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 publication2017-03-23 13:45:39 UTC
MaintainerBenjamin M. Taylor <b.taylor1@lancaster.ac.uk>
LicenseGPL-3
Version1.1

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

Functions

allocate Man page
alpha Man page
B Man page
basehazard Man page
basehazard.basehazardspec Man page
baseHazST Man page
baselinehazard Man page
betapriorGauss Man page
blockDiag Man page
boxplotRisk Man page
Bspline.construct Man page
BsplineHaz Man page
checkSurvivalData Man page
circulant Man page
circulantij Man page
circulant.matrix Man page
circulant.numeric Man page
covmodel Man page
CSplot Man page
cumbasehazard Man page
cumbasehazard.basehazardspec Man page
cumulativeBspline.construct Man page
density_PP Man page
densityquantile Man page
densityquantile.basehazardspec Man page
densityquantile_PP Man page
derivindepGaussianprior Man page
derivindepGaussianpriorST Man page
derivpsplineprior Man page
distinfo Man page
distinfo.basehazardspec Man page
estimateY Man page
etapriorGauss Man page
Et_PP Man page
EvalCov Man page
ExponentialCovFct Man page
exponentialHaz Man page
FFTgrid Man page
fixedpars Man page
fixmatrix Man page
fixParHaz Man page
frailtylag1 Man page
fs Man page
fstimes Man page
gamma2risk Man page
GammafromY Man page
GammaFromY_SPDE Man page
gencens Man page
getBackground Man page
getbb Man page
getBbasis Man page
getcov Man page
getgrd Man page
getGrid Man page
getleneta Man page
getOptCellwidth Man page
getparranges Man page
getsurvdata Man page
gompertzHaz Man page
gradbasehazard Man page
gradbasehazard.basehazardspec Man page
gradcumbasehazard Man page
gradcumbasehazard.basehazardspec Man page
grid2spdf Man page
grid2spix Man page
grid2spts Man page
gridY Man page
gridY_polygonal Man page
guess_t Man page
hasNext Man page
hasNext.iter Man page
hazardexceedance Man page
hazardpars Man page
hazard_PP Man page
hessbasehazard Man page
hessbasehazard.basehazardspec Man page
hesscumbasehazard Man page
hesscumbasehazard.basehazardspec Man page
imputationModel Man page
Independent Man page
indepGaussianprior Man page
indepGaussianpriorST Man page
inference.control Man page
insert Man page
invtransformweibull Man page
is.burnin Man page
is.retain Man page
iteration Man page
logPosterior Man page
logPosterior_gridded Man page
logPosterior_polygonal Man page
logPosterior_SPDE Man page
loop.mcmc Man page
makehamHaz Man page
maxlikparamPHsurv Man page
MCE Man page
mcmcLoop Man page
mcmcpars Man page
mcmcPriors Man page
mcmcProgressNone Man page
mcmcProgressPrint Man page
mcmcProgressTextBar Man page
midpts Man page
multiWayHaz Man page
neighLocs Man page
neighOrder Man page
nextStep Man page
NonSpatialLogLikelihood_or_gradient Man page
omegapriorGauss Man page
omegapriorGaussST Man page
optifix Man page
plot.FFTgrid Man page
plotsurv Man page
polyadd Man page
polymult Man page
posteriorcov Man page
predict.mcmcspatsurv Man page
print.mcmc Man page
print.mcmcspatsurv Man page
print.mlspatsurv Man page
print.textSummary Man page
priorposterior Man page
proposalVariance Man page
proposalVariance_gridded Man page
proposalVariance_polygonal Man page
proposalVariance_SPDE Man page
PsplineHaz Man page
psplineprior Man page
psplineRWprior Man page
QuadApprox Man page
quantile.mcmcspatsurv Man page
quantile.mlspatsurv Man page
randompars Man page
reconstruct.bs Man page
reconstruct.bs.coxph Man page
reconstruct.bs.mcmcspatsurv Man page
resetLoop Man page
residuals.mcmcspatsurv Man page
setTxtProgressBar2 Man page
setupHazard Man page
setupPrecMatStruct Man page
showGrid Man page
simsurv Man page
spatialpars Man page
spatsurv Man page
spatsurv-package Man page
spatsurvVignette Man page
SPDE Man page
SPDEprec Man page
SpikedExponentialCovFct Man page
spplot1 Man page
spplot_compare Man page
Summarise Man page
summary.mcmc Man page
summary.mcmcspatsurv Man page
surv3d Man page
survival_PP Man page
survspat Man page
survspatNS Man page
textSummary Man page
timevaryingPL Man page
tpowHaz Man page
transformweibull Man page
txtProgressBar2 Man page
urlTemplate Man page
vcov.mcmcspatsurv Man page
vcov.mlspatsurv Man page
weibullHaz Man page
YfromGamma Man page
YFromGamma_SPDE Man page

Files

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/TPSHaz.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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