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

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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.

Author
Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Date of publication
2015-07-28 00:15:30
Maintainer
Arnošt Komárek <arnost.komarek@mff.cuni.cz>
License
GPL (>= 2)
Version
2.6
URLs

View on CRAN

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...

Files in this package

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