| spatsurv-package {spatsurv} | R Documentation |
spatsurv
Description
An R package for spatially correlated parametric proportional hazards survial analysis.
Usage
spatsurv
Format
An object of class logical of length 1.
Details
| Package: | spatsurv |
| Type: | Package |
| Title: | Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models |
| Version: | 2.0-1 |
| Date: | 2023-10-18 |
| Author: | Benjamin M. Taylor and Barry S. Rowlingson Additional contributions Ziyu Zheng |
| Maintainer: | Benjamin M. Taylor <benjamin.taylor.software@gmail.com> |
| Description: | 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>. |
| License: | GPL-3 |
| Imports: | survival, sp, spatstat.explore, spatstat.geom, spatstat.random, raster, iterators, fields, Matrix, stringr, sf, RColorBrewer, methods, lubridate |
| Suggests: | rgl |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| NeedsCompilation: | no |
| Packaged: | 2022-11-22 14:11:17 UTC; taylorb7 |
| Depends: | R (>= 2.10) |
| Repository: | CRAN |
| Date/Publication: | 2022-11-22 14:30:02 UTC |
Index of help topics:
.onAttach .onAttach function
B B function
Bspline.construct Bspline.construct function
BsplineHaz BsplineHaz function
CSplot CSplot function
Et_PP Et_PP function
EvalCov EvalCov function
ExponentialCovFct ExponentialCovFct function
FFTgrid FFTgrid function
GammaFromY_SPDE GammaFromY_SPDE function
GammafromY GammafromY function
Independent Independent function
MCE MCE function
NonSpatialLogLikelihood_or_gradient
NonSpatialLogLikelihood_or_gradient function
PsplineHaz PsplineHaz function
QuadApprox QuadApprox function
SPDE SPDE function
SPDEprec SPDEprec function
SpikedExponentialCovFct
SpikedExponentialCovFct function
Summarise Summarise function
TwoWayHazAdditive TwoWayHazAdditive function
YFromGamma_SPDE YFromGamma_SPDE function
YfromGamma YfromGamma function
allocate allocate function
alpha alpha function
baseHazST baseHazST function
basehazard basehazard function
basehazard.basehazardspec
basehazard.basehazardspec function
baselinehazard baselinehazard function
baselinehazard_multiWay
baselinehazard_multiWay function
betapriorGauss betapriorGauss function
blockDiag A function to
boxplotRisk boxplotRisk function
checkSurvivalData checkSurvivalData function
circulant circulant function
circulant.matrix circulant.matrix function
circulant.numeric circulant.numeric function
circulantij circulantij function
covmodel covmodel 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
exponentialHaz exponentialHaz function
fixParHaz fixParHaz function
fixedpars fixedpars function
fixmatrix fixmatrix function
frailtylag1 frailtylag1 function
fs London Fire Brigade property
fstimes London Fire Brigade response times to dwelling
fires, 2009
gamma2risk gamma2risk function
gencens gencens function
getBbasis getBbasis function
getGrid getGrid function
getOptCellwidth getOptCellwidth function
getbb getbb function
getcov getcov function
getgrd getgrd function
getleneta getleneta 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
hazard_PP hazard_PP function
hazardexceedance hazardexceedance function
hazardpars hazardpars function
hessbasehazard hessbasehazard function
hessbasehazard.basehazardspec
hessbasehazard.basehazardspec function
hesscumbasehazard hesscumbasehazard function
hesscumbasehazard.basehazardspec
hesscumbasehazard.basehazardspec function
imputationModel imputationModel 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_SPDE logPosterior_SPDE function
logPosterior_gridded logPosterior_gridded function
logPosterior_polygonal
logPosterior_polygonal function
loop.mcmc loop over an iterator
makehamHaz makehamHaz function
maxlikparamPHsurv maxlikparamPHsurv function
mcmcLoop iterator for MCMC loops
mcmcPriors mcmcPriors function
mcmcProgressNone null progress monitor
mcmcProgressPrint printing progress monitor
mcmcProgressTextBar text bar progress monitor
mcmcpars mcmcpars function
midpts midpts function
multiWayHaz multiWayHaz function
neighLocs neighLocs function
neighOrder neighOrder function
nextStep next step of an MCMC chain
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_SPDE proposalVariance_SPDE function
proposalVariance_gridded
proposalVariance_gridded function
proposalVariance_polygonal
proposalVariance_polygonal function
psplineRWprior psplineRWprior function
psplineprior psplineprior 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
rootWeibullHaz rootWeibullHaz 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
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
vcov.mcmcspatsurv vcov.mcmcspatsurv function
vcov.mlspatsurv vcov.mlspatsurv function
weibullHaz weibullHaz function
Dependencies
The package spatsurv depends upon some other important contributions to CRAN in order to operate; their uses here are indicated:
survival, sp, spatstat, raster, iterators, RandomFields, fields, rgl, Matrix, stringr, RColorBrewer, geostatsp.
Citation
To cite use of spatsurv, the user may refer to the following work:
Benjamin M. Taylor and Barry S. Rowlingson (2017).
spatsurv: An R Package for Bayesian Inference with Spatial Survival Models.
Journal of Statistical Software, 77(4), 1-32, doi:10.18637/jss.v077.i04.
references
X
Author(s)
Benjamin Taylor, Health and Medicine, Lancaster University, Barry Rowlingson, Health and Medicine, Lancaster University
[Package spatsurv version 2.0-1 Index]