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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
Version
0.0-60
0.0-51
0.0-48
Install
install.packages('glmBfp')
Monthly Downloads
53
Version
0.0-60
License
GPL (>= 2)
Maintainer
Isaac Gravestock
Last Published
June 16th, 2020
Functions in glmBfp (0.0-60)
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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