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RBesT (version 1.6-6)

R Bayesian Evidence Synthesis Tools

Description

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) for details on applying this package while Neuenschwander et al. (2010) and Schmidli et al. (2014) explain details on the methodology.

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Version

Install

install.packages('RBesT')

Monthly Downloads

1,151

Version

1.6-6

License

GPL (>= 3)

Maintainer

Sebastian Weber

Last Published

March 3rd, 2023

Functions in RBesT (1.6-6)

dlink<-

Transform Densities with a link function
decision2S_boundary

Decision Boundary for 2 Sample Designs
decision1S

Decision Function for 1 Sample Designs
dBetaBinomial

Beta-Binomial Probabilities
fill

Fill numeric objects
decision2S

Decision Function for 2 Sample Designs
decision1S_boundary

Decision Boundary for 1 Sample Designs
forest_plot

Forest Plot
ess

Effective Sample Size for a Conjugate Prior
gMAP

Meta-Analytic-Predictive Analysis for Generalized Linear Models
likelihood

Read and Set Likelihood to the Corresponding Conjugate Prior
mix

Mixture Distributions
mixcombine

Combine Mixture Distributions
mixbeta

Beta Mixture Density
lodds

Logit (log-odds) and inverse-logit function.
integrate_density_log

internal function used for integration of densities which appears to be much more stable from -Inf to +Inf in the logit space while the density to be integrated recieves inputs from 0 to 1 such that the inverse distribution function must be used. The integral solved is int_x dmix(mix,x) integrand(x) where integrand must be given as log and we integrate over the support of mix.
mixdiff

Difference of mixture distributions
oc2S

Operating Characteristics for 2 Sample Design
log_inv_logit

Numerically stable log of the inv_logit function
plot.EM

Diagnostic plots for EM fits
logLik.EM

Extract log likelihood from fitted EM objects
plot.gMAP

Diagnostic plots for gMAP analyses
plot.mix

Plot mixture distributions
knn

k nearest neighbor algorithm for multi-variate data
oc1S

Operating Characteristics for 1 Sample Design
mixnorm

Normal Mixture Density
mixlink

takes x and transforms it according to the defined link function of the mixture
mixgamma

The Gamma Mixture Distribution
mixfit

Fit of Mixture Densities to Samples
mixdist3

Utility function to instantiate 2 parameter mixture densities.
pos1S

Probability of Success for a 1 Sample Design
robustify

Robustify Mixture Priors
pos2S

Probability of Success for 2 Sample Design
predict.gMAP

Predictions from gMAP analyses
uniroot_int

Find root of univariate function of integers
transplant

Transplant.
support

Support of Distributions
postmix

Conjugate Posterior Analysis
preddist

Predictive Distributions for Mixture Distributions
Curry

Functional programming utilities
RBesT-package

R Bayesian Evidence Synthesis Tools
AS

Ankylosing Spondylitis.
SimSum

Summarize Arrays
BinaryExactCI

Exact Confidence interval for Binary Proportion
crohn

Crohn's disease.
colitis

Ulcerative Colitis.
colVars

Fast column-wise calculation of unbiased variances
chains2sample

Scrambles the order of a mcmc array object for usage as a mcmc sample. It is advisable to set order once per mcmc run, otherwise correlations in the mcmc sample will be lost.
automixfit

Automatic Fitting of Mixtures of Conjugate Distributions to a Sample