Package: spatsurv 2.0-1

spatsurv: Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models

Bayesian inference for parametric proportional hazards spatial survival models; flexible spatial survival models. See Benjamin M. Taylor, Barry S. Rowlingson (2017) <doi:10.18637/jss.v077.i04>.

Authors:Benjamin M. Taylor and Barry S. Rowlingson Additional contributions Ziyu Zheng

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NEWS

# Install 'spatsurv' in R:
install.packages('spatsurv', repos = c('https://bentaylor1.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • fs - London Fire Brigade property
  • fstimes - London Fire Brigade response times to dwelling fires, 2009

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

139 exports 1 stars 1.00 score 50 dependencies 2 mentions 8 scripts 1.3k downloads

Last updated 11 months agofrom:70dda73bf5. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-winOKSep 13 2024
R-4.5-linuxOKSep 13 2024
R-4.4-winOKSep 13 2024
R-4.4-macOKSep 13 2024
R-4.3-winOKSep 13 2024
R-4.3-macOKSep 13 2024

Exports:allocatealphaBbasehazardbaseHazSTbaselinehazardbaselinehazard_multiWaybetapriorGaussblockDiagboxplotRiskBspline.constructBsplineHazcheckSurvivalDatacirculantcirculantijcovmodelCSplotcumbasehazardcumulativeBspline.constructdensity_PPdensityquantiledensityquantile_PPderivindepGaussianpriorderivindepGaussianpriorSTderivpsplinepriordistinfoestimateYEt_PPetapriorGaussEvalCovExponentialCovFctexponentialHazFFTgridfixedparsfixmatrixfixParHazfrailtylag1gamma2riskGammafromYGammaFromY_SPDEgencensgetbbgetBbasisgetcovgetgrdgetGridgetlenetagetOptCellwidthgetparrangesgetsurvdatagompertzHazgradbasehazardgradcumbasehazardgrid2spdfgrid2spixgrid2sptsgridYgridY_polygonalguess_thasNexthazard_PPhazardexceedancehazardparshessbasehazardhesscumbasehazardimputationModelIndependentindepGaussianpriorindepGaussianpriorSTinference.controlinsertinvtransformweibullis.burninis.retainiterationlogPosteriorlogPosterior_griddedlogPosterior_polygonallogPosterior_SPDEloop.mcmcmakehamHazmaxlikparamPHsurvMCEmcmcLoopmcmcparsmcmcPriorsmcmcProgressNonemcmcProgressPrintmcmcProgressTextBarmidptsmultiWayHazneighLocsneighOrdernextStepNonSpatialLogLikelihood_or_gradientomegapriorGaussomegapriorGaussSToptifixplotsurvpolyaddpolymultposteriorcovpriorposteriorproposalVarianceproposalVariance_griddedproposalVariance_polygonalproposalVariance_SPDEPsplineHazpsplinepriorpsplineRWpriorQuadApproxrandomparsreconstruct.bsresetLooprootWeibullHazsetTxtProgressBar2setupHazardsetupPrecMatStructshowGridsimsurvspatialparsspatsurvVignetteSPDESPDEprecSpikedExponentialCovFctSummarisesurv3dsurvival_PPsurvspatsurvspatNStextSummarytimevaryingPLtpowHaztransformweibullTwoWayHazAdditivetxtProgressBar2weibullHazYfromGammaYFromGamma_SPDE

Dependencies:abindclassclassIntclicpp11DBIdeldirdotCall64e1071fieldsgenericsgluegoftestiteratorsKernSmoothlatticelifecyclelubridatemagrittrmapsMASSMatrixnlmepolyclipproxyrasterRColorBrewerRcpprlangs2sfspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivaltensorterratimechangeunitsvctrsviridisLitewk

Readme and manuals

Help Manual

Help pageTopics
spatsurvspatsurv-package spatsurv
.onAttach function.onAttach
allocate functionallocate
alpha functionalpha
B functionB
basehazard functionbasehazard
basehazard.basehazardspec functionbasehazard.basehazardspec
baseHazST functionbaseHazST
baselinehazard functionbaselinehazard
baselinehazard_multiWay functionbaselinehazard_multiWay
betapriorGauss functionbetapriorGauss
A function toblockDiag
boxplotRisk functionboxplotRisk
Bspline.construct functionBspline.construct
BsplineHaz functionBsplineHaz
checkSurvivalData functioncheckSurvivalData
circulant functioncirculant
circulant.matrix functioncirculant.matrix
circulant.numeric functioncirculant.numeric
circulantij functioncirculantij
covmodel functioncovmodel
CSplot functionCSplot
cumbasehazard functioncumbasehazard
cumbasehazard.basehazardspec functioncumbasehazard.basehazardspec
cumulativeBspline.construct functioncumulativeBspline.construct
density_PP functiondensity_PP
densityquantile functiondensityquantile
densityquantile_PP functiondensityquantile_PP
densityquantile.basehazardspec functiondensityquantile.basehazardspec
derivindepGaussianprior functionderivindepGaussianprior
derivindepGaussianpriorST functionderivindepGaussianpriorST
derivpsplineprior functionderivpsplineprior
distinfo functiondistinfo
distinfo.basehazardspec functiondistinfo.basehazardspec
estimateY functionestimateY
Et_PP functionEt_PP
etapriorGauss functionetapriorGauss
EvalCov functionEvalCov
ExponentialCovFct functionExponentialCovFct
exponentialHaz functionexponentialHaz
FFTgrid functionFFTgrid
fixedpars functionfixedpars
fixmatrix functionfixmatrix
fixParHaz functionfixParHaz
frailtylag1 functionfrailtylag1
London Fire Brigade propertyfs
London Fire Brigade response times to dwelling fires, 2009fstimes
gamma2risk functiongamma2risk
GammafromY functionGammafromY
GammaFromY_SPDE functionGammaFromY_SPDE
gencens functiongencens
getbb functiongetbb
getBbasis functiongetBbasis
getcov functiongetcov
getgrd functiongetgrd
getGrid functiongetGrid
getleneta functiongetleneta
getOptCellwidth functiongetOptCellwidth
getparranges functiongetparranges
getsurvdata functiongetsurvdata
gompertzHaz functiongompertzHaz
gradbasehazard functiongradbasehazard
gradbasehazard.basehazardspec functiongradbasehazard.basehazardspec
gradcumbasehazard functiongradcumbasehazard
gradcumbasehazard.basehazardspec functiongradcumbasehazard.basehazardspec
grid2spdf functiongrid2spdf
grid2spix functiongrid2spix
grid2spts functiongrid2spts
gridY functiongridY
gridY_polygonal functiongridY_polygonal
guess_t functionguess_t
generic hasNext methodhasNext
hasNext.iter functionhasNext.iter
hazard_PP functionhazard_PP
hazardexceedance functionhazardexceedance
hazardpars functionhazardpars
hessbasehazard functionhessbasehazard
hessbasehazard.basehazardspec functionhessbasehazard.basehazardspec
hesscumbasehazard functionhesscumbasehazard
hesscumbasehazard.basehazardspec functionhesscumbasehazard.basehazardspec
imputationModel functionimputationModel
Independent functionIndependent
indepGaussianprior functionindepGaussianprior
indepGaussianpriorST functionindepGaussianpriorST
inference.control functioninference.control
insert functioninsert
invtransformweibull functioninvtransformweibull
is this a burn-in iteration?is.burnin
do we retain this iteration?is.retain
iteration numberiteration
logPosterior functionlogPosterior
logPosterior_gridded functionlogPosterior_gridded
logPosterior_polygonal functionlogPosterior_polygonal
logPosterior_SPDE functionlogPosterior_SPDE
loop over an iteratorloop.mcmc
makehamHaz functionmakehamHaz
maxlikparamPHsurv functionmaxlikparamPHsurv
MCE functionMCE
iterator for MCMC loopsmcmcLoop
mcmcpars functionmcmcpars
mcmcPriors functionmcmcPriors
null progress monitormcmcProgressNone
printing progress monitormcmcProgressPrint
text bar progress monitormcmcProgressTextBar
midpts functionmidpts
multiWayHaz functionmultiWayHaz
neighLocs functionneighLocs
neighOrder functionneighOrder
next step of an MCMC chainnextStep
NonSpatialLogLikelihood_or_gradient functionNonSpatialLogLikelihood_or_gradient
omegapriorGauss functionomegapriorGauss
omegapriorGaussST functionomegapriorGaussST
optifix functionoptifix
plot.FFTgrid functionplot.FFTgrid
plotsurv functionplotsurv
polyadd functionpolyadd
polymult functionpolymult
posteriorcov functionposteriorcov
predict.mcmcspatsurv functionpredict.mcmcspatsurv
print.mcmc functionprint.mcmc
print.mcmcspatsurv functionprint.mcmcspatsurv
print.mlspatsurv functionprint.mlspatsurv
print.textSummary functionprint.textSummary
priorposterior functionpriorposterior
proposalVariance functionproposalVariance
proposalVariance_gridded functionproposalVariance_gridded
proposalVariance_polygonal functionproposalVariance_polygonal
proposalVariance_SPDE functionproposalVariance_SPDE
PsplineHaz functionPsplineHaz
psplineprior functionpsplineprior
psplineRWprior functionpsplineRWprior
QuadApprox functionQuadApprox
quantile.mcmcspatsurv functionquantile.mcmcspatsurv
quantile.mlspatsurv functionquantile.mlspatsurv
randompars functionrandompars
reconstruct.bs functionreconstruct.bs
reconstruct.bs.coxph functionreconstruct.bs.coxph
reconstruct.bs.mcmcspatsurv functionreconstruct.bs.mcmcspatsurv
reset iteratorresetLoop
resuiduals.mcmcspatsurv functionresiduals.mcmcspatsurv
rootWeibullHaz functionrootWeibullHaz
set the progress barsetTxtProgressBar2
setupHazard functionsetupHazard
setupPrecMatStruct functionsetupPrecMatStruct
showGrid functionshowGrid
simsurv functionsimsurv
spatialpars functionspatialpars
spatsurvVignette functionspatsurvVignette
SPDE functionSPDE
SPDEprec functionSPDEprec
SpikedExponentialCovFct functionSpikedExponentialCovFct
Summarise functionSummarise
summary.mcmc functionsummary.mcmc
summary.mcmcspatsurv functionsummary.mcmcspatsurv
Spatial Survival Plot in 3Dsurv3d
survival_PP functionsurvival_PP
survspat functionsurvspat
survspatNS functionsurvspatNS
textSummary functiontextSummary
timevaryingPL functiontimevaryingPL
tpowHaz functiontpowHaz
transformweibull functiontransformweibull
TwoWayHazAdditive functionTwoWayHazAdditive
A text progress bar with labeltxtProgressBar2
vcov.mcmcspatsurv functionvcov.mcmcspatsurv
vcov.mlspatsurv functionvcov.mlspatsurv
weibullHaz functionweibullHaz
YfromGamma functionYfromGamma
YFromGamma_SPDE functionYFromGamma_SPDE