glmBfp: Bayesian Fractional Polynomials for GLMs

Implements the Bayesian paradigm for fractional polynomials in generalized linear models. See package 'bfp' for the treatment of normal models.

AuthorIsaac Gravestock [aut, cre], Daniel Sabanes Bove [aut], David Maisonave [ctb], Terry Therneau [ctb], R Core Team [ctb]
Date of publication2016-07-07 13:37:21
MaintainerIsaac Gravestock <isaac.gravestock@uzh.ch>
LicenseGPL (>= 2)
Version0.0-48

View on CRAN

Man pages

as.data.frame.GlmBayesMfp: Convert a GlmBayesMfp object into a data frame

boxTidwell: Box Tidwell transformation

computeModels: Compute model information for a given list of model...

constructNewdataMatrix: Construct the covariates matrix for new data based on an...

convert2Mcmc: Convert samples to mcmc objects

coxTBF: Fit Cox models using glmBayesMfp

cppBfgs: Interface to the internal C++ optimization routine "bfgs"

cppOptimize: Interface to the internal C++ optimization routine "optimize"

CustomGPrior: Constructor for the custom g-prior class

CustomGPrior-class: The custom g-prior class

empiricalHpd: Construct an empirical HPD interval from samples

evalZdensity: Evaluate the (negative log) unnormalized marginal z density...

Extract.GlmBayesMfp: Extract method for GlmBayesMfp objects

formula: Mark a covariate for transformation with fractional...

fpScale: Shift and scale a covariate vector (if wished) to have...

fpTrans: Transform formula variables

getDesignMatrix: Construct the design matrix for a given bfp GLM model

getFamily: Helper function for glmBayesMfp: Extracts an S3 family object

getFpTransforms: Get the FP transforms matrix of a given covariate vector

getGenerator: Internal helper function which gets the generator (and...

getLogGPrior: Helper function for glmBayesMfp: Returns the normalized log g...

getLogMargLikEstimate: Compute the Chib-Jeliazkov log marginal likelihood estimate...

getMarginalZ: Construct a (smooth) marginal z density approximation from a...

getModelCoefs: Estimate shrunken coefficients from GlmBayesMfp object for...

getUncenteredDesignMatrix: Construct the design matrix for a given bfp GLM model

glmBayesMfp: Bayesian model inference for fractional polynomial GLMs and...

GlmBayesMfpSamples-class: Class for samples from a single GlmBayesMfp model or a model...

GlmBayesMfpSamples-subsetting: Subset method for GlmBayesMfpSamples objects

glmBfp-package: Bayesian inference for fractional polynomial models from the...

GPrior-class: The virtual g-prior class

HypergPrior: Constructor for the hyper-g prior class

HypergPrior-class: The hyper-g prior class

HypergPrior-initialize: Initialization method for the "HypergPrior" class

IncInvGammaGPrior: Constructor for the incomplete inverse gamma g-prior class

IncInvGammaGPrior-class: The incomplete inverse gamma g-prior class

IncInvGammaGPrior-initialize: Initialization method for the "IncInvGammaGPrior" class

inclusionProbs: Compute posterior inclusion probabilites based on GlmBayesMfp...

InvGammaGPrior: Constructor for the inverse gamma g-prior class

InvGammaGPrior-class: The inverse gamma g-prior class

InvGammaGPrior-initialize: Initialization method for the "InvGammaGPrior" class

is.bool: Predicate checking for a boolean option

logMargLiks: Extract the log marginal likelihood estimates from a...

logPriors: Extract the log prior values from a GlmBayesMfp object

McmcOptions: Constructor for class McmcOptions

McmcOptions-class: Class for the three canonical MCMC options

plotCurveEstimate: Function for plotting a fractional polynomial curve estimate

posteriors: Extract posterior model probability estimates from a...

predict.TBFcox: Prediction methods for CoxTBF objects

predict.TBFcox.BMA: Prediction methods for CoxTBF objects for BMA models

predict.TBFcox.sep: Prediction methods for CoxTBF objects with separate estimates

print.GlmBayesMfp: Print a GlmBayesMfp object.

sampleBma: Produce posterior samples from a Bayesian model average over...

sampleGlm: Produce posterior samples from one GLM / Cox model

sampleSize: Compute the number of samples for a given MCMC options triple

scrHpd: Calculate an SCB from a samples matrix

testCox: Test the Cox model computation for the TBF approach

writeFormula: Construct a survival formula based on a glmBfp object with...

Files in this package

glmBfp
glmBfp/TODO
glmBfp/inst
glmBfp/inst/CITATION
glmBfp/inst/doc
glmBfp/inst/doc/examples.Rnw
glmBfp/inst/doc/examples.pdf
glmBfp/inst/doc/examples.R
glmBfp/configure.ac
glmBfp/tests
glmBfp/tests/optimization.R
glmBfp/src
glmBfp/src/linalgInterface.cpp
glmBfp/src/gpriors.h
glmBfp/src/evalZdensity.cpp
glmBfp/src/optimize.cpp
glmBfp/src/design.h
glmBfp/src/zdensity.cpp
glmBfp/src/zdensity.h
glmBfp/src/dataStructure.cpp
glmBfp/src/iwls.cpp
glmBfp/src/sampleGlm.cpp
glmBfp/src/optimize.h
glmBfp/src/linalgInterface.h
glmBfp/src/sum.h
glmBfp/src/iwls.h
glmBfp/src/gpriors.cpp
glmBfp/src/glmBayesMfp.cpp
glmBfp/src/Makevars.in
glmBfp/src/types.h
glmBfp/src/fpUcHandling.cpp
glmBfp/src/fpUcHandling.h
glmBfp/src/distributions.cpp
glmBfp/src/rcppExport.h
glmBfp/src/combinatorics.cpp
glmBfp/src/bfgs.cpp
glmBfp/src/coxfit.cpp
glmBfp/src/combinatorics.h
glmBfp/src/design.cpp
glmBfp/src/links.h
glmBfp/src/functionWraps.cpp
glmBfp/src/bfgs.h
glmBfp/src/dataStructure.h
glmBfp/src/Makevars.win
glmBfp/src/RcppExports.cpp
glmBfp/src/distributions.h
glmBfp/src/predBMA.cpp
glmBfp/src/functionWraps.h
glmBfp/src/coxfit.h
glmBfp/NAMESPACE
glmBfp/R
glmBfp/R/GlmBayesMfpSamples-methods.R glmBfp/R/getModelCoefs.R glmBfp/R/getMarginalZ.R glmBfp/R/evalZdensity.R glmBfp/R/computeModels.R glmBfp/R/GlmBayesMfp-methods.R glmBfp/R/helpers.R glmBfp/R/plotCurveEstimate.R glmBfp/R/McmcOptions-methods.R glmBfp/R/fpScale.R glmBfp/R/getFpTransforms.R glmBfp/R/writeFormula.R glmBfp/R/formula.R glmBfp/R/coxTBF.R glmBfp/R/McmcOptions-class.R glmBfp/R/hpds.R glmBfp/R/constructNewdataMatrix.R glmBfp/R/getLogMargLikEstimate.R glmBfp/R/getFamily.R glmBfp/R/uncenteredDesignMatrix.R glmBfp/R/optimize.R glmBfp/R/fpTrans.R glmBfp/R/glmBayesMfp.R glmBfp/R/getLogGPrior.R glmBfp/R/RcppExports.R glmBfp/R/testCox.R glmBfp/R/sampleBma.R glmBfp/R/glmBfp-package.R glmBfp/R/predictCoxTBF.R glmBfp/R/getDesignMatrix.R glmBfp/R/GPrior-classes.R glmBfp/R/posteriors.R glmBfp/R/sampleGlm.R glmBfp/R/inclusionProbs.R glmBfp/R/GlmBayesMfpSamples-class.R
glmBfp/vignettes
glmBfp/vignettes/examples.Rnw
glmBfp/vignettes/examples.bib
glmBfp/MD5
glmBfp/build
glmBfp/build/vignette.rds
glmBfp/DESCRIPTION
glmBfp/configure
glmBfp/ChangeLog
glmBfp/man
glmBfp/man/GlmBayesMfpSamples-subsetting.Rd glmBfp/man/getLogGPrior.Rd glmBfp/man/getMarginalZ.Rd glmBfp/man/getFamily.Rd glmBfp/man/HypergPrior-initialize.Rd glmBfp/man/sampleBma.Rd glmBfp/man/fpTrans.Rd glmBfp/man/cppOptimize.Rd glmBfp/man/constructNewdataMatrix.Rd glmBfp/man/IncInvGammaGPrior.Rd glmBfp/man/formula.Rd glmBfp/man/InvGammaGPrior.Rd glmBfp/man/print.GlmBayesMfp.Rd glmBfp/man/evalZdensity.Rd glmBfp/man/scrHpd.Rd glmBfp/man/convert2Mcmc.Rd glmBfp/man/getDesignMatrix.Rd glmBfp/man/GlmBayesMfpSamples-class.Rd glmBfp/man/fpScale.Rd glmBfp/man/IncInvGammaGPrior-initialize.Rd glmBfp/man/empiricalHpd.Rd glmBfp/man/predict.TBFcox.sep.Rd glmBfp/man/boxTidwell.Rd glmBfp/man/sampleGlm.Rd glmBfp/man/plotCurveEstimate.Rd glmBfp/man/Extract.GlmBayesMfp.Rd glmBfp/man/inclusionProbs.Rd glmBfp/man/glmBayesMfp.Rd glmBfp/man/computeModels.Rd glmBfp/man/IncInvGammaGPrior-class.Rd glmBfp/man/as.data.frame.GlmBayesMfp.Rd glmBfp/man/predict.TBFcox.Rd glmBfp/man/coxTBF.Rd glmBfp/man/getUncenteredDesignMatrix.Rd glmBfp/man/predict.TBFcox.BMA.Rd glmBfp/man/logPriors.Rd glmBfp/man/McmcOptions-class.Rd glmBfp/man/sampleSize.Rd glmBfp/man/CustomGPrior.Rd glmBfp/man/getLogMargLikEstimate.Rd glmBfp/man/getFpTransforms.Rd glmBfp/man/logMargLiks.Rd glmBfp/man/glmBfp-package.Rd glmBfp/man/is.bool.Rd glmBfp/man/CustomGPrior-class.Rd glmBfp/man/InvGammaGPrior-class.Rd glmBfp/man/cppBfgs.Rd glmBfp/man/testCox.Rd glmBfp/man/HypergPrior.Rd glmBfp/man/getGenerator.Rd glmBfp/man/McmcOptions.Rd glmBfp/man/HypergPrior-class.Rd glmBfp/man/writeFormula.Rd glmBfp/man/InvGammaGPrior-initialize.Rd glmBfp/man/GPrior-class.Rd glmBfp/man/getModelCoefs.Rd glmBfp/man/posteriors.Rd
glmBfp/cleanup

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