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OncoBayes2 0.8-9 - July 20th,
2023
Bug fixes
- resolve compilation from source issues on some platforms triggered
by changes in rstantools
OncoBayes2 0.8-8 - March 3rd,
2023
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 - August
24th, 2022
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 - May 2nd,
2022
- 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 -
February 28th, 2022
- fix issue with example_model not exposing properly objects when
running with silent=TRUE
OncoBayes2 0.8-4 -
February 18th, 2022
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 - October
7th, 2021
- Make Stan model compile with 2.27+ (lupmf postfix for variables is
not allowed)
OncoBayes2 0.8-2 -
September 13th, 2021
- 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 -
September 1st, 2021
OncoBayes2 0.8-0 - August
31st, 2021
- 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 - May 7th,
2021
- 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 - May 7th,
2020
- Drop RBesT dependency
- Avoid setting the ggplot2 theme upon package load
- Enhance SBC runs to monitor and report sampler diagnostics
OncoBayes2 0.6-4 - April 7th,
2020
- Add Operation Qualification script (run-oq.R in inst/extra)
- Add saturating interaction model (blrm_formula_saturating) and
associated tests
OncoBayes2 0.6-3 - March
18th, 2020
- 2nd attempt to work around issues found by clang sanitizer in Stan
model.
OncoBayes2 0.6-2 - March 9th,
2020
- Work around issues found by clang sanitizer in Stan model.
OncoBayes2 0.6-1 - March 4th,
2020
- 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 -
February 11th, 2020
- 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 -
December 12th, 2019
- 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 -
December 9th, 2019
- 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 -
November 29th, 2019
- Support summary.blrm_trial(…) syntax passing into
summary.blrmfit()
OncoBayes2 0.5-5 -
November 22nd, 2019
- Fixed Roxygen for posterior_predict
OncoBayes2 0.5-4 -
November 18th, 2019
- fix vignette documentation
- correct blrm trial co-data example
- fix test issues per CRAN checks on macosx-old-r run
OncoBayes2 0.5-3 -
November 15th, 2019
- 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 - August
28th, 2019
- run in all examples the example code (remove dontrun sections)
OncoBayes2 0.4-3 - August
27th, 2019
- 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 - August
27th, 2019
- 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 - July 31st,
2019
- Correct external package loading in examples
OncoBayes2 0.2-0 - July 27th,
2019
- 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 - May 15th,
2018
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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