spatsurv: Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models
Version 1.1

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

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("spatsurv")

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

B Man page Source code
Bspline.construct Man page Source code
BsplineHaz Man page Source code
CSplot Man page Source code
Et_PP Man page Source code
EvalCov Man page Source code
ExponentialCovFct Man page Source code
FFTgrid Man page Source code
GammaFromY_SPDE Man page Source code
GammafromY Man page Source code
Independent Man page Source code
MCE Man page Source code
NonSpatialLogLikelihood_or_gradient Man page Source code
PsplineHaz Man page Source code
QuadApprox Man page Source code
SPDE Man page Source code
SPDEprec Man page Source code
SpikedExponentialCovFct Man page Source code
Summarise Man page Source code
YFromGamma_SPDE Man page Source code
YfromGamma Man page Source code
allocate Man page Source code
alpha Man page Source code
baseHazST Man page Source code
basehazard Man page Source code
basehazard.basehazardspec Man page Source code
baselinehazard Man page Source code
betapriorGauss Man page Source code
blockDiag Man page Source code
boxplotRisk Man page Source code
checkSurvivalData Man page Source code
circulant Man page Source code
circulant.matrix Man page Source code
circulant.numeric Man page Source code
circulantij Man page Source code
covmodel Man page Source code
cumbasehazard Man page Source code
cumbasehazard.basehazardspec Man page Source code
cumulativeBspline.construct Man page Source code
dat2coords Source code
density_PP Man page Source code
densityquantile Man page Source code
densityquantile.basehazardspec Man page Source code
densityquantile_PP Man page Source code
derivindepGaussianprior Man page Source code
derivindepGaussianpriorST Man page Source code
derivpsplineprior Man page Source code
distinfo Man page Source code
distinfo.basehazardspec Man page Source code
estimateY Man page Source code
etapriorGauss Man page Source code
exponentialHaz Man page Source code
fixParHaz Man page Source code
fixedpars Man page Source code
fixmatrix Man page Source code
frailtylag1 Man page Source code
fs Man page
fstimes Man page
gamma2risk Man page Source code
gencens Man page Source code
getBackground Man page Source code
getBbasis Man page Source code
getGrid Man page Source code
getOptCellwidth Man page Source code
getbb Man page Source code
getcov Man page Source code
getgrd Man page Source code
getleneta Man page Source code
getparranges Man page Source code
getsurvdata Man page Source code
gompertzHaz Man page Source code
gradbasehazard Man page Source code
gradbasehazard.basehazardspec Man page Source code
gradcumbasehazard Man page Source code
gradcumbasehazard.basehazardspec Man page Source code
grid2spdf Man page Source code
grid2spix Man page Source code
grid2spts Man page Source code
gridY Man page Source code
gridY_polygonal Man page Source code
guess_t Man page Source code
hasNext Man page Source code
hasNext.iter Man page Source code
hazard_PP Man page Source code
hazardexceedance Man page Source code
hazardpars Man page Source code
hessbasehazard Man page Source code
hessbasehazard.basehazardspec Man page Source code
hesscumbasehazard Man page Source code
hesscumbasehazard.basehazardspec Man page Source code
imputationModel Man page Source code
indepGaussianprior Man page Source code
indepGaussianpriorST Man page Source code
inference.control Man page Source code
insert Man page Source code
invtransformweibull Man page Source code
is.burnin Man page Source code
is.retain Man page Source code
iteration Man page Source code
logPosterior Man page Source code
logPosterior_SPDE Man page Source code
logPosterior_gridded Man page Source code
logPosterior_polygonal Man page Source code
loop.mcmc Man page Source code
makehamHaz Man page Source code
maxlikparamPHsurv Man page Source code
mcmcLoop Man page Source code
mcmcPriors Man page Source code
mcmcProgressNone Man page Source code
mcmcProgressPrint Man page Source code
mcmcProgressTextBar Man page Source code
mcmcpars Man page Source code
midpts Man page Source code
multiWayHaz Man page Source code
neighLocs Man page Source code
neighOrder Man page Source code
nextStep Man page Source code
omegapriorGauss Man page Source code
omegapriorGaussST Man page Source code
onAttach Source code
optifix Man page Source code
plot.FFTgrid Man page Source code
plotsurv Man page Source code
polyadd Man page Source code
polymult Man page Source code
posteriorcov Man page Source code
predict.mcmcspatsurv Man page Source code
print.mcmc Man page Source code
print.mcmcspatsurv Man page Source code
print.mlspatsurv Man page Source code
print.textSummary Man page Source code
priorposterior Man page Source code
proposalVariance Man page Source code
proposalVariance_SPDE Man page Source code
proposalVariance_gridded Man page Source code
proposalVariance_polygonal Man page Source code
psplineRWprior Man page Source code
psplineprior Man page Source code
quantile.mcmcspatsurv Man page Source code
quantile.mlspatsurv Man page Source code
randompars Man page Source code
reconstruct.bs Man page Source code
reconstruct.bs.coxph Man page Source code
reconstruct.bs.mcmcspatsurv Man page Source code
resetLoop Man page Source code
residuals.mcmcspatsurv Man page Source code
setTxtProgressBar2 Man page Source code
setupHazard Man page Source code
setupPrecMatStruct Man page Source code
showGrid Man page Source code
simsurv Man page Source code
spatialpars Man page Source code
spatsurv Man page
spatsurv-package Man page
spatsurvVignette Man page Source code
spplot1 Man page Source code
spplot_compare Man page Source code
summary.mcmc Man page Source code
summary.mcmcspatsurv Man page Source code
surv3d Man page Source code
survival_PP Man page Source code
survspat Man page Source code
survspatNS Man page Source code
textSummary Man page Source code
timevaryingPL Man page Source code
tpowHaz Man page Source code
transformweibull Man page Source code
txtProgressBar2 Man page Source code
urlTemplate Man page Source code
vcov.mcmcspatsurv Man page Source code
vcov.mlspatsurv Man page Source code
weibullHaz Man page Source code

Files

inst
inst/CITATION
tests
tests/iteratorTest.R
tests/test_survspat.R
tests/test_sim_ana.R
tests/test_QuadApprox.R
NAMESPACE
NEWS
data
data/fstimes.rda
data/fs.rda
R
R/spatsurv.R
R/log_posteriors_and_derivatives.R
R/TPSHaz.R
R/survsim.R
R/log_posteriors_and_derivatives_SPDE.R
R/PsplineHaz.R
R/survspatNS.R
R/spatsurvMisc.R
R/covarianceFunctions.R
R/BsplineHaz.R
R/makeham.R
R/spatgrid.R
R/survspat.R
R/calibratemcmc.R
R/RWprior.R
R/gompertz.R
R/log_posteriors_and_derivatives_gridded.R
R/baseHazST.R
R/GMRF.R
R/optifix.R
R/surv3d.R
R/outputSummary.R
R/txtProgressBar2.R
R/plottingfunctions.R
R/maplayers.R
R/tpow.R
R/postprocessing.R
R/exponential.R
R/mcmcIterator.R
R/splineFunctions.R
R/circulant.R
R/multiWayHaz.R
R/mcmcProgress.R
R/partial_likelihood.R
R/spatial_imputation.R
R/mcmcPriors.R
R/weibull.R
R/basehazardspec.R
R/baseHazST_prior.R
R/zzz.R
R/nonspatial_log_likelihood_and_derivatives.R
R/log_posteriors_and_derivatives_polygonal.R
README.md
MD5
DESCRIPTION
man
man/priorposterior.Rd
man/densityquantile_PP.Rd
man/plot.FFTgrid.Rd
man/spplot_compare.Rd
man/cumulativeBspline.construct.Rd
man/circulant.matrix.Rd
man/gompertzHaz.Rd
man/frailtylag1.Rd
man/setTxtProgressBar2.Rd
man/densityquantile.Rd
man/Summarise.Rd
man/fixmatrix.Rd
man/blockDiag.Rd
man/indepGaussianpriorST.Rd
man/vcov.mcmcspatsurv.Rd
man/logPosterior.Rd
man/fstimes.Rd
man/quantile.mlspatsurv.Rd
man/hessbasehazard.basehazardspec.Rd
man/textSummary.Rd
man/survival_PP.Rd
man/logPosterior_polygonal.Rd
man/nextStep.Rd
man/gradbasehazard.Rd
man/print.mcmc.Rd
man/polymult.Rd
man/circulantij.Rd
man/reconstruct.bs.coxph.Rd
man/covmodel.Rd
man/gradcumbasehazard.basehazardspec.Rd
man/reconstruct.bs.Rd
man/getsurvdata.Rd
man/makehamHaz.Rd
man/invtransformweibull.Rd
man/MCE.Rd
man/omegapriorGaussST.Rd
man/iteration.Rd
man/weibullHaz.Rd
man/GammaFromY_SPDE.Rd
man/optifix.Rd
man/tpowHaz.Rd
man/hesscumbasehazard.Rd
man/BsplineHaz.Rd
man/mcmcProgressNone.Rd
man/guess_t.Rd
man/cumbasehazard.basehazardspec.Rd
man/betapriorGauss.Rd
man/getOptCellwidth.Rd
man/setupPrecMatStruct.Rd
man/spatsurv-package.Rd
man/getBackground.Rd
man/logPosterior_SPDE.Rd
man/grid2spts.Rd
man/gridY.Rd
man/gamma2risk.Rd
man/GammafromY.Rd
man/gridY_polygonal.Rd
man/spplot1.Rd
man/cumbasehazard.Rd
man/gencens.Rd
man/is.burnin.Rd
man/print.mcmcspatsurv.Rd
man/gradbasehazard.basehazardspec.Rd
man/proposalVariance_polygonal.Rd
man/timevaryingPL.Rd
man/spatsurvVignette.Rd
man/ExponentialCovFct.Rd
man/density_PP.Rd
man/inference.control.Rd
man/logPosterior_gridded.Rd
man/posteriorcov.Rd
man/distinfo.Rd
man/neighLocs.Rd
man/hazardpars.Rd
man/YfromGamma.Rd
man/mcmcLoop.Rd
man/fixParHaz.Rd
man/vcov.mlspatsurv.Rd
man/simsurv.Rd
man/indepGaussianprior.Rd
man/NonSpatialLogLikelihood_or_gradient.Rd
man/hessbasehazard.Rd
man/Bspline.construct.Rd
man/summary.mcmc.Rd
man/plotsurv.Rd
man/urlTemplate.Rd
man/fixedpars.Rd
man/spatialpars.Rd
man/multiWayHaz.Rd
man/hesscumbasehazard.basehazardspec.Rd
man/fs.Rd
man/circulant.Rd
man/SpikedExponentialCovFct.Rd
man/checkSurvivalData.Rd
man/showGrid.Rd
man/proposalVariance_SPDE.Rd
man/resetLoop.Rd
man/psplineprior.Rd
man/setupHazard.Rd
man/derivindepGaussianprior.Rd
man/estimateY.Rd
man/grid2spix.Rd
man/baselinehazard.Rd
man/circulant.numeric.Rd
man/polyadd.Rd
man/loop.mcmc.Rd
man/getbb.Rd
man/SPDEprec.Rd
man/insert.Rd
man/allocate.Rd
man/hasNext.iter.Rd
man/EvalCov.Rd
man/survspatNS.Rd
man/hazard_PP.Rd
man/alpha.Rd
man/surv3d.Rd
man/boxplotRisk.Rd
man/etapriorGauss.Rd
man/derivindepGaussianpriorST.Rd
man/neighOrder.Rd
man/getleneta.Rd
man/survspat.Rd
man/Et_PP.Rd
man/maxlikparamPHsurv.Rd
man/mcmcPriors.Rd
man/basehazard.Rd
man/summary.mcmcspatsurv.Rd
man/grid2spdf.Rd
man/print.textSummary.Rd
man/is.retain.Rd
man/txtProgressBar2.Rd
man/hasNext.Rd
man/densityquantile.basehazardspec.Rd
man/QuadApprox.Rd
man/CSplot.Rd
man/getgrd.Rd
man/PsplineHaz.Rd
man/YFromGamma_SPDE.Rd
man/getparranges.Rd
man/print.mlspatsurv.Rd
man/B.Rd
man/hazardexceedance.Rd
man/transformweibull.Rd
man/baseHazST.Rd
man/FFTgrid.Rd
man/SPDE.Rd
man/basehazard.basehazardspec.Rd
man/predict.mcmcspatsurv.Rd
man/residuals.mcmcspatsurv.Rd
man/mcmcProgressPrint.Rd
man/quantile.mcmcspatsurv.Rd
man/mcmcProgressTextBar.Rd
man/omegapriorGauss.Rd
man/midpts.Rd
man/imputationModel.Rd
man/distinfo.basehazardspec.Rd
man/Independent.Rd
man/psplineRWprior.Rd
man/gradcumbasehazard.Rd
man/randompars.Rd
man/proposalVariance.Rd
man/getGrid.Rd
man/derivpsplineprior.Rd
man/reconstruct.bs.mcmcspatsurv.Rd
man/getBbasis.Rd
man/getcov.Rd
man/mcmcpars.Rd
man/exponentialHaz.Rd
man/proposalVariance_gridded.Rd
spatsurv documentation built on May 19, 2017, 10:15 a.m.