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RBesT (version 1.6-3)

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.

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Version

Install

install.packages('RBesT')

Monthly Downloads

1,532

Version

1.6-3

License

GPL (>= 3)

Maintainer

Sebastian Weber

Last Published

November 24th, 2021

Functions in RBesT (1.6-3)

BinaryExactCI

Exact Confidence interval for Binary Proportion
ess

Effective Sample Size for a Conjugate Prior
dlink<-

Transform Densities with a link function
decision1S_boundary

Decision Boundary for 1 Sample Designs
gMAP

Meta-Analytic-Predictive Analysis for Generalized Linear Models
forest_plot

Forest Plot
decision2S_boundary

Decision Boundary for 2 Sample Designs
decision1S

Decision Function for 1 Sample Designs
dBetaBinomial

Beta-Binomial Probabilities
fill

Fill numeric objects
likelihood

Read and Set Likelihood to the Corresponding Conjugate Prior
log_inv_logit

Numerically stable log of the inv_logit function
mixgamma

The Gamma Mixture Distribution
logLik.EM

Extract log likelihood from fitted EM objects
log_colSum_exp

Matrix version of log_sum_exp
mixlink

takes x and transforms it according to the defined link function of the mixture
decision2S

Decision Function for 2 Sample Designs
log_sum_exp

Numerically stable summation of logs
plot.EM

Diagnostic plots for EM fits
oc2S

Operating Characteristics for 2 Sample Design
lodds

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

Normal Mixture Density
mix

Mixture Distributions
support

Support of Distributions
oc1S

Operating Characteristics for 1 Sample Design
transplant

Transplant.
mixcombine

Combine Mixture Distributions
knn

k nearest neighbor algorithm for multi-variate data
uniroot_int

Find root of univariate function of integers
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.
postmix

Conjugate Posterior Analysis
mixbeta

Beta Mixture Density
predict.gMAP

Predictions from gMAP analyses
robustify

Robustify Mixture Priors
preddist

Predictive Distributions for Mixture Distributions
mixfit

Fit of Mixture Densities to Samples
mixdist3

Utility function to instantiate 2 parameter mixture densities.
mixdiff

Difference of mixture distributions
pos2S

Probability of Success for 2 Sample Design
pos1S

Probability of Success for a 1 Sample Design
plot.gMAP

Diagnostic plots for gMAP analyses
plot.mix

Plot mixture distributions
AS

Ankylosing Spondylitis.
RBesT-package

R Bayesian Evidence Synthesis Tools
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.
Curry

Functional programming utilities
colVars

Fast column-wise calculation of unbiased variances
colitis

Ulcerative Colitis.
SimSum

Summarize Arrays
crohn

Crohn's disease.
automixfit

Automatic Fitting of Mixtures of Conjugate Distributions to a Sample