spatsurv: Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models

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

Author
Benjamin M. Taylor and Barry S. Rowlingson Additional contributions Ziyu Zheng
Date of publication
2016-10-24 17:14:26
Maintainer
Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
License
GPL-3
Version
0.9-14

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