# glmBfp v0.0-51

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## Bayesian Fractional Polynomials for GLMs

Implements the Bayesian paradigm for fractional polynomials in generalized linear models, described by Held, Gravestock, Sabanes Bove (2015) <doi:10.1214/14-STS510>. See package 'bfp' for the treatment of normal models.

## Functions in glmBfp

 Name Description CustomGPrior-class The custom g-prior class CustomGPrior Constructor for the custom g-prior class Extract.GlmBayesMfp Extract method for GlmBayesMfp objects GPrior-class The virtual g-prior class HypergPrior-class The hyper-g prior class HypergPrior-initialize Initialization method for the "HypergPrior" class HypergPrior Constructor for the hyper-g prior class IncInvGammaGPrior-class The incomplete inverse gamma g-prior class GlmBayesMfpSamples-class Class for samples from a single GlmBayesMfp model or a model average GlmBayesMfpSamples-subsetting Subset method for GlmBayesMfpSamples objects McmcOptions Constructor for class McmcOptions as.data.frame.GlmBayesMfp Convert a GlmBayesMfp object into a data frame coxTBF Fit Cox models using glmBayesMfp InvGammaGPrior-class The inverse gamma g-prior class InvGammaGPrior-initialize Initialization method for the "InvGammaGPrior" class constructNewdataMatrix Construct the covariates matrix for new data based on an existing GlmBayesMfp object InvGammaGPrior Constructor for the inverse gamma g-prior class McmcOptions-class Class for the three canonical MCMC options cppOptimize Interface to the internal C++ optimization routine "optimize" empiricalHpd Construct an empirical HPD interval from samples cppBfgs Interface to the internal C++ optimization routine "bfgs" getLogGPrior Helper function for glmBayesMfp: Returns the normalized log g prior density getLogMargLikEstimate Compute the Chib-Jeliazkov log marginal likelihood estimate from the MCMC output logPriors Extract the log prior values from a GlmBayesMfp object convert2Mcmc Convert samples to mcmc objects boxTidwell Box Tidwell transformation computeModels Compute model information for a given list of model configurations and glmBayesMfp output. fpScale Shift and scale a covariate vector (if wished) to have positive and small numbers. getDesignMatrix Construct the design matrix for a given bfp GLM model getFamily Helper function for glmBayesMfp: Extracts an S3 family object glmBfp-package Bayesian inference for fractional polynomial models from the GLM and Cox family inclusionProbs Compute posterior inclusion probabilites based on GlmBayesMfp object fpTrans Transform formula variables getFpTransforms Get the FP transforms matrix of a given covariate vector getGenerator Internal helper function which gets the generator (and normalizing constant) posteriors Extract posterior model probability estimates from a GlmBayesMfp object getUncenteredDesignMatrix Construct the design matrix for a given bfp GLM model glmBayesMfp Bayesian model inference for fractional polynomial GLMs and Cox models predict.TBFcox Prediction methods for CoxTBF objects predict.TBFcox.sep Prediction methods for CoxTBF objects with separate estimates sampleGlm Produce posterior samples from one GLM / Cox model sampleSize Compute the number of samples for a given MCMC options triple writeFormula Construct a survival formula based on a glmBfp object with censInd not null. IncInvGammaGPrior-initialize Initialization method for the "IncInvGammaGPrior" class IncInvGammaGPrior Constructor for the incomplete inverse gamma g-prior class evalZdensity Evaluate the (negative log) unnormalized marginal z density in a given model. bfp Mark a covariate for transformation with fractional polynomials getMarginalZ Construct a (smooth) marginal z density approximation from a model information list getModelCoefs Estimate shrunken coefficients from GlmBayesMfp object for Cox model is.bool Predicate checking for a boolean option logMargLiks Extract the log marginal likelihood estimates from a GlmBayesMfp object scrHpd Calculate an SCB from a samples matrix testCox Test the Cox model computation for the TBF approach plotCurveEstimate Function for plotting a fractional polynomial curve estimate print.GlmBayesMfp Print a GlmBayesMfp object. sampleBma Produce posterior samples from a Bayesian model average over GLMs / Cox models predict.TBFcox.BMA Prediction methods for CoxTBF objects for BMA models No Results!