hypergsplines: Bayesian model selection with penalised splines and hyper-g prior
Version 0.0-40

This R-package implements Bayesian model selection with penalised splines, using a hyper-g prior for the parameters in the normal additive and the generalised additive model.

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AuthorDaniel Sabanes Bove <daniel.sabanesbove@ifspm.uzh.ch>
Date of publication2013-11-21 18:18:42
MaintainerDaniel Sabanes Bove <daniel.sabanesbove@ifspm.uzh.ch>
LicenseGPL (>= 2)
Version0.0-40
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("hypergsplines", repos="http://R-Forge.R-project.org")

Man pages

aggregateModelsTable: Aggregate the models found by exhaustive or stochastic search
calculateModel: Calculate intermediate information for a specific model
checkModelConfigs: Check coherency of model configurations with data
CustomGPrior: Constructor for the custom g-prior class
CustomGPrior-class: The custom g-prior class
dinvGamma: Density function for the inverse gamma distribution
empiricalHpd: Construct an empirical HPD interval from samples
exhaustive: Evaluate all possible models
expWithConst: Exponentiate a vector of values plus a constant
getBmaSamples: Get posterior samples from the Bayesian Model Average (BMA)
getComputation: Collect the computation options
getFamily: Helper function for glmModelData: Extracts an S3 family...
getFitSamples: Extract fit samples on linear predictor scale from posterior...
getFunctionSamples: Extract function values samples from posterior coefficients...
getInclusionProbs: Extract posterior inclusion probabilities from the models...
getLogModelPrior: Get the log prior probability for a model
getMcmc: Collect the MCMC options
getQmatrix: Compute the Q matrix necessary for the offsets for survival...
getRhos: Compute the penalty parameters corresponding to degrees of...
getSamples: Get posterior samples for a specific model configuration
getSearch: Collect the search options, todo: really use this in the...
glmGetSamples: Get posterior samples for a specific model configuration for...
glmModelData: Process the data needed for modelling
GPrior-class: The virtual g-prior class
hyp2f1: Gauss hypergeometric function
HypergnPrior: Constructor for the "HypergnPrior" class
HypergnPrior-class: The hyper-g/n prior class
HypergnPrior-initialize: Initialization method for the "HypergnPrior" class
HypergPrior: Constructor for the hyper-g prior class
HypergPrior-class: The hyper-g prior class
HypergPrior-initialize: Initialization method for the "HypergPrior" class
hypergsplines-package: Bayesian model selection with penalized splines and hyper-g...
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
is.posInt: Predicate checking for a scalar positive integer
is.scalar: Predicate checking for a scalar
linApproxDens: Test the C++ object class LinApproxDens
logBFhypergn: Compute the log Bayes Factor against the null model under...
logHyp2f1Laplace: Laplace approximation to the Gauss hypergeometric function
makeBasis: Construction of quantile-based linear spline basis
modelData: Process the data needed for modelling
pinvGamma: Cumulative distribution function for the inverse gamma...
plotCurveEstimate: Plot function value estimates
postOptimize: Post-optimizing a good model
qinvGamma: Quantile function for the inverse gamma distribution
rinvGamma: Generate random numbers from the inverse gamma distribution
rshrinkage: Sample from the model-specific posterior of the shrinkage...
scrBesag: Simultaneous credible band computation
scrHpd: Calculate an SCB from a samples matrix
stochSearch: Stochastic search for models with high posterior probability
survModelData: Process the data needed for survival models

Functions

CustomGPrior Man page Source code
CustomGPrior-class Man page
GPrior-class Man page
HypergPrior Man page Source code
HypergPrior-class Man page
HypergPrior-initialize Man page
HypergnPrior Man page Source code
HypergnPrior-class Man page
HypergnPrior-initialize Man page
InvGammaGPrior Man page Source code
InvGammaGPrior-class Man page
InvGammaGPrior-initialize Man page
aggregateModelsTable Man page Source code
calculateModel Man page Source code
checkModelConfigs Man page Source code
dinvGamma Man page Source code
empiricalHpd Man page Source code
exhaustive Man page Source code
expWithConst Man page Source code
getBmaSamples Man page Source code
getComputation Man page Source code
getFamily Man page Source code
getFitSamples Man page Source code
getFunctionSamples Man page Source code
getInclusionProbs Man page Source code
getLogModelPrior Man page Source code
getMcmc Man page Source code
getQmatrix Man page Source code
getRhos Man page Source code
getSamples Man page Source code
getSearch Man page Source code
glmGetSamples Man page Source code
glmModelData Man page Source code
hyp2f1 Man page Source code
hypergsplines Man page
hypergsplines-package Man page
initialize,HypergPrior-method Man page
initialize,HypergnPrior-method Man page
initialize,InvGammaGPrior-method Man page
is.bool Man page Source code
is.posInt Man page Source code
is.scalar Man page Source code
linApproxDens Man page Source code
logBFhypergn Man page Source code
logHyp2f1Laplace Man page Source code
makeBasis Man page Source code
modelData Man page Source code
pinvGamma Man page Source code
plotCurveEstimate Man page Source code
postOptimize Man page Source code
qinvGamma Man page Source code
rinvGamma Man page Source code
rshrinkage Man page Source code
scrBesag Man page Source code
scrHpd Man page Source code
stochSearch Man page Source code
survModelData Man page Source code

Files

ChangeLog
DESCRIPTION
NAMESPACE
R
R/GPrior-classes.R
R/aggregateModelsTable.R
R/calculateModel.R
R/exhaustive.R
R/getBmaSamples.R
R/getFamily.R
R/getFitSamples.R
R/getFunctionSamples.R
R/getInclusionProbs.R
R/getLogModelPrior.R
R/getQmatrix.R
R/getRhos.R
R/getSamples.R
R/glmGetSamples.R
R/glmModelData.R
R/helpers.R
R/hpds.R
R/hyp2f1.R
R/hypergsplines-package.R
R/invGamma.R
R/linApproxDens.R
R/logBFhypergn.R
R/makeBasis.R
R/modelData.R
R/options.R
R/plotCurveEstimate.R
R/postOptimize.R
R/rshrinkage.R
R/stochSearch.R
R/survModelData.R
build
build/vignette.rds
examples
examples/aggregateModelsTable.R
examples/calculateModel.R
examples/exhaustive.R
examples/getBmaSamples.R
examples/getFitSamples.R
examples/getFunctionSamples.R
examples/getInclusionProbs.R
examples/getLogModelPrior.R
examples/getRhos.R
examples/getSamples.R
examples/glmGetSamples.R
examples/glmModelData.R
examples/hyp2f1.R
examples/makeBasis.R
examples/modelData.R
examples/plotCurveEstimate.R
examples/postOptimize.R
examples/stochSearch.R
examples/survModelData.R
inst
inst/CITATION
inst/doc
inst/doc/examples.R
inst/doc/examples.Rnw
inst/doc/examples.bib
inst/doc/examples.pdf
man
man/CustomGPrior-class.Rd
man/CustomGPrior.Rd
man/GPrior-class.Rd
man/HypergPrior-class.Rd
man/HypergPrior-initialize.Rd
man/HypergPrior.Rd
man/HypergnPrior-class.Rd
man/HypergnPrior-initialize.Rd
man/HypergnPrior.Rd
man/InvGammaGPrior-class.Rd
man/InvGammaGPrior-initialize.Rd
man/InvGammaGPrior.Rd
man/aggregateModelsTable.Rd
man/calculateModel.Rd
man/checkModelConfigs.Rd
man/dinvGamma.Rd
man/empiricalHpd.Rd
man/exhaustive.Rd
man/expWithConst.Rd
man/getBmaSamples.Rd
man/getComputation.Rd
man/getFamily.Rd
man/getFitSamples.Rd
man/getFunctionSamples.Rd
man/getInclusionProbs.Rd
man/getLogModelPrior.Rd
man/getMcmc.Rd
man/getQmatrix.Rd
man/getRhos.Rd
man/getSamples.Rd
man/getSearch.Rd
man/glmGetSamples.Rd
man/glmModelData.Rd
man/hyp2f1.Rd
man/hypergsplines-package.Rd
man/is.bool.Rd
man/is.posInt.Rd
man/is.scalar.Rd
man/linApproxDens.Rd
man/logBFhypergn.Rd
man/logHyp2f1Laplace.Rd
man/makeBasis.Rd
man/modelData.Rd
man/pinvGamma.Rd
man/plotCurveEstimate.Rd
man/postOptimize.Rd
man/qinvGamma.Rd
man/rinvGamma.Rd
man/rshrinkage.Rd
man/scrBesag.Rd
man/scrHpd.Rd
man/stochSearch.Rd
man/survModelData.Rd
src
src/Makevars
src/Makevars.win
src/aggregateModelsTable.cpp
src/backsolve.cpp
src/backsolve.h
src/calculateModel.cpp
src/dataStructure.cpp
src/dataStructure.h
src/distributions.cpp
src/distributions.h
src/exhaustive.cpp
src/exhaustive2.cpp
src/functionWraps.cpp
src/functionWraps.h
src/getLogMargLikEst.cpp
src/getLogMargLikEst.h
src/getRho.cpp
src/getRho.h
src/glmExhaustive.cpp
src/glmGetSamples.cpp
src/glmLogMargLik.cpp
src/glmStochSearch.cpp
src/gpriors.h
src/hyp2f1.cpp
src/hyp2f1.h
src/iwls.cpp
src/iwls.h
src/linApproxDens.cpp
src/linApproxDens.h
src/linalgInterface.cpp
src/linalgInterface.h
src/links.h
src/logBFhyperg.cpp
src/logBFhyperg.h
src/logBFhypergn.cpp
src/logBFhypergn.h
src/logMargLik.cpp
src/optimize.h
src/random.cpp
src/random.h
src/rcppExport.h
src/stochSearch.cpp
src/sum.cpp
src/sum.h
src/types.h
src/zdensity.cpp
src/zdensity.h
hypergsplines documentation built on May 21, 2017, 3:48 a.m.