glmBfp: Bayesian Fractional Polynomials for GLMs

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

Author
Isaac Gravestock [aut, cre], Daniel Sabanes Bove [aut], David Maisonave [ctb], Terry Therneau [ctb], R Core Team [ctb]
Date of publication
2016-10-19 15:45:17
Maintainer
Isaac Gravestock <isaac.gravestock@uzh.ch>
License
GPL (>= 2)
Version
0.0-49

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