Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models

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Documentation for package ‘spatsurv’ version 2.0-1

• DESCRIPTION file.
• Package NEWS.

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