Learn R Programming
⚠️There's a newer version (1.8-2) of this package.Take me there.

RBesT (version 1.7-3)

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.

Copy Link

Version

Install

install.packages('RBesT')

Monthly Downloads

1,532

Version

1.7-3

License

GPL (>= 3)

Maintainer

Sebastian Weber

Last Published

January 8th, 2024

Functions in RBesT (1.7-3)

decision2S

Decision Function for 2 Sample Designs
gMAP

Meta-Analytic-Predictive Analysis for Generalized Linear Models
forest_plot

Forest Plot
decision1S_boundary

Decision Boundary for 1 Sample Designs
ess

Effective Sample Size for a Conjugate Prior
dBetaBinomial

Beta-Binomial Probabilities
decision1S

Decision Function for 1 Sample Designs
lodds

Logit (log-odds) and inverse-logit function.
logLik.EM

Extract log likelihood from fitted EM objects
dlink<-

Transform Densities with a link 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.
likelihood

Read and Set Likelihood to the Corresponding Conjugate Prior
mixbeta

Beta Mixture Density
mix

Mixture Distributions
mixfit

Fit of Mixture Densities to Samples
log_inv_logit

Numerically stable log of the inv_logit function
knn

k nearest neighbor algorithm for multi-variate data
mixdist3

Utility function to instantiate 2 parameter mixture densities.
mixplot

Plot mixture distributions
mixmvnorm

Multivariate Normal Mixture Density
mixstanvar

Mixture distributions as brms priors
mixgamma

The Gamma Mixture Distribution
mixnorm

Normal Mixture Density
mixlink

takes x and transforms it according to the defined link function of the mixture
plot.EM

Diagnostic plots for EM fits
oc1S

Operating Characteristics for 1 Sample Design
plot.gMAP

Diagnostic plots for gMAP analyses
mixcombine

Combine Mixture Distributions
uniroot_int

Find root of univariate function of integers
predict.gMAP

Predictions from gMAP analyses
robustify

Robustify Mixture Priors
transplant

Transplant.
postmix

Conjugate Posterior Analysis
preddist

Predictive Distributions for Mixture Distributions
mixdiff

Difference of mixture distributions
oc2S

Operating Characteristics for 2 Sample Design
pos1S

Probability of Success for a 1 Sample Design
pos2S

Probability of Success for 2 Sample Design
support

Support of Distributions
Curry

Functional programming utilities
RBesT-package

R Bayesian Evidence Synthesis Tools
BinaryExactCI

Exact Confidence interval for Binary Proportion
automixfit

Automatic Fitting of Mixtures of Conjugate Distributions to a Sample
crohn

Crohn's disease.
AS

Ankylosing Spondylitis.
colitis

Ulcerative Colitis.
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.
colVars

Fast column-wise calculation of unbiased variances
SimSum

Summarize Arrays
decision2S_boundary

Decision Boundary for 2 Sample Designs
fill

Fill numeric objects