NEWS

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OncoBayes2 0.9-0 (2025-03-01)

Enhancements

• Introduce mixture prior arguments for blrm_exnex. These replace the existing arguments for prior specification, which are now deprecated and will be removed in the next main version increase of the package.
• Add experimental as_draws* functions allowing to extract samples in the posterior draws format from blrmfit objects.
• Improve error messages when Stan fails to sample.

Bug fixes

• Added several plot improvements and bug fixes. Fixed an issue leading to jagged curves in plot_toxicity_intervals_stacked(), and another leading to wrongly ordered facets in plot_toxicity_intervals(). Ensured consistent bayesplot themeing across all plots.
• Fixed sampling of model prior whenever EXNEX is used.
• Simulation-based calibration performance was increased by roughly an order of magnitude.
• Fixed issues for BLRMs without interaction term and cmdstan 2.36.0
• Results of model runs with the cmdstanr backend are now loaded using the brms package instead of rstan. This fixes issues with loading results from cmdstan 2.36.0
• The intervals reported by the summary() function using the interval_prob argument by default now include the lower end as a closed interval for calls where predictive = FALSE. For the default underdosing interval, this includes the probability of exactly 0 now.
• Fixed an issue relating to an incompatibility of upcoming R 4.5.0 on macOS when using C23 with rstan.

OncoBayes2 0.8-10

Enhancements

• Updated Stan model file syntax to use new array syntax as required by Stan >=2.33. This upgrades the minimal Stan version to 2.26.
• Start compressing plots in vignette to slim down file size.

OncoBayes2 0.8-9 (2023-07-20)

Bug fixes

• resolve compilation from source issues on some platforms triggered by changes in rstantools

OncoBayes2 0.8-8 (2023-03-03)

Enhancements

• upon package load OncoBayes2 will now report the date of the release and the respective git commit hash used to create the sources of the package.

Bug fixes

• ensure compatibility with posterior 1.4.0 (posterior returns num() formatted columns, which OncoBayes2 is not supporting)
• ensure C++17 compatiblity per CRAN (triggers an issue with clang 16)

OncoBayes2 0.8-7 (2022-08-25)

Enhancements

• add warning messages when printing blrmfit objects for divergent transitions or non-convergence of parameters
• add diagnostic extraction functions nuts_params, rhat, log_posterior and neff_ratio for blrmfit objects as defined in bayesplot
• speedup pp_data by about 25% which is used in all posterior summary functions
• add ewoc_check summary routine for blrm_trial objects. The returned summary contains MCMC diagnostics and accuracy estimates of the EWOC metric as defined for the trial. This allows to assess the MCMC estimation error for EWOC.
• added warning for imprecise estimates of the EWOC metric whenever blrm_trial objects are printed.

Bug fixes

• fix broken exclusion of unnecessary random variables whenever save_warmup=FALSE.

OncoBayes2 0.8-6 (2022-05-02)

• allow cmdstanr as new backend for blrm_exnex. The Stan model file is written with the function cmdstanr::write_stan_file to disk such that the model binaries can be cached if the user defines the global option cmdstanr_write_stan_file_dir. See ?cmdstanr::write_stan_file (requires cmdstanr >= 0.5.0)

OncoBayes2 0.8-5 (2022-03-01)

• fix issue with example_model not exposing properly objects when running with silent=TRUE

OncoBayes2 0.8-4 (2022-02-18)

• Switch SBC runs to use clustermq in lieu of batchtools. Also now use L'Ecuyer CMG as rng engine during SBC runs.

• add critical_quantile function allowing to calculate critical doses which fulfill conditions like EWOC.

OncoBayes2 0.8-3

• Make Stan model compile with 2.27+ (lupmf postfix for variables is not allowed)

OncoBayes2 0.8-2 (2021-09-14)

• Drop unneccessary random variables from the posterior whenever save_warmup=FALSE. This decreases the size of the posterior in memory by ~60% for the combo2 example.

OncoBayes2 0.8-1 (2021-09-02)

• Address CRAN comments

OncoBayes2 0.8-0

• Significantly speedup Stan model by dropping normalization of binomial
• The default interaction model for blrm_trial is now saturating (blrm_formula_saturating) in logit space, improving behavior for combinations with antagonistic toxicity.
• blrm_trial simplified prior now defaults to ENXEX off, and prior parameter defaults have been updated.
• New save_warmup argument to blrm_exnex can be used to disable saving of warmup samples, which defaults to the OncoBayes2.MC.save_warmup option, which defaults to TRUE in line with previous versions. NOTE: Starting with the next version 0.9.0 the new default will be FALSE!
• Do not crash for summary(trial, "data_prediction") if blrm_trial has NULL or 0-row data
• Spurious warning for dose_id NA on blrm_trial instantiation removed
• Spurious warning for dose not prespecified on summary(..., newdata=...) removed
• New plot function plot_toxicity_intervals_stacked(), which visualizes model posterior or predictive probabilities in discrete intervals, over a continuous range of doses
• Automated visual regression testing implemented using the vdiffr package
• Fix in plot_toxicity_curve to avoid overplotting if newdata contains columns other than grouping variables and doses (e.g. dose_id)
• Avoid re-parsing model formula whenever newdata is not used in respective functions. This prevents that changes to global variables (like dref) have any effect whenever the fitted data only is used.

OncoBayes2 0.7-0 (2021-05-07)

• Catch data specification errors for wrongly nested groups/strata
• BLRM trials now also print toxicity probability intervals and the EWOC setting
• The blrm_formula_linear and blrm_formula_saturating interaction model formula generators can now be customized to generate specific interactions using the specific_interaction_terms argument.
• Add predictive summaries to summary method.
• Switch predictive outputs to be based on averaging sampling density. This avoids the need for additional sampling for predictive summaries.
• Add plotting methods for blrmfit and blrm_trial objects.

OncoBayes2 0.6-5 (2020-05-07)

• Drop RBesT dependency
• Avoid setting the ggplot2 theme upon package load
• Enhance SBC runs to monitor and report sampler diagnostics

OncoBayes2 0.6-4 (2020-04-07)

• Add Operation Qualification script (run-oq.R in inst/extra)
• Add saturating interaction model (blrm_formula_saturating) and associated tests

OncoBayes2 0.6-3 (2020-03-19)

• 2nd attempt to work around issues found by clang sanitizer in Stan model.

OncoBayes2 0.6-2

• Work around issues found by clang sanitizer in Stan model.

OncoBayes2 0.6-1

• Fix issue with upcoming R 4.0 which changes stringsAsFactors default to FALSE
• Fix for upcoming tibble 3.0 upgrade which changes conventions of growing factors within tibbles

OncoBayes2 0.6-0 (2020-02-11)

• Fix issue with model outputs when EXNEX is being used. We recommend all users to upgrade to this version. The SBC runs now include checks for the per-group estimates to avoid a regression of the bug.
• Correct printing of prior information wrt. to summaries of number of strata and groups.

OncoBayes2 0.5-8 (2019-12-12)

• Merge data with same group and dosing in blrm_trial before passing into blrm_exnex for improved performance
• Ensure consistent sorting of this data to improve reproducibility of output with respect to input data permutations
• speedup Stan model which now skips data rows with no cases
• correct blrm_exnex documentation to reflect correctly exchangability model used for the interaction model

OncoBayes2 0.5-7

• Improve numerical stability of log_inv_logit function, preventing NaNs in the output of pp_data and resulting errors in summary()

OncoBayes2 0.5-6

• Support summary.blrm_trial(...) syntax passing into summary.blrmfit()

OncoBayes2 0.5-5

• Fixed Roxygen for posterior_predict

OncoBayes2 0.5-4 (2019-11-19)

• fix vignette documentation
• correct blrm trial co-data example
• fix test issues per CRAN checks on macosx-old-r run

OncoBayes2 0.5-3 (2019-11-15)

• new blrm_trial function which facilitates dose-escalation trial conduct by combining key trial design features
• new add_data argument to update function which adds data to existing model objects of class blrmfit or blrm_trial
• various smaller bug fixes

OncoBayes2 0.4-4 (2019-08-29)

• run in all examples the example code (remove dontrun sections)

OncoBayes2 0.4-3

• use message instead of cat in functions using printing except summary or print
• suppress by default messages from Stan, can be enable with verbose=TRUE
• make examples run with very short sampling

OncoBayes2 0.4-2

• Correct loading and exporting of methods
• Add tidybayes example for continuous use and visutalization of model
• Allow multiple central probability widths in prob argument of summary method

OncoBayes2 0.3-0

• Correct external package loading in examples

OncoBayes2 0.2-0

• Added function prior_summary
• Restructured print output
• Added examples single-agent, combo2 and combo3 along with example data sets
• A lot more documentation on reference pages
• New vignette on standard use case of blrm_exnex in Oncology
• Qualified blrm_exnex model with Simulation Based Calibration

OncoBayes2 0.1-0

• Initial release