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RBesT (version 1.5-4)

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

1,397

Version

1.5-4

License

GPL (>= 3)

Maintainer

Sebastian Weber

Last Published

October 23rd, 2019

Functions in RBesT (1.5-4)

automixfit

Automatic Fitting of Mixtures of Conjugate Distributions to a Sample
ess

Effective Sample Size for a Conjugate Prior
dBetaBinomial

Beta-Binomial Probabilities
decision2S

Decision Function for 2 Sample Designs
dlink<-

Transform Densities with a link function
forest_plot

Forest Plot
fill

Fill numeric objects
decision2S_boundary

Decision Boundary for 2 Sample Designs
decision1S_boundary

Decision Boundary for 1 Sample Designs
decision1S

Decision Function for 1 Sample Designs
gMAP

Meta-Analytic-Predictive Analysis for Generalized Linear Models
log_sum_exp

Numerically stable summation of logs
lodds

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

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

Extract log likelihood from fitted EM objects
mixlink

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

Matrix version of log_sum_exp
mixnorm

Normal Mixture Density
plot.gMAP

Diagnostic plots for gMAP analyses
mixcombine

Combine Mixture Distributions
plot.EM

Diagnostic plots for EM fits
mixbeta

Beta Mixture Density
mixfit

Fit of Mixture Densities to Samples
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.
preddist

Predictive Distributions for Mixture Distributions
robustify

Robustify Mixture Priors
mix

Mixture Distributions
support

Support of Distributions
plot.mix

Plot mixture distributions
mixgamma

The Gamma Mixture Distribution
pos1S

Probability of Success for a 1 Sample Design
uniroot_int

Find root of univariate function of integers
transplant

Transplant.
predict.gMAP

Predictions from gMAP analyses
oc2S

Operating Characteristics for 2 Sample Design
oc1S

Operating Characteristics for 1 Sample Design
knn

k nearest neighbor algorithm for multi-variate data
mixdiff

Difference of mixture distributions
pos2S

Probability of Success for 2 Sample Design
mixdist3

Utility function to instantiate 2 parameter mixture densities.
postmix

Conjugate Posterior Analysis
colitis

Ulcerative Colitis.
AS

Ankylosing Spondylitis.
colVars

Fast column-wise calculation of unbiased variances
SimSum

Summarize Arrays
crohn

Crohn's disease.
RBesT-package

R Bayesian Evidence Synthesis Tools
Curry

Functional programming utilities
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.
BinaryExactCI

Exact Confidence interval for Binary Proportion