RBesT 1.6-4 - August 5th, 2022

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 - November 23rd, 2021

update references to JSS publication

RBesT 1.6-2 - September 3rd, 2021

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

RBesT 1.6-1 - May 28th, 2020

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 - March 27th, 2020

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 - October 22nd, 2019

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 - August 28th, 2019

Fix vignette MAP for variances (missing definition)

RBesT 1.5-2 - August 28th, 2019

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 - August 28th, 2019

Work around compiler warning with clang on fedora platform

RBesT 1.5-0 - August 15th, 2019

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 - July 27th, 2019

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 - April 3nd, 2019

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 - November 16th, 2018

Address issue for build process on MacOS.

RBesT 1.3-6 - November 14th, 2018

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

RBesT 1.3-5 - November 13th, 2018

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 - October 16th, 2018

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 - February 2nd, 2018

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 - January 25th, 2018

Adjust numerical tolerances to pass tests for no long double case

RBesT 1.3-1 - December 21st, 2017

Add Trustees of Columbia copyright for respective files in DESCRIPTION

RBesT 1.3-0 - December 21st, 2017

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 - August 21st, 2017

Fix plotting procedures to work with bayesplot 1.3.0

RBesT 1.2-2 - July 12th, 2017

Further speedup example runtimes.

RBesT 1.2-1 - July 12th, 2017

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

RBesT 1.2-0 - July 3rd, 2017

First CRAN release.
Update of documentation.

RBesT 1.1-0 - May 15th, 2017

Redesign of reference scale handling for normal case.
Enable standard error as sufficient statistic in 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 argument to which enables designs based on log-odds decisions or relative risks.
New graphical vignette and new forest plot function.
Use as standard plotting package.

RBesT 1.0-0 - March 10th, 2016

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 function.

RBesT 0.9-2 - Oct 28th 2015

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

RBesT 0.9-1 - Sept 3rd 2015

Minor typo fixes.

RBesT 0.9-0 - Sept 1st 2015

First release.