glmBfp: Bayesian Fractional Polynomials for GLMs
Version 0.0-48

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("glmBfp")

Getting started

Package overview

Popular man pages

constructNewdataMatrix: Construct the covariates matrix for new data based on an...
coxTBF: Fit Cox models using glmBayesMfp
cppOptimize: Interface to the internal C++ optimization routine "optimize"
getDesignMatrix: Construct the design matrix for a given bfp GLM model
getFpTransforms: Get the FP transforms matrix of a given covariate vector
IncInvGammaGPrior: Constructor for the incomplete inverse gamma g-prior class
plotCurveEstimate: Function for plotting a fractional polynomial curve estimate
See all...

All man pages Function index File listing

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...

Functions

'\%bt\%' Man page
CustomGPrior Man page Source code
CustomGPrior-class Man page
Extract.GlmBayesMfp Man page
GPrior-class Man page
GlmBayesMfp Man page
GlmBayesMfpSamples-class Man page
GlmBayesMfpSamples-subsetting Man page
HypergPrior Man page Source code
HypergPrior-class Man page
HypergPrior-initialize Man page
IncInvGammaGPrior Man page Source code
IncInvGammaGPrior-class Man page
IncInvGammaGPrior-initialize Man page
InvGammaGPrior Man page Source code
InvGammaGPrior-class Man page
InvGammaGPrior-initialize Man page
McmcOptions Man page Source code
McmcOptions-class Man page
[,GlmBayesMfpSamples,ANY,missing,missing-method Man page
[.GlmBayesMfp Man page
\%bt\% Man page
as.data.frame.GlmBayesMfp Man page Source code
bfp Man page Source code
boxTidwell Man page
computeModels Man page Source code
constructNewdataMatrix Man page Source code
convert2Mcmc Man page Source code
coxTBF Man page Source code
cppBfgs Man page Source code
cppOptimize Man page Source code
empiricalHpd Man page Source code
evalZdensity Man page Source code
fpScale Man page Source code
fpTrans Man page Source code
getDesignMatrix Man page Source code
getFamily Man page Source code
getFpTransforms Man page Source code
getGenerator Man page Source code
getLogGPrior Man page Source code
getLogMargLikEstimate Man page Source code
getMarginalZ Man page Source code
getModelCoefs Man page Source code
getUncenteredDesignMatrix Man page Source code
glmBayesMfp Man page Source code
glmBfp Man page
glmBfp-package Man page
inclusionProbs Man page Source code
initialize,HypergPrior-method Man page
initialize,IncInvGammaGPrior-method Man page
initialize,InvGammaGPrior-method Man page
is.bool Man page Source code
logMargLiks Man page Source code
logPriors Man page Source code
plotCurveEstimate Man page Source code
posteriors Man page Source code
predBMAcpp Source code
predict.TBFcox Man page Source code
predict.TBFcox.BMA Man page Source code
predict.TBFcox.sep Man page Source code
print.GlmBayesMfp Man page Source code
sampleBma Man page Source code
sampleGlm Man page Source code
sampleSize Man page Source code
scrHpd Man page Source code
testCox Man page Source code
uc Man page
writeFormula Man page Source code

Files

TODO
inst
inst/CITATION
inst/doc
inst/doc/examples.Rnw
inst/doc/examples.pdf
inst/doc/examples.R
configure.ac
tests
tests/optimization.R
src
src/linalgInterface.cpp
src/gpriors.h
src/evalZdensity.cpp
src/optimize.cpp
src/design.h
src/zdensity.cpp
src/zdensity.h
src/dataStructure.cpp
src/iwls.cpp
src/sampleGlm.cpp
src/optimize.h
src/linalgInterface.h
src/sum.h
src/iwls.h
src/gpriors.cpp
src/glmBayesMfp.cpp
src/Makevars.in
src/types.h
src/fpUcHandling.cpp
src/fpUcHandling.h
src/distributions.cpp
src/rcppExport.h
src/combinatorics.cpp
src/bfgs.cpp
src/coxfit.cpp
src/combinatorics.h
src/design.cpp
src/links.h
src/functionWraps.cpp
src/bfgs.h
src/dataStructure.h
src/Makevars.win
src/RcppExports.cpp
src/distributions.h
src/predBMA.cpp
src/functionWraps.h
src/coxfit.h
NAMESPACE
R
R/GlmBayesMfpSamples-methods.R
R/getModelCoefs.R
R/getMarginalZ.R
R/evalZdensity.R
R/computeModels.R
R/GlmBayesMfp-methods.R
R/helpers.R
R/plotCurveEstimate.R
R/McmcOptions-methods.R
R/fpScale.R
R/getFpTransforms.R
R/writeFormula.R
R/formula.R
R/coxTBF.R
R/McmcOptions-class.R
R/hpds.R
R/constructNewdataMatrix.R
R/getLogMargLikEstimate.R
R/getFamily.R
R/uncenteredDesignMatrix.R
R/optimize.R
R/fpTrans.R
R/glmBayesMfp.R
R/getLogGPrior.R
R/RcppExports.R
R/testCox.R
R/sampleBma.R
R/glmBfp-package.R
R/predictCoxTBF.R
R/getDesignMatrix.R
R/GPrior-classes.R
R/posteriors.R
R/sampleGlm.R
R/inclusionProbs.R
R/GlmBayesMfpSamples-class.R
vignettes
vignettes/examples.Rnw
vignettes/examples.bib
MD5
build
build/vignette.rds
DESCRIPTION
configure
ChangeLog
man
man/GlmBayesMfpSamples-subsetting.Rd
man/getLogGPrior.Rd
man/getMarginalZ.Rd
man/getFamily.Rd
man/HypergPrior-initialize.Rd
man/sampleBma.Rd
man/fpTrans.Rd
man/cppOptimize.Rd
man/constructNewdataMatrix.Rd
man/IncInvGammaGPrior.Rd
man/formula.Rd
man/InvGammaGPrior.Rd
man/print.GlmBayesMfp.Rd
man/evalZdensity.Rd
man/scrHpd.Rd
man/convert2Mcmc.Rd
man/getDesignMatrix.Rd
man/GlmBayesMfpSamples-class.Rd
man/fpScale.Rd
man/IncInvGammaGPrior-initialize.Rd
man/empiricalHpd.Rd
man/predict.TBFcox.sep.Rd
man/boxTidwell.Rd
man/sampleGlm.Rd
man/plotCurveEstimate.Rd
man/Extract.GlmBayesMfp.Rd
man/inclusionProbs.Rd
man/glmBayesMfp.Rd
man/computeModels.Rd
man/IncInvGammaGPrior-class.Rd
man/as.data.frame.GlmBayesMfp.Rd
man/predict.TBFcox.Rd
man/coxTBF.Rd
man/getUncenteredDesignMatrix.Rd
man/predict.TBFcox.BMA.Rd
man/logPriors.Rd
man/McmcOptions-class.Rd
man/sampleSize.Rd
man/CustomGPrior.Rd
man/getLogMargLikEstimate.Rd
man/getFpTransforms.Rd
man/logMargLiks.Rd
man/glmBfp-package.Rd
man/is.bool.Rd
man/CustomGPrior-class.Rd
man/InvGammaGPrior-class.Rd
man/cppBfgs.Rd
man/testCox.Rd
man/HypergPrior.Rd
man/getGenerator.Rd
man/McmcOptions.Rd
man/HypergPrior-class.Rd
man/writeFormula.Rd
man/InvGammaGPrior-initialize.Rd
man/GPrior-class.Rd
man/getModelCoefs.Rd
man/posteriors.Rd
cleanup
glmBfp documentation built on May 19, 2017, 6:44 a.m.

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