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RBesT (version 1.6-1)

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

1.6-1

License

GPL (>= 3)

Maintainer

Sebastian Weber

Last Published

May 28th, 2020

Functions in RBesT (1.6-1)

automixfit

Automatic Fitting of Mixtures of Conjugate Distributions to a Sample
decision1S

Decision Function for 1 Sample Designs
dBetaBinomial

Beta-Binomial Probabilities
decision2S_boundary

Decision Boundary for 2 Sample Designs
forest_plot

Forest Plot
dlink<-

Transform Densities with a link function
gMAP

Meta-Analytic-Predictive Analysis for Generalized Linear Models
ess

Effective Sample Size for a Conjugate Prior
decision1S_boundary

Decision Boundary for 1 Sample Designs
log_inv_logit

Numerically stable log of the inv_logit function
log_sum_exp

Numerically stable summation of logs
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.
decision2S

Decision Function for 2 Sample Designs
fill

Fill numeric objects
lodds

Logit (log-odds) and inverse-logit function.
oc2S

Operating Characteristics for 2 Sample Design
mixdist3

Utility function to instantiate 2 parameter mixture densities.
mixfit

Fit of Mixture Densities to Samples
mixgamma

The Gamma Mixture Distribution
mixdiff

Difference of mixture distributions
plot.EM

Diagnostic plots for EM fits
mixcombine

Combine Mixture Distributions
log_colSum_exp

Matrix version of log_sum_exp
postmix

Conjugate Posterior Analysis
logLik.EM

Extract log likelihood from fitted EM objects
mixbeta

Beta Mixture Density
mix

Mixture Distributions
preddist

Predictive Distributions for Mixture Distributions
mixnorm

Normal Mixture Density
support

Support of Distributions
transplant

Transplant.
knn

k nearest neighbor algorithm for multi-variate data
oc1S

Operating Characteristics for 1 Sample Design
mixlink

takes x and transforms it according to the defined link function of the mixture
pos1S

Probability of Success for a 1 Sample Design
plot.gMAP

Diagnostic plots for gMAP analyses
plot.mix

Plot mixture distributions
pos2S

Probability of Success for 2 Sample Design
uniroot_int

Find root of univariate function of integers
predict.gMAP

Predictions from gMAP analyses
robustify

Robustify Mixture Priors
BinaryExactCI

Exact Confidence interval for Binary Proportion
AS

Ankylosing Spondylitis.
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.
colVars

Fast column-wise calculation of unbiased variances
RBesT-package

R Bayesian Evidence Synthesis Tools
Curry

Functional programming utilities
crohn

Crohn's disease.
colitis

Ulcerative Colitis.