NEWS

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RBesT 1.12-0 (2026-09-18)

Enhancements

• A WebAssembly/webR build of RBesT and its dependency closure is now produced as a mountable library image.
• gMAP now samples the group random effects in a sum-to-zero parametrization whenever the model has an intercept, normal random effects and a single tau stratum. The data-free common shift shared by the intercept and the random effects is marginalized analytically using an orthonormal basis of the sum-to-zero subspace, which removes the ridge between beta[1] and mean(eps) that made the posterior hard to explore. The model is mathematically unchanged and all outputs keep their previous meaning; only the sampling geometry differs. Student-t random effects, several tau strata and intercept-free models continue to use the previous parametrization. Set options(RBesT.MC.s2z = FALSE) to use the conventional parametrization. Many thanks to Sean Pinkney and Nikolai Vetr for presenting the approch at StanCon 2026.
• Automatic partial centering is now the default for all gMAP model variants (options(RBesT.MC.ncp = 3)). Before sampling, fixed-effort Gaussian quadrature estimates the posterior median of each heterogeneity stratum and converts it to per-group Fisher-information centering fractions. If the fixed numerical checks do not agree, gMAP warns and uses the exact non-centered model parametrization. RBesT.MC.ncp = 0 and 1 keep their existing meanings (centered / non-centered); RBesT.MC.ncp = 2 keeps its existing endpoint threshold but now bases its centered/non-centered decision on the same quadrature fractions instead of a cruder scalar heterogeneity guess (see below). Partial centering is independent of whether the model is eligible for the sum-to-zero representation. To restore the pre-1.12 sampling scheme, set options(RBesT.MC.s2z = FALSE, RBesT.MC.ncp = 1). Man thanks to Sean Pinkney for the implementation in brms used as template.
• Reuse the partial-centering quadrature to scale log(tau), fixed effects, and group effects for sampling. Fixed-effect locations remain pooled-GLM estimates, while group locations and scales enter an exact affine reparametrization. If quadrature is unavailable, gMAP warns and uses heuristic sampler-scaling estimates. The statistical model, reported summaries, and numeric init argument are unchanged.
• Lower the default adapt_delta for gMAP from 0.99 to 0.95 (options(RBesT.MC.control)). The sum-to-zero parametrization no longer needs the very conservative target acceptance rate that the old geometry required, and the lower target draws the same effective sample size from substantially fewer gradient evaluations. Should divergent transitions still occur, the reported warning now recommends raising adapt_delta to 0.99. Setting options(RBesT.MC.s2z = FALSE) also restores the previous adapt_delta default of 0.99, since the legacy geometry needs the more conservative target acceptance rate.
• The variables of the posterior draws of a gMAP object are now ordered theta, tau, beta, theta_pred, theta_resp_pred, lp__. Their names, dimensions and meaning are unchanged and all RBesT functions access them by name, such that only code relying on the column order of as_draws*() output is affected.
• write_mix_json now warns whenever the requested precision (argument digits) is so low that a mixture weight is written as zero and it aborts with an error in case all mixture weights are written as zero. Reading a mixture with zero weighted components with read_mix_json works as before and keeps all components of the mixture.

Bugfixes

• Make read_mix_json robust against jsonlite 2.0.0 simplification behavior by using deterministic JSON parsing, fixing reads of normal mixtures with three or more components.

RBesT 1.11-0 (2026-08-04)

Enhancements

• Decision boundary estimation is now substantially faster. The fixed uniform grid sweep in decision2S_boundary / decision1S_boundary (and hence oc1S, oc2S, pos1S, pos2S) is replaced by an adaptive scheme that only solves where the boundary bends (normal) or fills provably constant runs of the monotone integer boundary without further root searches (binomial, Poisson). Boundary construction is roughly 10x faster for normal endpoints and up to orders of magnitude faster for near-flat discrete boundaries (e.g. large-n Poisson); normal oc2S/pos2S run about 2-3x faster. Boundary values are unchanged (identical for discrete, within ~1e-5 for normal). Set options(RBesT.decision2S_boundary = "grid") to restore the legacy sweep.
• Make the normal decision2S_boundary interpolant consistent with the adaptive point placement. Curved and mixture boundaries are now interpolated with a shape-preserving monotone Hermite spline (splinefun(method = "monoH.FC")) instead of a global cubic, which matches the adaptive tracer's curvature-graded points and avoids overshoot. For the provably-linear case (single-component priors with constant sigma, including multi-criteria and n2 = 0 decisions) the boundary is now built as an exact straight line from two solves rather than a grid, making these boundaries exact (previously accurate to ~1e-6). Operating characteristics / probability of success are unchanged to within tolerance.
• Lower the default decision boundary discretization density Ngrid from 10 to 5 in oc2S, pos2S, and decision2S_boundary for the normal case. Ngrid now sets the finest resolution of the adaptive scheme and the grid density of the "grid" fallback; for the grid path a coarser grid roughly halves the boundary cost. Either way the resulting operating characteristics / probability of success change by at most about 1e-5 across a range of mixture and exponential-family settings. Pass Ngrid = 10 to restore the previous behaviour.
• Consolidate all package references into a single BibTeX file at inst/REFERENCES.bib. Documentation now cites it via the Rdpack \insertRef macro (roxygen @references), and the vignettes and articles cite the same file through the R Markdown bibliography: field, removing duplicated per-file reference lists.

Bugfixes

• Fix the simulation based calibration (SBC) code under inst/sbc, which was shipped broken in 1.10-0: the gMAP posterior storage refactor removed the raw rstan stanfit fit slot, causing run_sbc_case to fail with no applicable method for '@' applied to an object of class "NULL". The SBC helper fit_rbest now reads sampler diagnostics and posterior draws from the stored posterior draws objects instead of the removed stanfit.

RBesT 1.10-0 (2026-07-02)

Enhancements

• Add a family argument to oc1S, oc2S, pos1S, pos2S, decision1S_boundary, and decision2S_boundary for the normal case. Under the normal approximation this allows operating characteristics, probability of success, and decision boundaries to be evaluated for arbitrary exponential family endpoints.
• Add a new article (vignette) demonstrating a futility interim analysis for a negative binomial endpoint, including grid-based operating characteristics for two-stage designs, MAP-prior borrowing on control at the interim, and conditional vs. predictive power.
• Use Gaussian quadrature (GQ) for numerical integration against mixture densities (Gauss-Hermite for normMix, Gauss-Jacobi for betaMix, Gauss-Laguerre for gammaMix), replacing adaptive Gauss-Kronrod integration on identity-link paths in oc2S, pos2S, dmixdiff, pmixdiff, and ess for deterministic and robust results. The node count is refined automatically (starting from RBesT.GQ_nodes) until successive estimates agree within max(RBesT.GQ_abs_tol, RBesT.GQ_rel_tol * |I|), falling through to adaptive integration if the node cap is reached. Non-identity link cases and betaMix ESS continue to use adaptive integration, which can also be restored globally with options(RBesT.integrate_method = "adaptive").
• Use modern posterior functions to produce posterior summaries. Note that this can change the numeric values wrt to previous versions (e.g. a modernized Rhat definition is used).
• Refactor gMAP posterior sample storage to use posterior draws objects plus aligned sampler diagnostics instead of relying on a raw rstan stanfit; update summaries, predictions, plotting, and posterior accessors accordingly. The previously stored fit slot has been removed.
• Enable default test coverage for gMAP related functions using compact approximate posterior draw fixtures, so these tests can run routinely without full MCMC fixture generation.

Bugfixes

• Make read_mix_json robust against jsonlite 2.0.0 simplification behavior by using deterministic JSON parsing, fixing reads of normal mixtures with three or more components.

RBesT 1.9-0 (2026-03-13)

Enhancements

• Reformat R sources using Air.
• Extend normal outcome functions to two-sided decisions: decision1S and decision2S now allow lower.tail to have as many elements as pc to allow the specification of two-sided decision boundaries (mixed lower.tail elements, i.e. some specifying "lower" and some "upper") to capture intermediate result scenarios.
• Introduce global option RBesT.MC.save_warmup, which is set to FALSE causing to drop warmup samples from the gMAP fit object. Note that the pre-1.9.0 behavior was to store the warmup samples (but these were not used). To restore the original behavior set options(RBesT.MC.save_warmup=TRUE) once globally.
• Add experimental as_draws* functions allowing to extract samples in the posterior draws format from gMAP objects.

Bugfixes

• Avoid use of size argument to ggplot2 routines, which have been deprecated.

RBesT 1.8-2 (2025-04-25)

Enhancements

• Add experimental write_mix_json and read_mix_json functions which write and read mixture objects as JSON to/from files.
• Add "msr" parametrization to mixmvnorm which allows to consturct multi-variate normal mixtures in a parametrization using the mean vector, standard deviations and the correlations. This functionality is based on the new msr2mvnorm utility function.
• Allow standard deviations of 0 for components of a multi-variate normal mixture.

RBesT 1.8-1 (2025-01-21)

Bugfixes

• Fixed an issue with the ess function for beta and gamma mixtures when used inside of lapply or sapply.

RBesT 1.8-0 (2025-01-08)

Enhancements

• Enable ESS calculation for normal mixture densities when used in the context of a standard one-parameter exponential family through the new family argument. For example, this can be used to calculate the ESS of a normal mixture density representing a logit transformed response scale.
• Reformat R sources using styler.

Bugfixes

• Correct boundary behavior of BinaryExactCI function whenever no responses or no non-responses are observed. Fixes issue #21.
• Stabilize internal beta mixture information function, which corrects unstable ESS ELIR computations. Addresses issue #22.

RBesT 1.7-4 (2024-11-21)

Enhancements

• Added for mixstanvar automatic generation of distribution functions allowing truncated priors in brms with mixtures
• Slight speed increase for Stan model by more efficient construction of likelihood. Also reducing object size of gMAP objects by avoiding to store redundant variables.
• Upgraded testthat edition to version 3.

Bugfixes

• Fix issue #18 of ESS ELIR aborting whenever one mixture component has zero weight.
• Fixed a rare issue when estimating ESS ELIR for beta mixtures. The calculation aborted due to boundary issues which are now avoided.
• Avoid over and underflow of beta-binomial distribution.
• Replace calls to deprecated ggplot2::qplot with respective calls to ggplot2::ggplot.
• Use new array notation for mixstanvar generated Stan code to make generated Stan programs compatible with Stan >= 2.33

RBesT 1.7-3 (2024-01-08)

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.
• Moved most vignettes to be articles to decrease size of R packages. Articles are available on the package homepage.

Bugfixes

• Added pngquant to system requirements of package as requested by CRAN.

RBesT 1.7-2 (2023-08-21)

Enhancements

• Add unit tests for mixstanvar function and disabled integration tests on CI/CD systems as these require significant resources due to the need to compile Stan models. The unit tests do ensure that things are correct from the RBesT side of things.
• Use new scheme of roxygen2 to document package documentation.

Bugfixes

• Make EM for normal and multivariate normal mixtures deterministic in that the resulting density does not depend on the random seed any longer, which is the intended behavior. Note that this change may cause that estimated normal / MVN mixtures will be numerically different as compared to the previous version. The estimated density itself is (statistically) still the very same.

RBesT 1.7-1 (2023-08-10)

Enhancements

• Allow use of mixture priors in brms models with the new adapter function mixstanvar.
• Allow use of named dimensions for multivariate normal mixtures.
• Add experimental diagnostic plots for mixture multivariate normal EM fits. These are subject to changes in future release and user feedback is very welcome.
• Compress png plots of vignettes saving ~40% in file size of the package sources.

Bugfixes

• Fix issue when plotting EM diagnostic debugging plots for normal mixtures.
• Comply with newer ggplot2 standards to not use aes_string.

RBesT 1.7-0 (2023-07-20)

Enhancements

• Implementation multivariate normal mixture support in a first version. This includes density evaluation, basic summary functions and multivariate normal EM fitting. Support is not yet as complete as for other densites, but will be expanded in upcoming releases.
• Change the default for the option constrain_gt1 of the EM for beta mixtures to TRUE. This will be default constrain the fitted parameters of each beta mixture component to be greater than unity as required for finite ESS elir calculations.

RBesT 1.6-7 (2023-06-29)

Bug fixes

• resolve compilation from source issues on some platforms triggered by changes in rstantools
• correct documentation on difference distribution and improve PoS with co-data vignette

RBesT 1.6-6 (2023-03-03)

Bug fixes

• ensure C++17 compatiblity per CRAN (triggers an issue with clang 16)
• fix links in README.md to now link to new public pkgdown web-site

RBesT 1.6-5 (2023-02-10)

Enhancements

• upon package load RBesT 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 that predict for new studies will sample the study specifc random effect per iteration only once. This is important for MAP priors with covariate effects (which are pooled over the studies).

RBesT 1.6-4 (2022-08-08)

Enhancements

• use clustermq inplace of batchtools for SBC runs. Also use L'Ecuyer CMG random number gen during SBC runs.
• expand introductory vignette with plot of ESS vs robust weight
• start using matrixStats to speed up EM algorithms & OCs
• avoid warning whenever 2S normal design expanded their domain when called repeatedly
• add mixdist plot when plotting a mixture resulting from *mixfit call
• add warning message when printing a gMAP analysis for which the Stan sampler had issues due to divergent transitions or non-convergence as indicated by large Rhat

Bug fixes

• mixture density evaluations (dmix) with a defined link function did not evaluate correctly, which was visible when plotting mixtures (with more than one component) with link functions

RBesT 1.6-3 (2021-11-24)

• update references to JSS publication

RBesT 1.6-2 (2021-09-03)

• link against RcppParallel to align with new Stan requirements
• address CRAN comments

RBesT 1.6-1 (2020-05-28)

• stabilize elir ESS integration by integrating per mixture component
• comply with forthcoming and stricter stanc3 Stan transpiler
• address some warnings from ggplot2 3.3.0

RBesT 1.6-0 (2020-03-28)

• fix CI system issues
• fix issues with normal decision2S_boundary when boundaries are grown
• add demo for 2S OC simulation code for time-to-event endpoint with constant hazard assumption
• drop tidyverse dependency
• expand SBC checks to include group specifc estimates
• stop setting the ggplot2 default theme when loading package. All plots now use the bayesplot theme which can be modified with bayesplot_theme_* functions. See ?bayesplot::bayesplot_theme_get.
• correct transformation issue in MAP for variances vignette - thanks to Ping Chen
• allow for constrained fitting of beta mixtures which have a & b parameters greater than 1. This is the new default behavior which the function will inform about. The informational message will be removed in a future release.
• introduced new mixecdf plot as diagnostic for EM fits

RBesT 1.5-4 (2019-10-23)

• Now really fix n2=0 case for 2S design functions for indirect comparisons
• Update package structure to new rstantools 2.0 system

RBesT 1.5-3 (2019-08-28)

• Fix vignette MAP for variances (missing definition)

RBesT 1.5-2

• Speedup example run time
• Avoid use of cat in functions and use message instead
• Replace dontrun in examples with donttest
• Require NOT_CRAN=true for tests to run

RBesT 1.5-1

• Work around compiler warning with clang on fedora platform

RBesT 1.5-0

• Fix indirect comparisons to work with normal/Poisson/binomial (inexact) to allow for n2=0 in oc2S calls.
• Make mixture quantile function more robust to work with very flat mixture priors.
• Align ESS Morita calculations with Neuenschwander B. et al., pre-print 2019; arXiv:1907.04185

RBesT 1.4-0 (2019-06-27)

• Introduce elir ESS method as new default for ESS
• Allow to sample prior predictive with gMAP (argument prior_PD)
• Switch internally to ab parametrized version of EM beta algorithm

RBesT 1.3-8 (2019-04-04)

• Use Simulation Based Calibration for gMAP model qualification
• Improve covariate handling (naming of data items)
• Speedup Stan model by avoiding matrix-vector products with many zeros
• Fix index issue with differential discounting when used with covariates
• Make initialization of EM algorithms more robust
• Avoid special build hacks on MacOS

RBesT 1.3-7 (2018-11-19)

• Address issue for build process on MacOS.

RBesT 1.3-6 (2018-11-15)

• Re-create vignettes with proper MCMC sampling.
• Automate R package build process using CI/CD.

RBesT 1.3-5 (2018-11-14)

• Corrected 1.3-4 release notes to include MAP for variances vignette
• Make build process more robust (updated src/Makevars{.win})
• Added probability of success at interim vignette
• Added probability of success with co-data vignette

RBesT 1.3-4 (2018-10-17)

• Make package work with rstan 2.18.1.
• Revert BetaBinomial implementation back to R functions.
• Bugfix for decision1S_boundary for normal case for extreme parameter configurations (fixes pos1S & oc1S as well).
• Bugfix for mixcombine and plot with normal mixtures without a sigma being defined.
• Bugfix for repeated calls to decision2S_boundary for normal endpoint (fixes pos2S & oc2S as well).
• Avoid use of deprecated bayesplot function arguments whenever divergencies occured.
• (corrected) Added MAP for variances vignette

RBesT 1.3-3 (2018-02-02)

• Change numerical equality testing to use expect_equal (which uses all.equal internally accounting for machine specifc tolerances) to pass tests for no long double case. Numerical tolerances are reverted back to 1.3-1 settings.

RBesT 1.3-2 (2018-01-25)

• Adjust numerical tolerances to pass tests for no long double case

RBesT 1.3-1 (2017-12-21)

• Add Trustees of Columbia copyright for respective files in DESCRIPTION

RBesT 1.3-0

• Added probability of success calculation for 1+2 sample case.
• Added decision1+2S_boundary functions (and deprecated use of y2 argument of oc functions)
• Added RBesT.integrate_args option for greater control over density integrations.
• Correct cumulative predictive of beta mixtures to return 0/1 for out-of-range values (instead of leaving those out).
• Deprecated functions oc1+2Sdecision which are replaced by decision1+2S.

RBesT 1.2-3 (2017-08-21)

• Fix plotting procedures to work with bayesplot 1.3.0

RBesT 1.2-2 (2017-07-12)

• Further speedup example runtimes.

RBesT 1.2-1

• Compactify reference PDF manual.
• Introduce sampling arguments to gMAP.
• Shorten runtime of examples.

RBesT 1.2-0

• First CRAN release.
• Update of documentation.

RBesT 1.1-0

• Redesign of reference scale handling for normal case.
• Enable standard error as sufficient statistic in \code{postmix} function.
• Introduced plotting options.
• Increased adapt_delta default and set stepsize+max_treedepth default.
• Added RBesT.MC.{ncp, init, rescale} option.
• Corrections for Poisson OC.
• pmixdiff function now integrates over full support.
• Added \code{link} argument to \code{oc2Sdecision} which enables designs based on log-odds decisions or relative risks.
• New graphical vignette and new forest plot function.
• Use \pkg{bayesplot} as standard plotting package.

RBesT 1.0-0

• Stabilize integration in pmixdiff for beta mixtures by logit transform.
• Set default adapt_delta to 0.975.
• Made RBesT compatible with ggplot2 2.0.
• Allowed n2=0 in \code{oc2S} function.

RBesT 0.9-2

• Corrected Poisson stratified estimates.
• Added warning on divergent transitions.
• Added the crohn dataset.

RBesT 0.9-1

• Minor typo fixes.

RBesT 0.9-0

• First release.