R Bayesian Evidence Synthesis Tools

Tool-set to support Bayesian evidence synthesis. This includes meta-analysis, (robust) prior derivation from historical data, operating characteristics and analysis (1 and 2 sample cases). Please refer to Neuenschwander et al. (2010) and Schmidli et al. (2014) for details on the methodology.


News

November 16th, 2018 (1.3-7)

  • Address issue for build process on MacOS.

November 14th, 2018 (1.3-6)

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

November 13th, 2018 (1.3-5)

  • 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

October 16th, 2018 (1.3-4)

  • 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

February 2nd, 2018 (1.3-3)

  • 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.

January 25th, 2018 (1.3-2)

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

December 21st, 2017 (1.3-1)

  • Add Trustees of Columbia copyright for respective files in DESCRIPTION

December 21st, 2017 (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.

August 21st, 2017 (1.2-3)

  • Fix plotting procedures to work with bayesplot 1.3.0

July 12th, 2017 (1.2-2)

  • Further speedup example runtimes.

July 12th, 2017 (1.2-1)

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

July 3rd, 2017 (1.2-0)

  • First CRAN release.
  • Update of documentation.

May 15th, 2017 (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.

March 10th, 2016 (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.

Oct 28th 2015 (0.9-2)

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

Sept 3rd 2015 (0.9-1)

  • Minor typo fixes.

Sept 1st 2015 (0.9-0)

  • First release.

Reference manual

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install.packages("RBesT")

1.5-3 by Sebastian Weber, 23 days ago


Browse source code at https://github.com/cran/RBesT


Authors: Novartis Pharma AG [cph] , Sebastian Weber [aut, cre] , Beat Neuenschwander [ctb] , Heinz Schmidli [ctb] , Baldur Magnusson [ctb] , Yue Li [ctb] , Satrajit Roychoudhury [ctb] , Trustees of Columbia University [cph] (src/init.cpp , tools/make_cc.R , R/stanmodels.R , src/Makevars , src/Makevars.win)


Documentation:   PDF Manual  


Task views:


GPL (>= 3) license


Imports assertthat, mvtnorm, Formula, checkmate, rstan, bayesplot, ggplot2, dplyr, stats, utils

Depends on Rcpp, methods

Suggests rmarkdown, knitr, testthat, foreach, tidyverse, purrr, rstanarm, scales, tools, broom, tidyr

Linking to StanHeaders, rstan, BH, Rcpp, RcppEigen

System requirements: GNU make, pandoc (>= 1.12.3), pandoc-citeproc


Imported by OncoBayes2.


See at CRAN