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Package: RBesT 1.10-0

Sebastian Weber

RBesT: 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 Weber et al. (2021) <doi:10.18637/jss.v100.i19> for details on applying this package while Neuenschwander et al. (2010) <doi:10.1177/1740774509356002> and Schmidli et al. (2014) <doi:10.1111/biom.12242> explain details on the methodology.

Authors:Novartis Pharma AG [cph], Sebastian Weber [aut, cre], Beat Neuenschwander [ctb], Heinz Schmidli [ctb], Baldur Magnusson [ctb], Yue Li [ctb], Satrajit Roychoudhury [ctb], Lukas A. Widmer [ctb], Daniel Sabanés Bové [ctb], Trustees of Columbia University [cph]

RBesT_1.10-0.tar.gz
RBesT_1.10-0.tar.gz(r-4.7-arm64)RBesT_1.10-0.tar.gz(r-4.7-x86_64)RBesT_1.10-0.tar.gz(r-4.6-arm64)RBesT_1.10-0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RBesT/json (API)

# Install 'RBesT' in R:

install.packages('RBesT', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/novartis/rbest/issues

Pkgdown/docs site:https://opensource.nibr.com

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

AS - Ankylosing Spondylitis.
asthma - Asthma exacerbation recurrent event data.
colitis - Ulcerative Colitis.
crohn - Crohn's disease.
transplant - Transplant.

On CRAN:

cpp

6.19 score 5 stars 6 packages 208 scripts 4.1k downloads 1 mentions 58 exports 63 dependencies

Last updated from:3b3d528405. Checks:5 OK, 1 FAIL. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	424
linux-devel-x86_64	OK	478
source / vignettes	OK	397
linux-release-arm64	OK	726
linux-release-x86_64	OK	414
wasm-release	FAIL	217

Exports:as_draws as_draws_array as_draws_df as_draws_list as_draws_matrix as_draws_rvars automixfit BinaryExactCI decision1S decision1S_boundary decision2S decision2S_boundary dmix dmixdiff ess forest_plot gMAP has_lower has_upper inv_logit likelihood likelihood<-logit lower mixbeta mixcombine mixfit mixgamma mixmvnorm mixnorm mixstanvar mn2beta mn2gamma mn2norm ms2beta ms2gamma msr2mvnorm nsamples oc1S oc1Sdecision oc2S oc2Sdecision pmix pmixdiff pos1S pos2S postmix preddist qmix qmixdiff read_mix_json rmix rmixdiff robustify sigma sigma<-upper write_mix_json

Dependencies:abind assertthat backports bayesplot BH callr checkmate cli cpp11 desc distributional dplyr farver Formula generics ggplot2 ggridges glue gridExtra gtable inline isoband jsonlite labeling lifecycle loo magrittr matrixStats mvtnorm numDeriv otel pillar pkgbuild pkgconfig plyr posterior processx ps purrr QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel reshape2 rlang rstan rstantools S7 scales StanHeaders statmod stringi stringr tensorA tibble tidyr tidyselect utf8 vctrs viridisLite withr

Getting started with RBesT (binary)

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2025-01-08
Started: 2017-07-12

Help page	Topics
R Bayesian Evidence Synthesis Tools	RBesT-package RBesT
Ankylosing Spondylitis.	AS
Asthma exacerbation recurrent event data.	asthma
Automatic Fitting of Mixtures of Conjugate Distributions to a Sample	automixfit
Exact Confidence interval for Binary Proportion	BinaryExactCI
Ulcerative Colitis.	colitis
Crohn's disease.	crohn
Decision Function for 1 Sample Designs	decision1S has_lower has_upper lower oc1Sdecision upper
Decision Boundary for 1 Sample Designs	decision1S_boundary decision1S_boundary.betaMix decision1S_boundary.gammaMix decision1S_boundary.normMix
Decision Function for 2 Sample Designs	decision2S oc2Sdecision
Decision Boundary for 2 Sample Designs	decision2S_boundary decision2S_boundary.betaMix decision2S_boundary.gammaMix decision2S_boundary.normMix
Transform 'gMAP' to 'draws' objects	as_draws as_draws.gMAP as_draws_array as_draws_array.gMAP as_draws_df as_draws_df.gMAP as_draws_list as_draws_list.gMAP as_draws_matrix as_draws_matrix.gMAP as_draws_rvars as_draws_rvars.gMAP draws-RBesT
Effective Sample Size for a Conjugate Prior	ess ess.betaMix ess.gammaMix ess.normMix
Forest Plot	forest_plot
Meta-Analytic-Predictive Analysis for Generalized Linear Models	as.matrix.gMAP coef.gMAP fitted.gMAP gMAP print.gMAP summary.gMAP
Read and Set Likelihood to the Corresponding Conjugate Prior	likelihood likelihood<-
Logit (log-odds) and inverse-logit function.	inv_logit lodds logit
Mixture Distributions	dmix mix pmix qmix rmix [[.mix
Beta Mixture Density	mixbeta mn2beta ms2beta print.betaBinomialMix print.betaMix summary.betaBinomialMix summary.betaMix
Combine Mixture Distributions	mixcombine
Difference of mixture distributions	dmixdiff mixdiff pmixdiff qmixdiff rmixdiff
Fit of Mixture Densities to Samples	mixfit mixfit.array mixfit.default mixfit.gMAP mixfit.gMAPpred
The Gamma Mixture Distribution	mixgamma mn2gamma ms2gamma print.gammaExpMix print.gammaMix print.gammaPoissonMix summary.gammaMix summary.gammaPoissonMix
Write and Read a Mixture Object with JSON	mixjson read_mix_json write_mix_json
Multivariate Normal Mixture Density	mixmvnorm msr2mvnorm print.mvnormMix sigma.mvnormMix summary.mvnormMix
Normal Mixture Density	mixnorm mn2norm print.normMix sigma sigma.normMix sigma<- summary.normMix
Plot mixture distributions	mixplot plot.mix plot.mvnormMix
Mixture distributions as 'brms' priors	mixstanvar
Return the number of posterior samples	nsamples nsamples.gMAP
Operating Characteristics for 1 Sample Design	oc1S oc1S.betaMix oc1S.gammaMix oc1S.normMix
Operating Characteristics for 2 Sample Design	oc2S oc2S.betaMix oc2S.gammaMix oc2S.normMix
Diagnostic plots for EM fits	plot.EM
Diagnostic plots for gMAP analyses	plot.gMAP
Probability of Success for a 1 Sample Design	pos1S pos1S.betaMix pos1S.gammaMix pos1S.normMix
Probability of Success for 2 Sample Design	pos2S pos2S.betaMix pos2S.gammaMix pos2S.normMix
Conjugate Posterior Analysis	postmix postmix.betaMix postmix.gammaMix postmix.normMix
Predictive Distributions for Mixture Distributions	preddist preddist.betaMix preddist.gammaMix preddist.mvnormMix preddist.normMix
Predictions from gMAP analyses	as.matrix.gMAPpred predict.gMAP print.gMAPpred summary.gMAPpred
Robustify Mixture Priors	robustify robustify.betaMix robustify.gammaMix robustify.normMix
Transplant.	transplant

Package: RBesT 1.10-0

RBesT: R Bayesian Evidence Synthesis Tools

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Readme and manuals

Help Manual

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