bayesSurv: Bayesian Survival Regression with Flexible Error and Random Effects Distributions
Version 2.6

Contains Bayesian implementations of Mixed-Effects Accelerated Failure Time (MEAFT) models for censored data. Those can be not only right-censored but also interval-censored, doubly-interval-censored or misclassified interval-censored.

Browse man pages Browse package API and functions Browse package files

AuthorArnošt Komárek <arnost.komarek@mff.cuni.cz>
Date of publication2015-07-28 00:15:30
MaintainerArnošt Komárek <arnost.komarek@mff.cuni.cz>
LicenseGPL (>= 2)
Version2.6
URL http://msekce.karlin.mff.cuni.cz/~komarek
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("bayesSurv")

Man pages

bayesBisurvreg: Population-averaged accelerated failure time model for...
bayesBisurvreg.help: Helping function for Bayesian regression with smoothed...
bayesDensity: Summary for the density estimate based on the mixture...
bayesGspline: Summary for the density estimate based on the model with...
bayesHistogram: Smoothing of a uni- or bivariate histogram using Bayesian...
bayesHistogram.help: Helping function for Bayesian smoothing of (bi)-variate...
bayessurvreg1: A Bayesian survival regression with an error distribution...
bayessurvreg1.files2init: Read the initial values for the Bayesian survival regression...
bayessurvreg1.help: Helping function for Bayesian survival regression models,...
bayessurvreg2: Cluster-specific accelerated failure time model for...
bayessurvreg2.help: Helping functions for Bayesian regression with an error...
bayessurvreg3: Cluster-specific accelerated failure time model for...
bayessurvreg3.help: Helping functions for Bayesian regression with an error...
bayessurvreg.help: Helping function for Bayesian survival regression models.
cgd: Chronic Granulomatous Disease data
credible.region: Compute a simultaneous credible region (rectangle) from a...
densplot2: Probability density function estimate from MCMC output
files2coda: Read the sampled values from the Bayesian survival regression...
files.Gspline: Write headers to or clean files with sampled G-spline
give.init: Check and possibly fill in initial values for the G-spline,...
give.summary: Brief summary for the chain(s) obtained using the MCMC.
marginal.bayesGspline: Summary for the marginal density estimates based on the...
plot.bayesDensity: Plot an object of class bayesDensity
plot.bayesGspline: Plot an object of class bayesGspline
plot.marginal.bayesGspline: Plot an object of class marginal.bayesGspline
predictive: Compute predictive quantities based on a Bayesian survival...
predictive2: Compute predictive quantities based on a Bayesian survival...
print.bayesDensity: Print a summary for the density estimate based on the...
rMVNorm: Sample from the multivariate normal distribution
rWishart: Sample from the Wishart distribution
sampleCovMat: Compute a sample covariance matrix.
sampled.kendall.tau: Estimate of the Kendall's tau from the bivariate model
scanFN: Read Data Values
simult.pvalue: Compute a simultaneous p-value from a sample for a vector...
tandmob2: Signal Tandmobiel data, version 2
tandmobRoos: Signal Tandmobiel data, version Roos
traceplot2: Trace plot of MCMC output.
vecr2matr: Transform single component indeces to double component...

Functions

bayesBisurvreg Man page Source code
bayesBisurvreg.checkStore Man page Source code
bayesBisurvreg.help Man page
bayesBisurvreg.priorBeta Man page Source code
bayesBisurvreg.priorInit Man page Source code
bayesBisurvreg.writeHeaders Man page Source code
bayesDensity Man page Source code
bayesGspline Man page Source code
bayesHistogram Man page Source code
bayesHistogram.checkStore Man page Source code
bayesHistogram.design Man page Source code
bayesHistogram.help Man page
bayesHistogram.priorInit Man page Source code
bayesHistogram.writeHeaders Man page Source code
bayessurvreg.checknsimul Man page Source code
bayessurvreg.design Man page Source code
bayessurvreg.help Man page
bayessurvreg1 Man page Source code
bayessurvreg1.checkStore Man page Source code
bayessurvreg1.files2init Man page Source code
bayessurvreg1.help Man page
bayessurvreg1.priorBeta Man page Source code
bayessurvreg1.priorInit Man page Source code
bayessurvreg1.priorb Man page Source code
bayessurvreg1.revjump Man page Source code
bayessurvreg1.writeHeaders Man page Source code
bayessurvreg2 Man page Source code
bayessurvreg2.checkStore Man page Source code
bayessurvreg2.help Man page
bayessurvreg2.priorBeta Man page Source code
bayessurvreg2.priorInit Man page Source code
bayessurvreg2.priorb Man page Source code
bayessurvreg2.writeHeaders Man page Source code
bayessurvreg3 Man page Source code
bayessurvreg3.checkStore Man page Source code
bayessurvreg3.checkrho Man page Source code
bayessurvreg3.help Man page
bayessurvreg3.priorBeta Man page Source code
bayessurvreg3.priorInit Man page Source code
bayessurvreg3.priorb Man page Source code
bayessurvreg3.priorinitNb Man page Source code
bayessurvreg3.writeHeaders Man page Source code
bayessurvreg3Para Man page Source code
cgd Man page
clean.Gspline Man page Source code
credible.region Man page Source code
densplot2 Man page Source code
files2coda Man page Source code
give.init.Gspline Man page Source code
give.init.r Man page Source code
give.init.y Man page Source code
give.init.y2 Man page Source code
give.summary Man page Source code
marginal.bayesGspline Man page Source code
onAttach Source code
plot.bayesDensity Man page Source code
plot.bayesGspline Man page Source code
plot.marginal.bayesGspline Man page Source code
predictive Man page Source code
predictive.control Man page Source code
predictive2 Man page Source code
predictive2.control Man page Source code
predictive2Para Man page Source code
print.bayesDensity Man page Source code
print.simult.pvalue Man page Source code
rMVNorm Man page Source code
rWishart Man page Source code
sampleCovMat Man page Source code
sampled.kendall.tau Man page Source code
scanFN Man page Source code
simult.pvalue Man page Source code
tandmob2 Man page
tandmobRoos Man page
traceplot2 Man page Source code
vecr2matr Man page Source code
write.headers.Gspline Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/index.html
inst/doc/IDsampled500.dat
inst/doc/ex-tandmobCS.R
inst/doc/ex-tandmobPA.R
inst/doc/ex-cgd.R
inst/doc/ex-tandmobMixture.R
inst/doc/IDsampled50.dat
src
src/templatefun_GS.h
src/logLikelihood.h
src/Makevars
src/GMRF_Gspline_Util.h
src/classRandomEff_rhoNorm.cpp
src/predictive.cpp
src/sampledKendallTau.h
src/List.h
src/regresResidual_GS.h
src/miscellaneous_GS.cpp
src/ARS2.h
src/randomLogLikelihood.h
src/constants.h
src/Gspline_update_lambda.cpp
src/bayessurvreg2.h
src/update_Data_GS.cpp
src/propVector.h
src/splitCombine.h
src/bayessurvreg1.h
src/arms.h
src/random.cpp
src/updateMeans.cpp
src/bayesHistogram.h
src/updateCovMatRandom.cpp
src/rhoNorm.cpp
src/Gspline_update_sigma.cpp
src/openFile.h
src/updateCovMatRandom.h
src/classCovMatrix.cpp
src/Gspline_update_gamma.cpp
src/update_sens_spec_misclassification.h
src/bayesBisurvreg.h
src/updateEta.cpp
src/bayesGspline.cpp
src/Gspline_update_Scale.cpp
src/mixMoments.h
src/cholesky.cpp
src/rhoNorm.h
src/newton_raphson.h
src/AK_BLAS_LAPACK.h
src/arms.cpp
src/bblocks.cpp
src/classBetaGamma.cpp
src/Gspline.cpp
src/Gspline_update_a.cpp
src/updateWeights.h
src/quantile.cpp
src/random.h
src/classCovMatrix.h
src/covMatrix.h
src/Slice_sampler2.cpp
src/updateRegres.cpp
src/MHproposal.cpp
src/Gspline.h
src/bayesGspline.h
src/updateVars.h
src/updateRandom.h
src/predictMisc.h
src/MHblocks.cpp
src/covMatrix.cpp
src/logLikelihood.cpp
src/in_output_GS.h
src/bblocks.h
src/updateEta.h
src/bayessurvreg1.cpp
src/ARS2.cpp
src/templatefun_GS.cpp
src/classBetaGamma.h
src/regresResidual_GS.cpp
src/miscellaneous.cpp
src/updateAlloc.h
src/bayessurvreg2.cpp
src/bayesDensity.cpp
src/mvtdist.h
src/GMRF.h
src/classBetaGammaExtend.cpp
src/in_output.cpp
src/classBetaGammaExtend.h
src/updateRegres.h
src/arrays2Mat.h
src/updateMeans.h
src/GMRF.cpp
src/moodyRing.h
src/update_sens_spec_misclassification.cpp
src/predictMisc.cpp
src/splitCombine.cpp
src/newton_raphson.cpp
src/bayessurvreg.h
src/MHproposal.h
src/updateAlloc.cpp
src/structRandomEff32.cpp
src/structRandomEff32.h
src/arrays2Mat.cpp
src/classCovMatrixExtend.h
src/templatefun.cpp
src/in_output.h
src/updateVars.cpp
src/mixMoments.cpp
src/marginal_bayesGspline.h
src/updateData.cpp
src/bayesBisurvreg.cpp
src/Mvtdist3.h
src/updateWeights.cpp
src/bayesDensity.h
src/sampledKendallTau.cpp
src/GMRF_Gspline.h
src/classRandomEff.h
src/List.cpp
src/classRandomEff.cpp
src/checkImputeData.cpp
src/Mvtdist3.cpp
src/miscellaneous.h
src/update_Alloc_GS.h
src/Gspline_update_Intcpt.cpp
src/cholesky.h
src/openFile.cpp
src/GMRF_Gspline.cpp
src/MHblocks.h
src/predictive.h
src/updateData.h
src/update_Data_GS.h
src/moodyRing.cpp
src/classCovMatrixExtend.cpp
src/predictive_GS.h
src/AK_BasicFun.h
src/GMRF_Gspline_Util.cpp
src/propVector.cpp
src/checkImputeData.h
src/predictive_GS.cpp
src/mvtdist.cpp
src/templatefun.h
src/randomLogLikelihood.cpp
src/birthDeath.cpp
src/qrdecomp.cpp
src/in_output_GS.cpp
src/updateRandom.cpp
src/miscellaneous_GS.h
src/Slice_sampler2.h
src/marginal_bayesGspline.cpp
src/birthDeath.h
src/quantile.h
src/AK_Error.h
src/classRandomEff_rhoNorm.h
src/qrdecomp.h
src/update_Alloc_GS.cpp
src/bayesHistogram.cpp
src/AK_BLAS_LAPACK.cpp
NAMESPACE
data
data/tandmob2.RData
data/tandmobRoos.RData
data/cgd.RData
R
R/traceplot2.R
R/bayessurvreg.design.R
R/bayessurvreg2.checkStore.R
R/bayesBisurvreg.priorBeta.R
R/bayesHistogram.design.R
R/bayessurvreg1.writeHeaders.R
R/predictive2.control.R
R/bayessurvreg3.priorinitNb.R
R/simult.pvalue.R
R/bayessurvreg3.priorInit.R
R/bayessurvreg3.R
R/give.init.Gspline.R
R/credible.region.R
R/rMVNorm.R
R/bayesBisurvreg.checkStore.R
R/bayessurvreg1.revjump.R
R/give.summary.R
R/bayesGspline.R
R/bayessurvreg2.writeHeaders.R
R/bayessurvreg3.checkStore.R
R/predictive2Para.R
R/densplot2.R
R/bayesBisurvreg.writeHeaders.R
R/bayessurvreg3.priorBeta.R
R/bayesDensity.R
R/bayessurvreg3.writeHeaders.R
R/give.init.r.R
R/bayesHistogram.writeHeaders.R
R/bayessurvreg1.checkStore.R
R/bayesHistogram.checkStore.R
R/predictive2.R
R/bayessurvreg1.priorBeta.R
R/bayessurvreg3.priorb.R
R/files.Gspline.R
R/bayessurvreg2.priorBeta.R
R/rWishart.R
R/bayessurvreg1.R
R/bayessurvreg1.files2init.R
R/sampleCovMat.R
R/sampled.kendall.tau.R
R/predictive.control.R
R/bayessurvreg2.R
R/predictive.R
R/bayessurvreg1.priorInit.R
R/bayessurvreg1.priorb.R
R/bayessurvreg2.priorb.R
R/bayesBisurvreg.priorInit.R
R/give.init.y.R
R/files2coda.R
R/bayessurvreg2.priorInit.R
R/bayesHistogram.R
R/marginal.bayesGspline.R
R/bayessurvreg.checknsimul.R
R/zzz.R
R/scanFN.R
R/bayessurvreg3.checkrho.R
R/bayessurvreg3Para.R
R/vecr2matr.R
R/bayesBisurvreg.R
R/bayesHistogram.priorInit.R
MD5
DESCRIPTION
man
man/bayesGspline.Rd
man/plot.bayesGspline.Rd
man/plot.bayesDensity.Rd
man/bayessurvreg2.help.Rd
man/predictive.Rd
man/print.bayesDensity.Rd
man/marginal.bayesGspline.Rd
man/give.init.Rd
man/bayesDensity.Rd
man/bayessurvreg.help.Rd
man/simult.pvalue.Rd
man/plot.marginal.bayesGspline.Rd
man/tandmob2.Rd
man/tandmobRoos.Rd
man/bayessurvreg2.Rd
man/give.summary.Rd
man/credible.region.Rd
man/bayesHistogram.help.Rd
man/vecr2matr.Rd
man/bayessurvreg3.Rd
man/files2coda.Rd
man/bayessurvreg1.Rd
man/sampleCovMat.Rd
man/densplot2.Rd
man/cgd.Rd
man/bayessurvreg1.help.Rd
man/bayesHistogram.Rd
man/traceplot2.Rd
man/rMVNorm.Rd
man/scanFN.Rd
man/rWishart.Rd
man/files.Gspline.Rd
man/bayessurvreg3.help.Rd
man/bayessurvreg1.files2init.Rd
man/sampled.kendall.tau.Rd
man/bayesBisurvreg.Rd
man/predictive2.Rd
man/bayesBisurvreg.help.Rd
CHANGES
bayesSurv documentation built on May 19, 2017, 8:57 p.m.