RBesT v1.5-4

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R Bayesian Evidence Synthesis Tools

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) <doi:10.1177/1740774509356002> and Schmidli et al. (2014) <doi:10.1111/biom.12242> for details on the methodology.

Functions in RBesT

Name Description
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
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Vignettes of RBesT

Name
PoS_codata.Rmd
PoS_interim.Rmd
customizing_plots.Rmd
introduction.Rmd
introduction_normal.Rmd
robustMAP.Rmd
variances_MAP.Rmd
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Details

Type Package
Date 2019-10-22
LinkingTo StanHeaders (>= 2.19.0), rstan (>= 2.19.2), BH (>= 1.69.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0)
License GPL (>= 3)
LazyData true
Biarch true
NeedsCompilation yes
VignetteBuilder knitr
SystemRequirements GNU make, pandoc (>= 1.12.3), pandoc-citeproc
Encoding UTF-8
RoxygenNote 6.1.1
Packaged 2019-10-23 15:41:28 UTC; weberse2
Repository CRAN
Date/Publication 2019-10-23 16:40:02 UTC

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