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RBesT (version 1.6-0)

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 Neuenschwander et al. (2010) and Schmidli et al. (2014) for details on the methodology.

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Version

Install

install.packages('RBesT')

Monthly Downloads

1,532

Version

1.6-0

License

GPL (>= 3)

Maintainer

Sebastian Weber

Last Published

March 28th, 2020

Functions in RBesT (1.6-0)

automixfit

Automatic Fitting of Mixtures of Conjugate Distributions to a Sample
forest_plot

Forest Plot
ess

Effective Sample Size for a Conjugate Prior
decision1S_boundary

Decision Boundary for 1 Sample Designs
decision2S_boundary

Decision Boundary for 2 Sample Designs
decision2S

Decision Function for 2 Sample Designs
dBetaBinomial

Beta-Binomial Probabilities
mixcombine

Combine Mixture Distributions
mixbeta

Beta Mixture Density
decision1S

Decision Function for 1 Sample Designs
fill

Fill numeric objects
gMAP

Meta-Analytic-Predictive Analysis for Generalized Linear Models
likelihood

Read and Set Likelihood to the Corresponding Conjugate Prior
logLik.EM

Extract log likelihood from fitted EM objects
mixdiff

Difference of mixture distributions
plot.mix

Plot mixture distributions
mixdist3

Utility function to instantiate 2 parameter mixture densities.
plot.EM

Diagnostic plots for EM fits
pos1S

Probability of Success for a 1 Sample Design
lodds

Logit (log-odds) and inverse-logit function.
plot.gMAP

Diagnostic plots for gMAP analyses
dlink<-

Transform Densities with a link function
oc1S

Operating Characteristics for 1 Sample Design
log_colSum_exp

Matrix version of log_sum_exp
robustify

Robustify Mixture Priors
mixnorm

Normal Mixture Density
preddist

Predictive Distributions for Mixture Distributions
knn

k nearest neighbor algorithm for multi-variate data
predict.gMAP

Predictions from gMAP analyses
mix

Mixture Distributions
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.
oc2S

Operating Characteristics for 2 Sample Design
log_sum_exp

Numerically stable summation of logs
mixgamma

The Gamma Mixture Distribution
mixlink

takes x and transforms it according to the defined link function of the mixture
pos2S

Probability of Success for 2 Sample Design
postmix

Conjugate Posterior Analysis
support

Support of Distributions
mixfit

Fit of Mixture Densities to Samples
transplant

Transplant.
uniroot_int

Find root of univariate function of integers
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
SimSum

Summarize Arrays
colVars

Fast column-wise calculation of unbiased variances
colitis

Ulcerative Colitis.
RBesT-package

R Bayesian Evidence Synthesis Tools
crohn

Crohn's disease.
BinaryExactCI

Exact Confidence interval for Binary Proportion
AS

Ankylosing Spondylitis.