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 publication2017-03-21 10:30:38
MaintainerIsaac Gravestock <isaac.gravestock@uzh.ch>
LicenseGPL (>= 2)
Version0.0-49

View on R-Forge

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

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

Files

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

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