spatsurv: Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models

Bayesian inference for parametric proportional hazards spatial survival models; flexible spatial survival models.

AuthorBenjamin M. Taylor and Barry S. Rowlingson Additional contributions Ziyu Zheng
Date of publication2016-10-24 17:14:26
MaintainerBenjamin M. Taylor <b.taylor1@lancaster.ac.uk>
LicenseGPL-3
Version0.9-14

View on CRAN

Man pages

allocate: allocate function

alpha: alpha function

B: B function

basehazard: basehazard function

basehazard.basehazardspec: basehazard.basehazardspec function

baseHazST: baseHazST function

baselinehazard: baselinehazard function

betapriorGauss: betapriorGauss function

blockDiag: A function to

boxplotRisk: boxplotRisk function

Bspline.construct: Bspline.construct function

BsplineHaz: BsplineHaz function

checkSurvivalData: checkSurvivalData function

circulant: circulant function

circulantij: circulantij function

circulant.matrix: circulant.matrix function

circulant.numeric: circulant.numeric function

covmodel: covmodel function

CSplot: CSplot function

cumbasehazard: cumbasehazard function

cumbasehazard.basehazardspec: cumbasehazard.basehazardspec function

cumulativeBspline.construct: cumulativeBspline.construct function

density_PP: density_PP function

densityquantile: densityquantile function

densityquantile.basehazardspec: densityquantile.basehazardspec function

densityquantile_PP: densityquantile_PP function

derivindepGaussianprior: derivindepGaussianprior function

derivindepGaussianpriorST: derivindepGaussianpriorST function

derivpsplineprior: derivpsplineprior function

distinfo: distinfo function

distinfo.basehazardspec: distinfo.basehazardspec function

estimateY: estimateY function

etapriorGauss: etapriorGauss function

Et_PP: Et_PP function

EvalCov: EvalCov function

ExponentialCovFct: ExponentialCovFct function

exponentialHaz: exponentialHaz function

FFTgrid: FFTgrid function

fixedpars: fixedpars function

fixmatrix: fixmatrix function

fixParHaz: fixParHaz function

frailtylag1: frailtylag1 function

fs: London Fire Brigade property

fstimes: London Fire Brigade response times to dwelling fires, 2009

gamma2risk: gamma2risk function

GammafromY: GammafromY function

GammaFromY_SPDE: GammaFromY_SPDE function

gencens: gencens function

getBackground: getBackground function

getbb: getbb function

getBbasis: getBbasis function

getcov: getcov function

getgrd: getgrd function

getGrid: getGrid function

getleneta: getleneta function

getOptCellwidth: getOptCellwidth function

getparranges: getparranges function

getsurvdata: getsurvdata function

gompertzHaz: gompertzHaz function

gradbasehazard: gradbasehazard function

gradbasehazard.basehazardspec: gradbasehazard.basehazardspec function

gradcumbasehazard: gradcumbasehazard function

gradcumbasehazard.basehazardspec: gradcumbasehazard.basehazardspec function

grid2spdf: grid2spdf function

grid2spix: grid2spix function

grid2spts: grid2spts function

gridY: gridY function

gridY_polygonal: gridY_polygonal function

guess_t: guess_t function

hasNext: generic hasNext method

hasNext.iter: hasNext.iter function

hazardexceedance: hazardexceedance function

hazardpars: hazardpars function

hazard_PP: hazard_PP function

hessbasehazard: hessbasehazard function

hessbasehazard.basehazardspec: hessbasehazard.basehazardspec function

hesscumbasehazard: hesscumbasehazard function

hesscumbasehazard.basehazardspec: hesscumbasehazard.basehazardspec function

imputationModel: imputationModel function

Independent: Independent function

indepGaussianprior: indepGaussianprior function

indepGaussianpriorST: indepGaussianpriorST function

inference.control: inference.control function

insert: insert function

invtransformweibull: invtransformweibull function

is.burnin: is this a burn-in iteration?

is.retain: do we retain this iteration?

iteration: iteration number

logPosterior: logPosterior function

logPosterior_gridded: logPosterior_gridded function

logPosterior_polygonal: logPosterior_polygonal function

logPosterior_SPDE: logPosterior_SPDE function

loop.mcmc: loop over an iterator

makehamHaz: makehamHaz function

maxlikparamPHsurv: maxlikparamPHsurv function

MCE: MCE function

mcmcLoop: iterator for MCMC loops

mcmcpars: mcmcpars function

mcmcPriors: mcmcPriors function

mcmcProgressNone: null progress monitor

mcmcProgressPrint: printing progress monitor

mcmcProgressTextBar: text bar progress monitor

midpts: midpts function

multiWayHaz: multiWayHaz function

neighLocs: neighLocs function

neighOrder: neighOrder function

nextStep: next step of an MCMC chain

NonSpatialLogLikelihood_or_gradient: NonSpatialLogLikelihood_or_gradient function

omegapriorGauss: omegapriorGauss function

omegapriorGaussST: omegapriorGaussST function

optifix: optifix function

plot.FFTgrid: plot.FFTgrid function

plotsurv: plotsurv function

polyadd: polyadd function

polymult: polymult function

posteriorcov: posteriorcov function

predict.mcmcspatsurv: predict.mcmcspatsurv function

print.mcmc: print.mcmc function

print.mcmcspatsurv: print.mcmcspatsurv function

print.mlspatsurv: print.mlspatsurv function

print.textSummary: print.textSummary function

priorposterior: priorposterior function

proposalVariance: proposalVariance function

proposalVariance_gridded: proposalVariance_gridded function

proposalVariance_polygonal: proposalVariance_polygonal function

proposalVariance_SPDE: proposalVariance_SPDE function

PsplineHaz: PsplineHaz function

psplineprior: psplineprior function

psplineRWprior: psplineRWprior function

QuadApprox: QuadApprox function

quantile.mcmcspatsurv: quantile.mcmcspatsurv function

quantile.mlspatsurv: quantile.mlspatsurv function

randompars: randompars function

reconstruct.bs: reconstruct.bs function

reconstruct.bs.coxph: reconstruct.bs.coxph function

reconstruct.bs.mcmcspatsurv: reconstruct.bs.mcmcspatsurv function

resetLoop: reset iterator

residuals.mcmcspatsurv: resuiduals.mcmcspatsurv function

setTxtProgressBar2: set the progress bar

setupHazard: setupHazard function

setupPrecMatStruct: setupPrecMatStruct function

showGrid: showGrid function

simsurv: simsurv function

spatialpars: spatialpars function

spatsurv-package: spatsurv

spatsurvVignette: spatsurvVignette function

SPDE: SPDE function

SPDEprec: SPDEprec function

SpikedExponentialCovFct: SpikedExponentialCovFct function

spplot1: spplot1 function

spplot_compare: spplot_compare function

Summarise: Summarise function

summary.mcmc: summary.mcmc function

summary.mcmcspatsurv: summary.mcmcspatsurv function

surv3d: Spatial Survival Plot in 3D

survival_PP: survival_PP function

survspat: survspat function

survspatNS: survspatNS function

textSummary: textSummary function

timevaryingPL: timevaryingPL function

tpowHaz: tpowHaz function

transformweibull: transformweibull function

txtProgressBar2: A text progress bar with label

urlTemplate: urlTemplate function

vcov.mcmcspatsurv: vcov.mcmcspatsurv function

vcov.mlspatsurv: vcov.mlspatsurv function

weibullHaz: weibullHaz function

YfromGamma: YfromGamma function

YFromGamma_SPDE: YFromGamma_SPDE function

Files in this package

spatsurv
spatsurv/inst
spatsurv/inst/CITATION
spatsurv/tests
spatsurv/tests/iteratorTest.R
spatsurv/tests/test_survspat.R
spatsurv/tests/test_sim_ana.R
spatsurv/tests/test_QuadApprox.R
spatsurv/NAMESPACE
spatsurv/NEWS
spatsurv/data
spatsurv/data/fstimes.rda
spatsurv/data/fs.rda
spatsurv/R
spatsurv/R/spatsurv.R spatsurv/R/log_posteriors_and_derivatives.R spatsurv/R/survsim.R spatsurv/R/log_posteriors_and_derivatives_SPDE.R spatsurv/R/PsplineHaz.R spatsurv/R/survspatNS.R spatsurv/R/spatsurvMisc.R spatsurv/R/covarianceFunctions.R spatsurv/R/BsplineHaz.R spatsurv/R/makeham.R spatsurv/R/spatgrid.R spatsurv/R/survspat.R spatsurv/R/calibratemcmc.R spatsurv/R/RWprior.R spatsurv/R/gompertz.R spatsurv/R/log_posteriors_and_derivatives_gridded.R spatsurv/R/baseHazST.R spatsurv/R/GMRF.R spatsurv/R/optifix.R spatsurv/R/surv3d.R spatsurv/R/outputSummary.R spatsurv/R/txtProgressBar2.R spatsurv/R/plottingfunctions.R spatsurv/R/maplayers.R spatsurv/R/tpow.R spatsurv/R/postprocessing.R spatsurv/R/exponential.R spatsurv/R/mcmcIterator.R spatsurv/R/splineFunctions.R spatsurv/R/circulant.R spatsurv/R/multiWayHaz.R spatsurv/R/mcmcProgress.R spatsurv/R/partial_likelihood.R spatsurv/R/spatial_imputation.R spatsurv/R/mcmcPriors.R spatsurv/R/weibull.R spatsurv/R/basehazardspec.R spatsurv/R/baseHazST_prior.R spatsurv/R/zzz.R spatsurv/R/nonspatial_log_likelihood_and_derivatives.R spatsurv/R/log_posteriors_and_derivatives_polygonal.R
spatsurv/README.md
spatsurv/MD5
spatsurv/DESCRIPTION
spatsurv/man
spatsurv/man/priorposterior.Rd spatsurv/man/densityquantile_PP.Rd spatsurv/man/plot.FFTgrid.Rd spatsurv/man/spplot_compare.Rd spatsurv/man/cumulativeBspline.construct.Rd spatsurv/man/circulant.matrix.Rd spatsurv/man/gompertzHaz.Rd spatsurv/man/frailtylag1.Rd spatsurv/man/setTxtProgressBar2.Rd spatsurv/man/densityquantile.Rd spatsurv/man/Summarise.Rd spatsurv/man/fixmatrix.Rd spatsurv/man/blockDiag.Rd spatsurv/man/indepGaussianpriorST.Rd spatsurv/man/vcov.mcmcspatsurv.Rd spatsurv/man/logPosterior.Rd spatsurv/man/fstimes.Rd spatsurv/man/quantile.mlspatsurv.Rd spatsurv/man/hessbasehazard.basehazardspec.Rd spatsurv/man/textSummary.Rd spatsurv/man/survival_PP.Rd spatsurv/man/logPosterior_polygonal.Rd spatsurv/man/nextStep.Rd spatsurv/man/gradbasehazard.Rd spatsurv/man/print.mcmc.Rd spatsurv/man/polymult.Rd spatsurv/man/circulantij.Rd spatsurv/man/reconstruct.bs.coxph.Rd spatsurv/man/covmodel.Rd spatsurv/man/gradcumbasehazard.basehazardspec.Rd spatsurv/man/reconstruct.bs.Rd spatsurv/man/getsurvdata.Rd spatsurv/man/makehamHaz.Rd spatsurv/man/invtransformweibull.Rd spatsurv/man/MCE.Rd spatsurv/man/omegapriorGaussST.Rd spatsurv/man/iteration.Rd spatsurv/man/weibullHaz.Rd spatsurv/man/GammaFromY_SPDE.Rd spatsurv/man/optifix.Rd spatsurv/man/tpowHaz.Rd spatsurv/man/hesscumbasehazard.Rd spatsurv/man/BsplineHaz.Rd spatsurv/man/mcmcProgressNone.Rd spatsurv/man/guess_t.Rd spatsurv/man/cumbasehazard.basehazardspec.Rd spatsurv/man/betapriorGauss.Rd spatsurv/man/getOptCellwidth.Rd spatsurv/man/setupPrecMatStruct.Rd spatsurv/man/spatsurv-package.Rd spatsurv/man/getBackground.Rd spatsurv/man/logPosterior_SPDE.Rd spatsurv/man/grid2spts.Rd spatsurv/man/gridY.Rd spatsurv/man/gamma2risk.Rd spatsurv/man/GammafromY.Rd spatsurv/man/gridY_polygonal.Rd spatsurv/man/spplot1.Rd spatsurv/man/cumbasehazard.Rd spatsurv/man/gencens.Rd spatsurv/man/is.burnin.Rd spatsurv/man/print.mcmcspatsurv.Rd spatsurv/man/gradbasehazard.basehazardspec.Rd spatsurv/man/proposalVariance_polygonal.Rd spatsurv/man/timevaryingPL.Rd spatsurv/man/spatsurvVignette.Rd spatsurv/man/ExponentialCovFct.Rd spatsurv/man/density_PP.Rd spatsurv/man/inference.control.Rd spatsurv/man/logPosterior_gridded.Rd spatsurv/man/posteriorcov.Rd spatsurv/man/distinfo.Rd spatsurv/man/neighLocs.Rd spatsurv/man/hazardpars.Rd spatsurv/man/YfromGamma.Rd spatsurv/man/mcmcLoop.Rd spatsurv/man/fixParHaz.Rd spatsurv/man/vcov.mlspatsurv.Rd spatsurv/man/simsurv.Rd spatsurv/man/indepGaussianprior.Rd spatsurv/man/NonSpatialLogLikelihood_or_gradient.Rd spatsurv/man/hessbasehazard.Rd spatsurv/man/Bspline.construct.Rd spatsurv/man/summary.mcmc.Rd spatsurv/man/plotsurv.Rd spatsurv/man/urlTemplate.Rd spatsurv/man/fixedpars.Rd spatsurv/man/spatialpars.Rd spatsurv/man/multiWayHaz.Rd spatsurv/man/hesscumbasehazard.basehazardspec.Rd spatsurv/man/fs.Rd spatsurv/man/circulant.Rd spatsurv/man/SpikedExponentialCovFct.Rd spatsurv/man/checkSurvivalData.Rd spatsurv/man/showGrid.Rd spatsurv/man/proposalVariance_SPDE.Rd spatsurv/man/resetLoop.Rd spatsurv/man/psplineprior.Rd spatsurv/man/setupHazard.Rd spatsurv/man/derivindepGaussianprior.Rd spatsurv/man/estimateY.Rd spatsurv/man/grid2spix.Rd spatsurv/man/baselinehazard.Rd spatsurv/man/circulant.numeric.Rd spatsurv/man/polyadd.Rd spatsurv/man/loop.mcmc.Rd spatsurv/man/getbb.Rd spatsurv/man/SPDEprec.Rd spatsurv/man/insert.Rd spatsurv/man/allocate.Rd spatsurv/man/hasNext.iter.Rd spatsurv/man/EvalCov.Rd spatsurv/man/survspatNS.Rd spatsurv/man/hazard_PP.Rd spatsurv/man/alpha.Rd spatsurv/man/surv3d.Rd spatsurv/man/boxplotRisk.Rd spatsurv/man/etapriorGauss.Rd spatsurv/man/derivindepGaussianpriorST.Rd spatsurv/man/neighOrder.Rd spatsurv/man/getleneta.Rd spatsurv/man/survspat.Rd spatsurv/man/Et_PP.Rd spatsurv/man/maxlikparamPHsurv.Rd spatsurv/man/mcmcPriors.Rd spatsurv/man/basehazard.Rd spatsurv/man/summary.mcmcspatsurv.Rd spatsurv/man/grid2spdf.Rd spatsurv/man/print.textSummary.Rd spatsurv/man/is.retain.Rd spatsurv/man/txtProgressBar2.Rd spatsurv/man/hasNext.Rd spatsurv/man/densityquantile.basehazardspec.Rd spatsurv/man/QuadApprox.Rd spatsurv/man/CSplot.Rd spatsurv/man/getgrd.Rd spatsurv/man/PsplineHaz.Rd spatsurv/man/YFromGamma_SPDE.Rd spatsurv/man/getparranges.Rd spatsurv/man/print.mlspatsurv.Rd spatsurv/man/B.Rd spatsurv/man/hazardexceedance.Rd spatsurv/man/transformweibull.Rd spatsurv/man/baseHazST.Rd spatsurv/man/FFTgrid.Rd spatsurv/man/SPDE.Rd spatsurv/man/basehazard.basehazardspec.Rd spatsurv/man/predict.mcmcspatsurv.Rd spatsurv/man/residuals.mcmcspatsurv.Rd spatsurv/man/mcmcProgressPrint.Rd spatsurv/man/quantile.mcmcspatsurv.Rd spatsurv/man/mcmcProgressTextBar.Rd spatsurv/man/omegapriorGauss.Rd spatsurv/man/midpts.Rd spatsurv/man/imputationModel.Rd spatsurv/man/distinfo.basehazardspec.Rd spatsurv/man/Independent.Rd spatsurv/man/psplineRWprior.Rd spatsurv/man/gradcumbasehazard.Rd spatsurv/man/randompars.Rd spatsurv/man/proposalVariance.Rd spatsurv/man/getGrid.Rd spatsurv/man/derivpsplineprior.Rd spatsurv/man/reconstruct.bs.mcmcspatsurv.Rd spatsurv/man/getBbasis.Rd spatsurv/man/getcov.Rd spatsurv/man/mcmcpars.Rd spatsurv/man/exponentialHaz.Rd spatsurv/man/proposalVariance_gridded.Rd

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