R: Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models

# Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models

## Documentation for package ‘spatsurv’ version 2.0-1

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I L M N O P Q R S T V W Y misc

spatsurv-package | spatsurv

## -- A --

allocate | allocate function
alpha | alpha function

## -- B --

B | B function
basehazard | basehazard function
basehazard.basehazardspec | basehazard.basehazardspec function
baseHazST | baseHazST function
baselinehazard | baselinehazard function
baselinehazard_multiWay | baselinehazard_multiWay function
betapriorGauss | betapriorGauss function
blockDiag | A function to
boxplotRisk | boxplotRisk function
Bspline.construct | Bspline.construct function
BsplineHaz | BsplineHaz function

## -- C --

checkSurvivalData | checkSurvivalData function
circulant | circulant function
circulant.matrix | circulant.matrix function
circulant.numeric | circulant.numeric function
circulantij | circulantij function
covmodel | covmodel function
CSplot | CSplot function
cumbasehazard | cumbasehazard function
cumbasehazard.basehazardspec | cumbasehazard.basehazardspec function
cumulativeBspline.construct | cumulativeBspline.construct function

## -- D --

densityquantile | densityquantile function
densityquantile.basehazardspec | densityquantile.basehazardspec function
densityquantile_PP | densityquantile_PP function
density_PP | density_PP function
derivindepGaussianprior | derivindepGaussianprior function
derivindepGaussianpriorST | derivindepGaussianpriorST function
derivpsplineprior | derivpsplineprior function
distinfo | distinfo function
distinfo.basehazardspec | distinfo.basehazardspec function

## -- E --

estimateY | estimateY function
etapriorGauss | etapriorGauss function
Et_PP | Et_PP function
EvalCov | EvalCov function
ExponentialCovFct | ExponentialCovFct function
exponentialHaz | exponentialHaz function

## -- F --

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

## -- G --

gamma2risk | gamma2risk function
GammafromY | GammafromY function
GammaFromY_SPDE | GammaFromY_SPDE function
gencens | gencens 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

## -- H --

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

## -- I --

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

## -- L --

logPosterior | logPosterior function
logPosterior_gridded | logPosterior_gridded function
logPosterior_polygonal | logPosterior_polygonal function
logPosterior_SPDE | logPosterior_SPDE function
loop.mcmc | loop over an iterator

## -- M --

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

## -- N --

neighLocs | neighLocs function
neighOrder | neighOrder function
nextStep | next step of an MCMC chain
NonSpatialLogLikelihood_or_gradient | NonSpatialLogLikelihood_or_gradient function

## -- O --

omegapriorGauss | omegapriorGauss function
omegapriorGaussST | omegapriorGaussST function
optifix | optifix function

## -- P --

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

## -- Q --

QuadApprox | QuadApprox function
quantile.mcmcspatsurv | quantile.mcmcspatsurv function
quantile.mlspatsurv | quantile.mlspatsurv function

## -- R --

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
rootWeibullHaz | rootWeibullHaz function

## -- S --

setTxtProgressBar2 | set the progress bar
setupHazard | setupHazard function
setupPrecMatStruct | setupPrecMatStruct function
showGrid | showGrid function
simsurv | simsurv function
spatialpars | spatialpars function
spatsurv | spatsurv
spatsurvVignette | spatsurvVignette function
SPDE | SPDE function
SPDEprec | SPDEprec function
SpikedExponentialCovFct | SpikedExponentialCovFct 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

## -- T --

textSummary | textSummary function
timevaryingPL | timevaryingPL function
tpowHaz | tpowHaz function
transformweibull | transformweibull function
TwoWayHazAdditive | TwoWayHazAdditive function
txtProgressBar2 | A text progress bar with label

## -- V --

vcov.mcmcspatsurv | vcov.mcmcspatsurv function
vcov.mlspatsurv | vcov.mlspatsurv function

## -- W --

weibullHaz | weibullHaz function

## -- Y --

YfromGamma | YfromGamma function
YFromGamma_SPDE | YFromGamma_SPDE function

## -- misc --

.onAttach | .onAttach function