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RBesT (version 1.4-0)

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

1,151

Version

1.4-0

License

GPL (>= 3) | file LICENSE

Maintainer

Sebastian Weber

Last Published

June 27th, 2019

Functions in RBesT (1.4-0)

BinaryExactCI

Exact Confidence interval for Binary Proportion
RBesT-package

R Bayesian Evidence Synthesis Tools
colVars

Fast column-wise calculation of unbiased variances
crohn

Crohn's disease.
Curry

Functional programming utilities
SimSum

Summarize Arrays
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.
colitis

Ulcerative Colitis.
AS

Ankylosing Spondylitis.
automixfit

Automatic Fitting of Mixtures of Conjugate Distributions to a Sample
decision2S_boundary

Decision Boundary for 2 Sample Designs
mixcombine

Combine Mixture Distributions
decision2S

Decision Function for 2 Sample Designs
decision1S_boundary

Decision Boundary for 1 Sample Designs
mixbeta

Beta Mixture Density
decision1S

Decision Function for 1 Sample Designs
dBetaBinomial

Beta-Binomial Probabilities
mixnorm

Normal Mixture Density
mixlink

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

Numerically stable summation of logs
mix

Mixture Distributions
mixdiff

Difference of mixture distributions
ess

Effective Sample Size for a Conjugate Prior
dlink<-

Transform Densities with a link function
mixdist3

Utility function to instantiate 2 parameter mixture densities.
fill

Fill numeric objects
likelihood

Read and Set Likelihood to the Corresponding Conjugate Prior
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.
mixgamma

The Gamma Mixture Distribution
predict.gMAP

Predictions from gMAP analyses
knn

k nearest neighbor algorithm for multi-variate data
mixfit

Fit of Mixture Densities to Samples
preddist

Predictive Distributions for Mixture Distributions
forest_plot

Forest Plot
log_colSum_exp

Matrix version of log_sum_exp
gMAP

Meta-Analytic-Predictive Analysis for Generalized Linear Models
logLik.EM

Extract log likelihood from fitted EM objects
oc1S

Operating Characteristics for 1 Sample Design
oc2S

Operating Characteristics for 2 Sample Design
robustify

Robustify Mixture Priors
pos1S

Probability of Success for a 1 Sample Design
plot.mix

Plot mixture distributions
support

Support of Distributions
lodds

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

Find root of univariate function of integers
transplant

Transplant.
plot.gMAP

Diagnostic plots for gMAP analyses
plot.EM

Diagnostic plots for EM fits
pos2S

Probability of Success for 2 Sample Design
postmix

Conjugate Posterior Analysis