May 2nd, 2022 (0.8-6)
* 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)
February 28th, 2022 (0.8-5)
* fix issue with example_model not exposing properly objects when
running with silent=TRUE
February 18th, 2022 (0.8-4)
* 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.
October 7th, 2021 (0.8-3)
* Make Stan model compile with 2.27+ (lupmf postfix for variables is
not allowed)
September 13th, 2021 (0.8-2)
* 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.
September 1st, 2021 (0.8-1)
* Address CRAN comments
August 31st, 2021 (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.
May 7th, 2021 (0.7-0)
* 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.
May 7th, 2020 (0.6-5)
* Drop RBesT dependency
* Avoid setting the ggplot2 theme upon package load
* Enhance SBC runs to monitor and report sampler diagnostics
April 7th, 2020 (0.6-4)
* Add Operation Qualification script (run-oq.R in inst/extra)
* Add saturating interaction model (blrm_formula_saturating) and associated tests
March 18th, 2020 (0.6-3)
* 2nd attempt to work around issues found by clang sanitizer in Stan model.
March 9th, 2020 (0.6-2)
* Work around issues found by clang sanitizer in Stan model.
March 4th, 2020 (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
February 11th, 2020 (0.6-0)
* 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.
December 12th, 2019 (0.5-8)
* 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
December 9th, 2019 (0.5-7)
* Improve numerical stability of log_inv_logit function, preventing
NaNs in the output of pp_data and resulting errors in summary()
November 29th, 2019 (0.5-6)
* Support summary.blrm_trial(...) syntax passing into summary.blrmfit()
November 22nd, 2019 (0.5-5)
* Fixed Roxygen for posterior_predict
November 18th, 2019 (0.5-4)
* fix vignette documentation
* correct blrm trial co-data example
* fix test issues per CRAN checks on macosx-old-r run
November 15th, 2019 (0.5-3)
* 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
August 28th, 2019 (0.4-4)
* run in all examples the example code (remove dontrun sections)
August 27th, 2019 (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
August 27th, 2019 (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
July 31st, 2019 (0.3-0)
* Correct external package loading in examples
July 27th, 2019 (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
May 15th, 2018 (0.1-0)
* Initial release