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 - April 25th,
2025
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 - January 20th,
2025
Bugfixes
Fixed an issue with the ess function for beta and gamma
mixtures when used inside of lapply or
sapply.
RBesT 1.8-0 - January 8th,
2025
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 - November 21st,
2024
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 - January 2nd,
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.
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 - August 21st,
2023
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 - August 8th,
2023
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 - July 19th, 2023
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 - June 26th, 2023
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 - March 3rd, 2023
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 - February 8th,
2023
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 - 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.