Add public pkgdown web-site and establish new GitHub homepage of
OnocBayes2
Bug fixes
Address formatting issues in roxgen2 documentation
OncoBayes2 0.9-3 - April
25th, 2025
Bug fixes
Fix issue with using multiple strata and the new argument
prior_tau_dist=NULL of blrm_exnex.
Fix issues with draws extraction functions which ignored the
inc_warmup argument.
OncoBayes2 0.9-2 - April 7th,
2025
Enhancements
Extend as_draws_* functions to blrm_trial
inputs.
Bug fixes
Ensure that the new option prior_tau_dist=NULL is
forwarded when used via blrm_trial to
blrm_exnex.
Make sure that rvars are exported as arrays when the
underyling parameter is structured.
OncoBayes2 0.9-1 - March
17th, 2025
Enhancements
Adding new vignette on how to derive MAP priors from historical
data.
New sample_map argument for blrm_exnex
function allows to sample MAP prior for all defined strata of the model.
When set to TRUE the posterior draws contain
map_log_beta and map_eta which correspond to
respective MAP priors per stratum for new trials.
Allow argument prior_tau_dist of
blrm_exnex to be set to NULL. This will
disable the hierarchical model structure entirely and this simplifies
specifying such models without a hierarchical structure (data will then
be pooled across groups).
Bug fixes
Fix issue whenever different number of mixture components are used
for prios on drug components.
Ensure that extracted posterior samples as draws objects have
labeled array dimensions.
Small efficiency improvement for Stan model.
OncoBayes2 0.9-0 -
February 28th, 2025
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 -
November 4th, 2024
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 - 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
Address CRAN comments
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