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glmBfp (version 0.0-60)

Bayesian Fractional Polynomials for GLMs

Description

Implements the Bayesian paradigm for fractional polynomials in generalized linear models, described by Held, Gravestock, Sabanes Bove (2015) . See package 'bfp' for the treatment of normal models.

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Version

Install

install.packages('glmBfp')

Monthly Downloads

35

Version

0.0-60

License

GPL (>= 2)

Maintainer

Isaac Gravestock

Last Published

June 16th, 2020

Functions in glmBfp (0.0-60)

GPrior-class

The virtual g-prior class
HypergPrior-class

The hyper-g prior class
CustomGPrior-class

The custom g-prior class
IncInvGammaGPrior-class

The incomplete inverse gamma g-prior class
HypergPrior

Constructor for the hyper-g prior class
Extract.GlmBayesMfp

Extract method for GlmBayesMfp objects
CustomGPrior

Constructor for the custom g-prior class
GlmBayesMfpSamples-class

Class for samples from a single GlmBayesMfp model or a model average
HypergPrior-initialize

Initialization method for the "HypergPrior" class
McmcOptions

Constructor for class McmcOptions
GlmBayesMfpSamples-subsetting

Subset method for GlmBayesMfpSamples objects
InvGammaGPrior-class

The inverse gamma g-prior class
constructNewdataMatrix

Construct the covariates matrix for new data based on an existing GlmBayesMfp object
convert2Mcmc

Convert samples to mcmc objects
getMarginalZ

Construct a (smooth) marginal z density approximation from a model information list
as.data.frame.GlmBayesMfp

Convert a GlmBayesMfp object into a data frame
InvGammaGPrior

Constructor for the inverse gamma g-prior class
cppOptimize

Interface to the internal C++ optimization routine "optimize"
InvGammaGPrior-initialize

Initialization method for the "InvGammaGPrior" class
predict.TBFcox

Prediction methods for CoxTBF objects
IncInvGammaGPrior-initialize

Initialization method for the "IncInvGammaGPrior" class
predict.TBFcox.sep

Prediction methods for CoxTBF objects with separate estimates
getLogGPrior

Helper function for glmBayesMfp: Returns the normalized log g prior density
boxTidwell

Box Tidwell transformation
IncInvGammaGPrior

Constructor for the incomplete inverse gamma g-prior class
getLogMargLikEstimate

Compute the Chib-Jeliazkov log marginal likelihood estimate from the MCMC output
getModelCoefs

Estimate shrunken coefficients from GlmBayesMfp object for Cox model
writeFormula

Construct a survival formula based on a glmBfp object with censInd not null.
computeModels

Compute model information for a given list of model configurations and glmBayesMfp output.
plotCurveEstimate

Function for plotting a fractional polynomial curve estimate
logPriors

Extract the log prior values from a GlmBayesMfp object
empiricalHpd

Construct an empirical HPD interval from samples
McmcOptions-class

Class for the three canonical MCMC options
evalZdensity

Evaluate the (negative log) unnormalized marginal z density in a given model.
coxTBF

Fit Cox models using glmBayesMfp
fpTrans

Transform formula variables
fpScale

Shift and scale a covariate vector (if wished) to have positive and small numbers.
sampleGlm

Produce posterior samples from one GLM / Cox model
predict.TBFcox.BMA

Prediction methods for CoxTBF objects for BMA models
posteriors

Extract posterior model probability estimates from a GlmBayesMfp object
cppBfgs

Interface to the internal C++ optimization routine "bfgs"
getUncenteredDesignMatrix

Construct the design matrix for a given bfp GLM model
getDesignMatrix

Construct the design matrix for a given bfp GLM model
glmBayesMfp

Bayesian model inference for fractional polynomial GLMs and Cox models
bfp

Mark a covariate for transformation with fractional polynomials
is.bool

Predicate checking for a boolean option
sampleSize

Compute the number of samples for a given MCMC options triple
glmBfp-package

Bayesian inference for fractional polynomial models from the GLM and Cox family
getFamily

Helper function for glmBayesMfp: Extracts an S3 family object
logMargLiks

Extract the log marginal likelihood estimates from a GlmBayesMfp object
inclusionProbs

Compute posterior inclusion probabilites based on GlmBayesMfp object
getGenerator

Internal helper function which gets the generator (and normalizing constant)
print.GlmBayesMfp

Print a GlmBayesMfp object.
testCox

Test the Cox model computation for the TBF approach
getFpTransforms

Get the FP transforms matrix of a given covariate vector
scrHpd

Calculate an SCB from a samples matrix
sampleBma

Produce posterior samples from a Bayesian model average over GLMs / Cox models