point() (#592)
• Add build check function on prior predictive and plot prior (#605)

Documentation

• Add quantile regression example (#608)

Deprecation

• Remove automatic_priors argument from Model (#603)
• Remove string option for data input in Model (#604)

Bambi 0.9.1

New features

• Add support for jax sampling via numpyro and blackjax samplers (#526)
• Add Laplace family (#524)
• Improve Laplace computation and integration (#555 and #563)

Maintenance and fixes

• Ensure order variable is preserved when ploting priors (#529)
• Treat offset accordingly (#534)
• Refactor tests to share data generation code (#531)

Documentation

• Update documentation following good inferencedata practices (#537)
• Add logos to repo and docs (#542)

Deprecation

• Deprecate method argument in favor of inference_method (#554)

New features

• Bambi now uses PyMC 4.0 as it's backend. Most if not all your previous model should run the same, without the need of any change.
• Add Plot Conditional Adjusted Predictions plot_cap (#517)

Maintenance and fixes

• Group specific terms now work with numeric of multiple columns (#516)

Bambi 0.8.0

New features

• Add VonMises ("vonmises") built-in family (#453)
• Model.predict() gains a new argument include_group_specific to determine if group-specific effects are considered when making predictions (#470)
• Add Multinomial ("multinomial") built-in family (#490)

Maintenance and fixes

• Add posterior predictive sampling method to "categorical" family (#458)
• Require Python >= 3.7.2 to fix NoReturn type bug in Python (#463)
• Fixed the wrong builtin link given by link="inverse" was wrong. It returned the same result as link="cloglog" (#472)
• Replaced plain dictionaries with namedtuples when same dictionary structure was repeated many times (#472)
• The function check_full_rank() in utils.py now checks the array is 2 dimensional (#472)
• Removed _extract_family_prior() from bambi/families as it was unnecesary (#472)
• Removed bambi/families/utils.py as it was unnecessary (#472)
• Removed external links and unused datasets (#483)
• Replaced "_coord_group_factor" with "__factor_dim" and "_coord_group_expr" with "__expr_dim" in dimension/coord names (#499)
• Fixed a bug related to modifying the types of the columns in the original data frame (#502)

Documentation

• Add circular regression example (#465)
• Add Categorical regression example (#457)
• Add Beta regression example (#442)
• Add Radon Example (#440)
• Fix typos and clear up writing in some docs (#462)
• Documented the module bambi/defaults (#472)
• Improved documentation and made it more consistent (#472)
• Cleaned Strack RRR example (#479)

Deprecation

• Removed old default priors (#474)
• Removed draws parameter from Model.predict() method (#504)

This is a patch release where we fix a bug related to the shape of 2 level categorical group-specific effects (#441)