`install.packages('glmBfp')`

53

0.0-60

GPL (>= 2)

June 16th, 2020

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